- galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 569483091092: Keep the sample's bar code incormation when editn the sample row in the non-admin user view.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1288731289 14400 # Node ID 56948309109207f932a113e464409432c7a38df7 # Parent 27c152bb441a0136720dbbc0c7cb293e581b8f5f Keep the sample's bar code incormation when editn the sample row in the non-admin user view. --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -153,6 +153,7 @@ <input type="text" name="sample_${current_sample_index}_barcode" value="${current_sample['barcode']}" size="10"/> %else: ${current_sample['barcode']} + <input type="hidden" name="sample_${current_sample_index}_barcode" value="${current_sample['barcode']}"/> %endif </td> %endif @@ -261,7 +262,7 @@ %elif sample: <tr><td>${current_sample_name}</td> - %if is_submitted or is_complete: + %if display_bar_code: <td>${current_sample_barcode}</td> %endif %if is_unsubmitted:

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galaxy-dist commit e000a6800e1c: trackster: Fix summary_tree data provider to reflect bottom level not being indexed anymore.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1288748135 14400 # Node ID e000a6800e1cbfa15a190bb2aff90a5956882a43 # Parent 56948309109207f932a113e464409432c7a38df7 trackster: Fix summary_tree data provider to reflect bottom level not being indexed anymore. - Fix a bug causing no display modes to appear. - Update "Visualize in Trackster" init code in root/history.mako Fix small typo in root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -32,7 +32,7 @@ <div class="toolTitleNoSection"> %endif <% encoded_id = key.lstrip( 'workflow_' ) %> - <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id, check_user=False )}" target="_parent"}">${_(workflow.name)}</a> + <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id, check_user=False )}" target="_parent">${_(workflow.name)}</a></div></%def> --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -677,7 +677,7 @@ var TiledTrack = function() { track.draw(); }; var mode_mapping = {}; - for (var i, len = track.display_modes.length; i < len; i++) { + for (var i = 0, len = track.display_modes.length; i < len; i++) { var mode = track.display_modes[i]; mode_mapping[mode] = function(mode) { return function() { change_mode(mode); }; --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -102,14 +102,14 @@ class SummaryTreeDataProvider( TracksDat level = ceil( log( resolution, st.block_size ) ) - 1 level = int(max( level, 0 )) - if level <= 0: + if level <= 1: return None stats = st.chrom_stats[chrom] results = st.query(chrom, int(start), int(end), level) if results == "detail": return None - elif results == "draw" or level <= 1: + elif results == "draw": return "no_detail" else: return results, stats[level]["max"], stats[level]["avg"], stats[level]["delta"] --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -157,29 +157,33 @@ TERMINAL_STATES = ${ h.to_json_string(TE // Trackster links function init_trackster_links() { - $("a.trackster").live( "click", function() { - var link = $(this), - hid = link.attr("id").split("_")[1]; // visualize_{id} - + // Add to trackster browser functionality + $(".trackster-add").live("click", function() { + var dataset = this, + dataset_jquery = $(this); $.ajax({ - url: "${h.url_for( controller='tracks', action='list_tracks' )}", - data: {'hid': hid}, - error: function() { alert( "Visualization error" ); }, - success: function(html) { - show_modal("Add Track — Select Dataset(s)", html, { - "New Browser": function() { - hide_modal(); + url: dataset_jquery.attr("data-url"), + dataType: "html", + error: function() { alert( "Could not add this dataset to browser." ); }, + success: function(table_html) { + var parent = window.parent; + parent.show_modal("Add to Browser:", table_html, { + "Cancel": function() { + parent.hide_modal(); }, - "Insert": function() { - hide_modal(); + "Insert into selected": function() { + $(parent.document).find('input[name=id]:checked').each(function() { + var vis_id = $(this).val(); + parent.location = dataset_jquery.attr("action-url") + "&id=" + vis_id; + }); }, - "Cancel": function() { - hide_modal(); + "Insert into new browser": function() { + parent.location = dataset_jquery.attr("new-url"); } }); } }); - }); + }); } init_trackster_links(); --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=50,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPa ttern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,d,c,b){this.container=a;this.vis_id=c;this.dbkey=b;this.ti tle=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClas s("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div />").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.wh ich)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey: this.dbkey}),dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}a.chrom_select.html(h);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var e=0,d=a.tracks.length;e<d;e++){a.tracks[e].is_overview=false}$(this).siblings().filter("canvas").remove(); $(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var i=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(i/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag ",function(i){var f=Math.min(i.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(i.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(j){var f=Math.min(j.clientX,this.drag_origin_x),d=Math.max(j.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),i=a.low;a.low=Math.round(f/g*h)+i;a.high=Math.round(d/g*h)+i;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+c ommatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counte r;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max _low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);th is.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.nav_container.height()-45);this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b ){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track").css("position","relative");i f(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.filtering_div.hide();this.filtering_div.bind("drag",function(i){i.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200 px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(k,l){var i=l.values;d.text("["+i[0]+"-"+i[1]+"]");a.low=i[0];a.high=i[1];c.draw(true)},change:function(i,k){a.control_element.slider("option","slide").call(a.control_element,i,k)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$(" <a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var b=this,j=b.view;if(b.hidden){return}if(b.display_modes!==undefined){if(b.mode_div===undefined){b.mode_div=$("<div class='right-float menubutton popup' />").appendTo(b.header_div);var e= b.display_modes[0];b.mode=e;b.mode_div.text(e);var c=function(i){b.mode_div.text(i);b.mode=i;b.tile_cache.clear();b.draw()};var a={};for(var f,h=b.display_modes.length;f<h;f++){var g=b.display_modes[f];a[g]=function(i){return function(){c(i)}}(g)}make_popupmenu(b.mode_div,a)}else{b.mode_div.hide()}}var d={};d["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();b.is_overview=true;b.set_overview();for(var i in j.tracks){if(j.tracks[i]!==b){j.tracks[i].is_overview=false}}};d["Edit configuration"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){b.update_options(b.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",b.gen_options(b.track_id),{Cancel:l,OK:i})};if(b.filters.length>0){d["Show filters"]=function(){var i;if(!b.filterin g_div.is(":visible")){i="Hide filters";b.filters_visible=true}else{i="Show filters";b.filters_visible=false}$("#"+b.name_div.attr("id")+"-menu").find("li").eq(2).text(i);b.filtering_div.toggle()}}d.Remove=function(){j.remove_track(b);if(j.num_tracks===0){$("#no-tracks").show()}};b.popup_menu=make_popupmenu(b.name_div,d);show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var k=this.view.low,g=this.view.high,h=g-k,f=this.view.resolution;var n=$("<div style='position: relative;'></div>"),o=this.content_div.width()/h;this.content_div.append(n);this.max_height=0;var b=Math.floor(k/f/DENSITY);var j={};while((b*DENSITY*f)<g){var l=this.content_div.width()+"_"+o+"_"+b;var e=this.tile_cache.get(l);if(!a&&e){var i=b*DENSITY*f;var d=(i-k)*o;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,n)}else{this.delayed_draw(this,l,k,g,b,f,n,o,j)}b+=1}var c=this;var m=setInterval(function( ){if(obj_length(j)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var p=0;p<c.filters.length;p++){c.filters[p].update_ui_elt()}clearInterval(m)}},50)},delayed_draw:function(c,h,g,e,b,d,i,j,f){var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|H ide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div. append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_ cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.verti cal_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b +1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,w=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(w)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(w);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;n.beginPath();n.fillStyle=this.prefs.colo r;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(d-(h-k)/m*d);n.fillRect(u,h,f,d-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,d)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></inp ut>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_px= 0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view. resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,b,q){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=q;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,y=[],h=0,n=this.view.max_low;var A=[];if(this.inc_slots[a].mode!==q){delete this.inc_slots[a];this.inc_slots[a]={mode:q,w_scale:m};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var v=0,w=g.length;v<w;v++){var f=g[v],l=f[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);A.push(this.inc_slots[a][l])}else{y.push(v)}}for(var v=0,w=y.length;v<w;v++){var f=g[y[v]],l=f[0],r=f[1],c=f[2],p=f[3],d=Math.floor((r-n)*m),e=Math.ceil((c-n)*m);if(p!==undefined&&!b){var s=CONTEXT.measureText(p).width;if(d-s<0){e+=s}else{d-=s}}var u=0;while(u<=MAX_FEATURE_DEPTH){var o=true;if(this.s_e_by_tile[a][u]!==undefined){for(var t=0,z=this.s_e_by_tile[a][u].length;t<z;t++){var x=this.s_e_by _tile[a][u][t];if(e>x[0]&&d<x[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][u]===undefined){this.s_e_by_tile[a][u]=[]}this.s_e_by_tile[a][u].push([d,e]);this.inc_slots[a][l]=u;h=Math.max(h,u);break}u++}}return h},rect_or_text:function(r,l,t,b,q,f,i,e){r.textAlign="center";var k=0,p=Math.round(l/2);for(var m=0,s=i.length;m<s;m++){var j=i[m],d="MIDNSHP"[j[0]],n=j[1];if(d==="H"||d==="S"){k-=n}var g=q+k,w=Math.floor(Math.max(0,(g-t)*l)),h=Math.floor(Math.max(0,(g+n-t)*l));switch(d){case"S":case"H":case"M":var o=f.slice(k,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+1,h-w,9);r.fillStyle=CONNECTOR_COLOR;for(var u=0,a=o.length;u<a;u++){if(g+u>=t&&g+u<=b){var v=Math.floor(Math.max(0,(g+u-t)*l));r.fillText(o[u],v+this.left_offset+p,e+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+4,h-w,3)}break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(w+this.left_ offset,e+5,h-w,1);break;case"D":r.fillStyle="red";r.fillRect(w+this.left_offset,e+4,h-w,3);break;case"P":case"I":break}k+=n}},draw_tile:function(ag,o,s,av){var N=o*DENSITY*ag,al=(o+1)*DENSITY*ag,M=al-N;var an=(!this.initial_canvas?"initial":N+"_"+al);var I=this.data_cache.get(an);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,al]]=true;this.get_data(N,al);return}var a=Math.ceil(M*av),ai=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,ae=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_info==="no_detail")),W=this.left_offset,au,D,aw;var q=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(q)}q=$(q);if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;aw=10}else{aw=(ae?this.vertical_nodetail_px:this.vertical_detail_px);var A=(av<0.0001?1/this.view.zoom_res:av);D=this.incremental_slots(A,I.data,ae,r)*aw+z;au=this.inc _slots[A]}}q.css({position:"absolute",top:0,left:(N-this.view.low)*av-W});q.get(0).width=a+W;q.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=q.get(0).getContext("2d");J.fillStyle=l;J.font=this.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Y=I.data,L=I.max,b=Math.ceil(I.delta*av);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var ap=0,H=Y.length;ap<H;ap++){var aa=Math.floor((Y[ap][0]-N)*av);var Z=Y[ap][1];if(!Z){continue}var am=Z/L*this.summary_draw_height;J.fillStyle="black";J.fillRect(aa+W,this.summary_draw_height-am,b,am);if(this.prefs.show_counts&&J.measureText(Z).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(Z,aa+W+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(q);return q}if(I.message){q.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fillS tyle="red";J.textAlign="left";J.fillText(I.message,100+W,aw)}var ad=false;if(I.data){ad=true;for(var ar=0;ar<this.filters.length;ar++){if(!this.filters[ar].applies_to(I.data[0])){ad=false}}}if(ad){q.addClass(FILTERABLE_CLASS)}var at=I.data;var ao=0;for(var ap=0,H=at.length;ap<H;ap++){var S=at[ap],R=S[0],aq=S[1],ac=S[2],O=S[3];if(au[R]===undefined){continue}var ab=false;var U;for(var ar=0;ar<this.filters.length;ar++){U=this.filters[ar];U.update_attrs(S);if(!U.keep(S)){ab=true;break}}if(ab){continue}if(aq<=al&&ac>=N){var af=Math.floor(Math.max(0,(aq-N)*av)),K=Math.ceil(Math.min(a,Math.max(0,(ac-N)*av))),X=(r==="Dense"?1:(1+au[R]))*aw;var G,aj,P=null,ax=null;if(I.dataset_type==="bai"){var v=S[4];J.fillStyle=l;if(S[5] instanceof Array){var E=Math.floor(Math.max(0,(S[5][0]-N)*av)),Q=Math.ceil(Math.min(a,Math.max(0,(S[5][1]-N)*av))),C=Math.floor(Math.max(0,(S[6][0]-N)*av)),w=Math.ceil(Math.min(a,Math.max(0,(S[6][1]-N)*av)));if(S[5][1]>=N&&S[5][0]<=al){this.rect_or_text(J,av,N,al,S [5][0],S[5][2],v,X)}if(S[6][1]>=N&&S[6][0]<=al){this.rect_or_text(J,av,N,al,S[6][0],S[6][2],v,X)}if(C>Q){J.fillStyle=CONNECTOR_COLOR;J.fillRect(Q+W,X+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,av,N,al,aq,O,v,X)}if(r!=="Dense"&&!ae&&aq>N){J.fillStyle=this.prefs.label_color;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+W,X+8)}else{J.textAlign="right";J.fillText(R,af-2+W,X+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(ae){J.fillStyle=l;J.fillRect(af+W,X+5,K-af,1)}else{var F=S[4],V=S[5],ah=S[6],h=S[7];if(V&&ah){P=Math.floor(Math.max(0,(V-N)*av));ax=Math.ceil(Math.min(a,Math.max(0,(ah-N)*av)))}if(r!=="Dense"&&O!==undefined&&aq>N){J.fillStyle=ai;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,af-2+W,X+8)}J.fillStyle=l}if(h){if(F){if(F=="+"){J.fillStyle=RIGHT_STRAND}else{if(F=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(af+W,X,K-af,10);J.fillStyle=l}for(var an=0 ,g=h.length;an<g;an++){var u=h[an],d=Math.floor(Math.max(0,(u[0]-N)*av)),T=Math.ceil(Math.min(a,Math.max((u[1]-N)*av)));if(d>T){continue}G=5;aj=3;J.fillRect(d+W,X+aj,T-d,G);if(P!==undefined&&!(d>ax||T<P)){G=9;aj=1;var ak=Math.max(d,P),B=Math.min(T,ax);J.fillRect(ak+W,X+aj,B-ak,G)}}}else{G=9;aj=1;J.fillRect(af+W,X+aj,K-af,G);if(S.strand){if(S.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(S.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(af+W,X,K-af,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(ae){J.fillStyle=l;J.fillRect(af+W,X+5,K-af,1)}else{var t=S[4],n=S[5],c=S[6];G=9;aj=1;J.fillRect(af+W,X,K-af,G);if(r!=="Dense"&&O!==undefined&&aq>N){J.fillStyle=ai;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,af-2+W,X+8)}J.fillStyle=l}var m=t+" / "+n;if(aq>N&&J.measureText(m).width<(K-af)){J.fillStyle="white";J.textAlign="center";J.fillText(m,W+af+(K-af)/2,X+8);J.fillStyle=l}}}}}ao++}}return q}, gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_co unts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=50,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPa ttern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,d,c,b){this.container=a;this.vis_id=c;this.dbkey=b;this.ti tle=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClas s("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div />").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.wh ich)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey: this.dbkey}),dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}a.chrom_select.html(h);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var e=0,d=a.tracks.length;e<d;e++){a.tracks[e].is_overview=false}$(this).siblings().filter("canvas").remove(); $(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var i=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(i/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag ",function(i){var f=Math.min(i.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(i.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(j){var f=Math.min(j.clientX,this.drag_origin_x),d=Math.max(j.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),i=a.low;a.low=Math.round(f/g*h)+i;a.high=Math.round(d/g*h)+i;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+c ommatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counte r;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max _low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);th is.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.nav_container.height()-45);this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b ){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track").css("position","relative");i f(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.filtering_div.hide();this.filtering_div.bind("drag",function(i){i.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200 px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(k,l){var i=l.values;d.text("["+i[0]+"-"+i[1]+"]");a.low=i[0];a.high=i[1];c.draw(true)},change:function(i,k){a.control_element.slider("option","slide").call(a.control_element,i,k)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$(" <a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var b=this,j=b.view;if(b.hidden){return}if(b.display_modes!==undefined){if(b.mode_div===undefined){b.mode_div=$("<div class='right-float menubutton popup' />").appendTo(b.header_div);var e= b.display_modes[0];b.mode=e;b.mode_div.text(e);var c=function(i){b.mode_div.text(i);b.mode=i;b.tile_cache.clear();b.draw()};var a={};for(var f=0,h=b.display_modes.length;f<h;f++){var g=b.display_modes[f];a[g]=function(i){return function(){c(i)}}(g)}make_popupmenu(b.mode_div,a)}else{b.mode_div.hide()}}var d={};d["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();b.is_overview=true;b.set_overview();for(var i in j.tracks){if(j.tracks[i]!==b){j.tracks[i].is_overview=false}}};d["Edit configuration"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){b.update_options(b.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",b.gen_options(b.track_id),{Cancel:l,OK:i})};if(b.filters.length>0){d["Show filters"]=function(){var i;if(!b.filter ing_div.is(":visible")){i="Hide filters";b.filters_visible=true}else{i="Show filters";b.filters_visible=false}$("#"+b.name_div.attr("id")+"-menu").find("li").eq(2).text(i);b.filtering_div.toggle()}}d.Remove=function(){j.remove_track(b);if(j.num_tracks===0){$("#no-tracks").show()}};b.popup_menu=make_popupmenu(b.name_div,d);show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var k=this.view.low,g=this.view.high,h=g-k,f=this.view.resolution;var n=$("<div style='position: relative;'></div>"),o=this.content_div.width()/h;this.content_div.append(n);this.max_height=0;var b=Math.floor(k/f/DENSITY);var j={};while((b*DENSITY*f)<g){var l=this.content_div.width()+"_"+o+"_"+b;var e=this.tile_cache.get(l);if(!a&&e){var i=b*DENSITY*f;var d=(i-k)*o;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,n)}else{this.delayed_draw(this,l,k,g,b,f,n,o,j)}b+=1}var c=this;var m=setInterval(functio n(){if(obj_length(j)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var p=0;p<c.filters.length;p++){c.filters[p].update_ui_elt()}clearInterval(m)}},50)},delayed_draw:function(c,h,g,e,b,d,i,j,f){var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show |Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_di v.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.dat a_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.ver tical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f= (b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,w=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(w)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(w);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;n.beginPath();n.fillStyle=this.prefs.co lor;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(d-(h-k)/m*d);n.fillRect(u,h,f,d-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,d)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></i nput>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_p x=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.vie w.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,b,q){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=q;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,y=[],h=0,n=this.view.max_low;var A=[];if(this.inc_slots[a].mode!==q){delete this.inc_slots[a];this.inc_slots[a]={mode:q,w_scale:m};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var v=0,w=g.length;v<w;v++){var f=g[v],l=f[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);A.push(this.inc_slots[a][l])}else{y.push(v)}}for(var v=0,w=y.length;v<w;v++){var f=g[y[v]],l=f[0],r=f[1],c=f[2],p=f[3],d=Math.floor((r-n)*m),e=Math.ceil((c-n)*m);if(p!==undefined&&!b){var s=CONTEXT.measureText(p).width;if(d-s<0){e+=s}else{d-=s}}var u=0;while(u<=MAX_FEATURE_DEPTH){var o=true;if(this.s_e_by_tile[a][u]!==undefined){for(var t=0,z=this.s_e_by_tile[a][u].length;t<z;t++){var x=this.s_e_ by_tile[a][u][t];if(e>x[0]&&d<x[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][u]===undefined){this.s_e_by_tile[a][u]=[]}this.s_e_by_tile[a][u].push([d,e]);this.inc_slots[a][l]=u;h=Math.max(h,u);break}u++}}return h},rect_or_text:function(r,l,t,b,q,f,i,e){r.textAlign="center";var k=0,p=Math.round(l/2);for(var m=0,s=i.length;m<s;m++){var j=i[m],d="MIDNSHP"[j[0]],n=j[1];if(d==="H"||d==="S"){k-=n}var g=q+k,w=Math.floor(Math.max(0,(g-t)*l)),h=Math.floor(Math.max(0,(g+n-t)*l));switch(d){case"S":case"H":case"M":var o=f.slice(k,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+1,h-w,9);r.fillStyle=CONNECTOR_COLOR;for(var u=0,a=o.length;u<a;u++){if(g+u>=t&&g+u<=b){var v=Math.floor(Math.max(0,(g+u-t)*l));r.fillText(o[u],v+this.left_offset+p,e+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+4,h-w,3)}break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(w+this.lef t_offset,e+5,h-w,1);break;case"D":r.fillStyle="red";r.fillRect(w+this.left_offset,e+4,h-w,3);break;case"P":case"I":break}k+=n}},draw_tile:function(ag,o,s,av){var N=o*DENSITY*ag,al=(o+1)*DENSITY*ag,M=al-N;var an=(!this.initial_canvas?"initial":N+"_"+al);var I=this.data_cache.get(an);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,al]]=true;this.get_data(N,al);return}var a=Math.ceil(M*av),ai=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,ae=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_info==="no_detail")),W=this.left_offset,au,D,aw;var q=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(q)}q=$(q);if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;aw=10}else{aw=(ae?this.vertical_nodetail_px:this.vertical_detail_px);var A=(av<0.0001?1/this.view.zoom_res:av);D=this.incremental_slots(A,I.data,ae,r)*aw+z;au=this.i nc_slots[A]}}q.css({position:"absolute",top:0,left:(N-this.view.low)*av-W});q.get(0).width=a+W;q.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=q.get(0).getContext("2d");J.fillStyle=l;J.font=this.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Y=I.data,L=I.max,b=Math.ceil(I.delta*av);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var ap=0,H=Y.length;ap<H;ap++){var aa=Math.floor((Y[ap][0]-N)*av);var Z=Y[ap][1];if(!Z){continue}var am=Z/L*this.summary_draw_height;J.fillStyle="black";J.fillRect(aa+W,this.summary_draw_height-am,b,am);if(this.prefs.show_counts&&J.measureText(Z).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(Z,aa+W+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(q);return q}if(I.message){q.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fil lStyle="red";J.textAlign="left";J.fillText(I.message,100+W,aw)}var ad=false;if(I.data){ad=true;for(var ar=0;ar<this.filters.length;ar++){if(!this.filters[ar].applies_to(I.data[0])){ad=false}}}if(ad){q.addClass(FILTERABLE_CLASS)}var at=I.data;var ao=0;for(var ap=0,H=at.length;ap<H;ap++){var S=at[ap],R=S[0],aq=S[1],ac=S[2],O=S[3];if(au[R]===undefined){continue}var ab=false;var U;for(var ar=0;ar<this.filters.length;ar++){U=this.filters[ar];U.update_attrs(S);if(!U.keep(S)){ab=true;break}}if(ab){continue}if(aq<=al&&ac>=N){var af=Math.floor(Math.max(0,(aq-N)*av)),K=Math.ceil(Math.min(a,Math.max(0,(ac-N)*av))),X=(r==="Dense"?1:(1+au[R]))*aw;var G,aj,P=null,ax=null;if(I.dataset_type==="bai"){var v=S[4];J.fillStyle=l;if(S[5] instanceof Array){var E=Math.floor(Math.max(0,(S[5][0]-N)*av)),Q=Math.ceil(Math.min(a,Math.max(0,(S[5][1]-N)*av))),C=Math.floor(Math.max(0,(S[6][0]-N)*av)),w=Math.ceil(Math.min(a,Math.max(0,(S[6][1]-N)*av)));if(S[5][1]>=N&&S[5][0]<=al){this.rect_or_text(J,av,N,al ,S[5][0],S[5][2],v,X)}if(S[6][1]>=N&&S[6][0]<=al){this.rect_or_text(J,av,N,al,S[6][0],S[6][2],v,X)}if(C>Q){J.fillStyle=CONNECTOR_COLOR;J.fillRect(Q+W,X+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,av,N,al,aq,O,v,X)}if(r!=="Dense"&&!ae&&aq>N){J.fillStyle=this.prefs.label_color;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+W,X+8)}else{J.textAlign="right";J.fillText(R,af-2+W,X+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(ae){J.fillStyle=l;J.fillRect(af+W,X+5,K-af,1)}else{var F=S[4],V=S[5],ah=S[6],h=S[7];if(V&&ah){P=Math.floor(Math.max(0,(V-N)*av));ax=Math.ceil(Math.min(a,Math.max(0,(ah-N)*av)))}if(r!=="Dense"&&O!==undefined&&aq>N){J.fillStyle=ai;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,af-2+W,X+8)}J.fillStyle=l}if(h){if(F){if(F=="+"){J.fillStyle=RIGHT_STRAND}else{if(F=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(af+W,X,K-af,10);J.fillStyle=l}for(var an =0,g=h.length;an<g;an++){var u=h[an],d=Math.floor(Math.max(0,(u[0]-N)*av)),T=Math.ceil(Math.min(a,Math.max((u[1]-N)*av)));if(d>T){continue}G=5;aj=3;J.fillRect(d+W,X+aj,T-d,G);if(P!==undefined&&!(d>ax||T<P)){G=9;aj=1;var ak=Math.max(d,P),B=Math.min(T,ax);J.fillRect(ak+W,X+aj,B-ak,G)}}}else{G=9;aj=1;J.fillRect(af+W,X+aj,K-af,G);if(S.strand){if(S.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(S.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(af+W,X,K-af,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(ae){J.fillStyle=l;J.fillRect(af+W,X+5,K-af,1)}else{var t=S[4],n=S[5],c=S[6];G=9;aj=1;J.fillRect(af+W,X,K-af,G);if(r!=="Dense"&&O!==undefined&&aq>N){J.fillStyle=ai;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,af-2+W,X+8)}J.fillStyle=l}var m=t+" / "+n;if(aq>N&&J.measureText(m).width<(K-af)){J.fillStyle="white";J.textAlign="center";J.fillText(m,W+af+(K-af)/2,X+8);J.fillStyle=l}}}}}ao++}}return q },gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_ counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});

1 0

galaxy-dist commit 37477f7d10e7: Data Libraries: Pre-generate and cache variables so that expensive functions like jQuery.siblings, jQuery.filter and jQuery.find only have to be called a minimum amount of times. Provides significant speedup to loading of large data libraries.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1288749068 14400 # Node ID 37477f7d10e7407186bd189fdec9e114e4b8f3d2 # Parent 4053c425b536b9878f6f8bdfac75453adec7bdf3 Data Libraries: Pre-generate and cache variables so that expensive functions like jQuery.siblings, jQuery.filter and jQuery.find only have to be called a minimum amount of times. Provides significant speedup to loading of large data libraries. --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -68,7 +68,7 @@ } } }; - + var save_folder_state = function() { var state = {}; $("tr.folderRow").each( function() { @@ -79,12 +79,17 @@ }; $("#library-grid").each(function() { - // Recursively fill in children and descendents of each row - var process_row = function(q, parents) { + + var child_of_parent_cache = {}; + // Recursively fill in children and descendents of each row + var process_row = function(q, parents) { // Find my index - var index = q.parent().children().index(q); + var parent = q.parent(), + this_level = child_of_parent_cache[parent] || (child_of_parent_cache[parent] = parent.children()); + + var index = this_level.index(q); // Find my immediate children - var children = q.siblings().filter("[parent='" + index + "']"); + var children = $(par_child_dict[index]); // Recursively handle them var descendents = children; children.each( function() { @@ -103,8 +108,7 @@ } save_folder_state(); }; - $(q).find("span.expandLink").click(expand_fn); - $(q).find("span.expandLink a").click(expand_fn); + $("." + q.attr("id") + "-click").click(expand_fn); // Check/uncheck boxes in subfolders. q.children("td").children("input[type=checkbox]").click( function() { if ( $(this).is(":checked") ) { @@ -112,15 +116,32 @@ } else { descendents.find("input[type=checkbox]").attr("checked", false); // If you uncheck a lower level checkbox, uncheck the boxes above it - // (since deselecting a child means the parent is not fully selected any - // more). + // (since deselecting a child means the parent is not fully selected any more). parents.children("td").children("input[type=checkbox]").attr("checked", false); } }); // return descendents for use by parent return descendents; - } - $(this).find("tbody tr").not("[parent]").each( function() { + } + + // Initialize dict[parent_id] = rows_which_have_that_parent_id_as_parent_attr + var par_child_dict = {}, + no_parent = []; + + $(this).find("tbody tr").each( function() { + if (this.hasAttribute("parent")) { + var parent = this.getAttribute("parent"); + if (par_child_dict[parent] !== undefined) { + par_child_dict[parent].push(this); + } else { + par_child_dict[parent] = [this]; + } + } else { + no_parent.push(this); + } + }); + + $(no_parent).each( function() { descendents = process_row( $(this), $([]) ); descendents.hide(); }); @@ -338,7 +359,8 @@ info_association, inherited = folder.get_info_association( restrict=True ) %> %if not root_folder and ( not folder.deleted or show_deleted ): - <tr id="folder-${trans.security.encode_id(folder.id)}" class="folderRow libraryOrFolderRow" + <% encoded_id = trans.security.encode_id(folder.id) %> + <tr id="folder-${encoded_id}" class="folderRow libraryOrFolderRow" %if parent is not None: parent="${parent}" style="display: none;" @@ -349,9 +371,9 @@ %if folder.deleted: <span class="libraryItem-error"> %endif - <span class="expandLink"><span class="rowIcon"></span> + <span class="expandLink folder-${encoded_id}-click"><span class="rowIcon"></span><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup"> - <a href="javascript:void(0);">${folder.name}</a> + <a class="folder-${encoded_id}-click" href="javascript:void(0);">${folder.name}</a></div> %if folder.deleted: </span>

1 0

galaxy-dist commit b7ac22fab158: First pass of bug fixes, anbd additional UI cleanup for Sample Tracking.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1288713844 14400 # Node ID b7ac22fab1588a565a07acc4972564c2b9198489 # Parent 667043341e81261a7fe587daa475110486b15292 First pass of bug fixes, anbd additional UI cleanup for Sample Tracking. --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -73,9 +73,10 @@ is_complete = request.is_complete is_unsubmitted = request.is_unsubmitted can_add_samples = is_unsubmitted - can_edit_or_delete_samples = is_unsubmitted and request.samples + can_edit_or_delete_samples = request.samples and not is_complete can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted can_reject_or_transfer = is_admin and request.is_submitted + can_submit = request.samples and is_unsubmitted %><br/><br/> @@ -87,7 +88,7 @@ %if editing_samples and can_add_samples: <li><a class="action-button" href="${h.url_for( controller='requests_common', action='add_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), add_sample_button='Add sample' )}">Add sample</a></li> %endif - %if is_unsubmitted: + %if can_submit: <li><a class="action-button" confirm="More samples cannot be added to this request after it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit request</a></li> %endif <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request actions</a></li> @@ -209,12 +210,12 @@ Click the <b>Save</b> button when you have finished editing the samples </div> %endif - %if request.samples and request.is_submitted: - <script type="text/javascript"> - // Updater - updater( {${ ",".join( [ '"%s" : "%s"' % ( s.id, s.state.name ) for s in request.samples ] ) }}); - </script> - %endif + ##%if request.samples and request.is_submitted: + ## <script type="text/javascript"> + ## // Updater + ## updater( {${ ",".join( [ '"%s" : "%s"' % ( s.id, s.state.name ) for s in request.samples ] ) }}); + ## </script> + ##%endif </form></div> %if is_unsubmitted and not editing_samples: --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -36,6 +36,12 @@ class Requests( BaseController ): action='edit_basic_request_info', cntrller='requests', **kwd ) ) + if operation == "edit_samples": + kwd[ 'editing_samples' ] = True + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='edit_samples', + cntrller='requests', + **kwd ) ) if operation == "view_request": return trans.response.send_redirect( web.url_for( controller='requests_common', action='view_request', --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -46,17 +46,6 @@ class RequestsGrid( grids.Grid ): .filter( model.RequestEvent.table.c.id.in_( select( columns=[ func.max( model.RequestEvent.table.c.id ) ], from_obj=model.RequestEvent.table, group_by=model.RequestEvent.table.c.request_id ) ) ) - def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - # TODO: is this method necessary? - accepted_filter_labels_and_vals = [ model.Request.states.get( state ) for state in model.Request.states ] - accepted_filter_labels_and_vals.append( "All" ) - accepted_filters = [] - for val in accepted_filter_labels_and_vals: - label = val.lower() - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args ) ) - return accepted_filters # Grid definition title = "Sequencing Requests" @@ -64,7 +53,6 @@ class RequestsGrid( grids.Grid ): model_class = model.Request default_sort_key = "-update_time" num_rows_per_page = 50 - preserve_state = True use_paging = True default_filter = dict( state="All", deleted="False" ) columns = [ @@ -379,14 +367,24 @@ class RequestsCommon( BaseController, Us sample_event_comment = "" event = trans.model.RequestEvent( request, request.states.SUBMITTED, sample_event_comment ) trans.sa_session.add( event ) - # change the state of each of the samples of thus request - new_state = request.type.states[0] + # Change the state of each of the samples of this request + # request.type.states is the list of SampleState objects configured + # by the admin for this RequestType. + trans.sa_session.add( event ) + trans.sa_session.flush() + # Samples will not have an associated SampleState until the request is submitted, at which + # time all samples of the request will be set to the first SampleState configured for the + # request's RequestType configured by the admin. + initial_sample_state_after_request_submitted = request.type.states[0] for sample in request.samples: - event = trans.model.SampleEvent( sample, new_state, 'Samples created.' ) + event_comment = 'Request submitted and sample state set to %s.' % request.type.states[0].name + event = trans.model.SampleEvent( sample, + initial_sample_state_after_request_submitted, + event_comment ) trans.sa_session.add( event ) trans.sa_session.add( request ) trans.sa_session.flush() - request.send_email_notification( trans, new_state ) + request.send_email_notification( trans, initial_sample_state_after_request_submitted ) message = 'The request has been submitted.' return trans.response.send_redirect( web.url_for( controller=cntrller, action='browse_requests', @@ -519,8 +517,6 @@ class RequestsCommon( BaseController, Us try: request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( id ) ) except: - message += "Invalid request ID (%s). " % str( id ) - status = 'error' ok_for_now = False if ok_for_now: request.deleted = True @@ -549,8 +545,6 @@ class RequestsCommon( BaseController, Us try: request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( id ) ) except: - message += "Invalid request ID (%s). " % str( id ) - status = 'error' ok_for_now = False if ok_for_now: request.deleted = False @@ -903,6 +897,7 @@ class RequestsCommon( BaseController, Us action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ), + editing_samples=True, status=status, message=message ) ) if is_admin: @@ -1024,7 +1019,7 @@ class RequestsCommon( BaseController, Us if sample_state_id in [ None, 'none' ]: message = "Select a new state from the <b>Change current state</b> list before clicking the <b>Save</b> button." kwd[ 'message' ] = message - del kwd[ 'save_changes_button' ] + del kwd[ 'save_samples_button' ] handle_error( **kwd ) sample_event_comment = util.restore_text( params.get( 'sample_event_comment', '' ) ) new_state = trans.sa_session.query( trans.model.SampleState ).get( trans.security.decode_id( sample_state_id ) ) @@ -1056,32 +1051,38 @@ class RequestsCommon( BaseController, Us folder_id = params.get( 'sample_0_folder_id', 'none' ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) self.__update_samples( trans, request, samples, **kwd ) - # See if all the samples' barcodes are in the same state, - # and if so send email if configured to. - common_state = request.samples_have_common_state - if common_state and common_state.id == request.type.states[1].id: - event = trans.model.RequestEvent( request, - request.states.SUBMITTED, - "All samples are in %s state." % common_state.name ) - trans.sa_session.add( event ) - trans.sa_session.flush() - request.send_email_notification( trans, request.type.states[1] ) + # Samples will not have an associated SampleState until the request is submitted, at which + # time all samples of the request will be set to the first SampleState configured for the + # request's RequestType defined by the admin. + if request.is_submitted: + # See if all the samples' barcodes are in the same state, and if so send email if configured to. + common_state = request.samples_have_common_state + if common_state and common_state.id == request.type.states[1].id: + event = trans.model.RequestEvent( request, + request.states.SUBMITTED, + "All samples are in %s state." % common_state.name ) + trans.sa_session.add( event ) + trans.sa_session.flush() + request.send_email_notification( trans, request.type.states[1] ) message = 'Changes made to the samples have been saved. ' else: - # Saving a newly created sample. + # Saving a newly created sample. The sample will not have an associated SampleState + # until the request is submitted, at which time all samples of the request will be + # set to the first SampleState configured for the request's RequestType configured + # by the admin ( i.e., the sample's SampleState would be set to request.type.states[0] ). for index in range( len( samples ) - len( request.samples ) ): sample_index = len( request.samples ) current_sample = samples[ sample_index ] form_values = trans.model.FormValues( request.type.sample_form, current_sample[ 'field_values' ] ) trans.sa_session.add( form_values ) trans.sa_session.flush() - s = trans.model.Sample( current_sample[ 'name' ], - '', - request, - form_values, - current_sample[ 'barcode' ], - current_sample[ 'library' ], - current_sample[ 'folder' ] ) + s = trans.model.Sample( name=current_sample[ 'name' ], + desc='', + request=request, + form_values=form_values, + bar_code='', + library=current_sample[ 'library' ], + folder=current_sample[ 'folder' ] ) trans.sa_session.add( s ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_common', @@ -1113,49 +1114,55 @@ class RequestsCommon( BaseController, Us if obj is not None: # obj will be None if the user checked sample check boxes and selected an action # to perform on multiple samples, but did not select certain samples. - sample_updated = False - # If this sample has values in kwd, then kwd will include a - # key whose value is this sample's ( possibly changed ) name. An - # example of this key is 'sample_0_name'. - for k, v in kwd.items(): - name_key = 'sample_%i_name' % index - if k == name_key: - sample_updated = True - break - if sample_updated: - id_index = index + 1 - if sample_operation == 'none': - # We are handling changes to a single sample. - library_id = params.get( 'sample_%i_library_id' % id_index, 'none' ) - folder_id = params.get( 'sample_%i_folder_id' % id_index, 'none' ) - # Update the corresponding sample's values as well as the sample_widget. - sample = request.samples[ index ] - sample.name = util.restore_text( params.get( 'sample_%i_name' % index, '' ) ) - # The bar_code field requires special handling because after a request is submitted, the - # state of a sample cannot be changed without a bar_code assocaited with the sample. - bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, '' ) ) - if not bar_code and not sample.bar_code: - # If this is a 'new' (still in its first state) sample, create an event - if sample.state.id == request.states[0].id: - event = trans.model.SampleEvent( sample, - request.type.states[1], - 'Sample added to the system' ) + sample = request.samples[ index ] + # See if any values in kwd are different from the values already associated with this sample. + id_index = index + 1 + if sample_operation == 'none': + # We are handling changes to a single sample. + library_id = params.get( 'sample_%i_library_id' % id_index, 'none' ) + folder_id = params.get( 'sample_%i_folder_id' % id_index, 'none' ) + # Update the corresponding sample's values as well as the sample_widget. + name = util.restore_text( params.get( 'sample_%i_name' % index, '' ) ) + # The bar_code field requires special handling because after a request is submitted, the + # state of a sample cannot be changed without a bar_code associated with the sample. Bar + # codes can only be added to a sample after the request is submitted. Also, a samples will + # not have an associated SampleState until the request is submitted, at which time the sample + # is automatically associated with the first SamplesState configured by the admin for the + # request's RequestType. + bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, '' ) ) + if bar_code: + bc_message = self.__validate_barcode( trans, sample, bar_code ) + if bc_message: + kwd[ 'message' ] = bc_message + del kwd[ 'save_samples_button' ] + handle_error( **kwd ) + if not sample.bar_code: + # If the sample's associated SampleState is still the initial state + # configured by the admin for the request's RequestType, this must be + # the first time a bar code was added to the sample, so change it's state + # to the next associated SampleState. + if sample.state.id == request.type.states[0].id: + event = trans.app.model.SampleEvent(sample, + request.type.states[1], + 'Bar code associated with the sample' ) trans.sa_session.add( event ) trans.sa_session.flush() - elif bar_code: - bc_message = self.__validate_barcode( trans, sample, bar_code ) - if bc_message: - kwd[ 'message' ] = bc_message - del kwd[ 'save_samples_button' ] - handle_error( **kwd ) + library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) + field_values = [] + for field_index in range( len( request.type.sample_form.fields ) ): + field_values.append( util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) ) + form_values = trans.sa_session.query( trans.model.FormValues ).get( sample.values.id ) + form_values.content = field_values + if sample.name != name or \ + sample.bar_code != bar_code or \ + sample.library != library or \ + sample.folder != folder or \ + form_values.content != field_values: + # Information about this sample has been changed. + sample.name = name sample.bar_code = bar_code - library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) sample.library = library sample.folder = folder - field_values = [] - for field_index in range( len( request.type.sample_form.fields ) ): - field_values.append( util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) ) - form_values = trans.sa_session.query( trans.model.FormValues ).get( sample.values.id ) form_values.content = field_values trans.sa_session.add_all( ( sample, form_values ) ) trans.sa_session.flush() --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -9,8 +9,6 @@ import logging, os, pexpect, ConfigParse log = logging.getLogger( __name__ ) - - class AdminRequestsGrid( RequestsGrid ): class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, request ): @@ -51,6 +49,7 @@ class RequestTypeGrid( grids.Grid ): return request_type.sample_form.name # Grid definition + webapp = "galaxy" title = "Sequencer Configurations" template = "admin/requests/grid.mako" model_class = model.RequestType @@ -103,6 +102,7 @@ class DataTransferGrid( grids.Grid ): def get_value( self, trans, grid, sample_dataset ): return sample_dataset.status # Grid definition + webapp = "galaxy" title = "Sample Datasets" template = "admin/requests/grid.mako" model_class = model.SampleDataset @@ -129,9 +129,19 @@ class DataTransferGrid( grids.Grid ): visible=False, filterable="standard" ) ) operations = [ - grids.GridOperation( "Start Transfer", allow_multiple=True, condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ) ), - grids.GridOperation( "Rename", allow_multiple=True, allow_popup=False, condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ) ), - grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ) ), + grids.GridOperation( "Transfer", + allow_multiple=True, + condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ), + url_args=dict( webapp="galaxy" ) ), + grids.GridOperation( "Rename", + allow_multiple=True, + allow_popup=False, + condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ), + url_args=dict( webapp="galaxy" ) ), + grids.GridOperation( "Delete", + allow_multiple=True, + condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ), + url_args=dict( webapp="galaxy" ) ) ] def apply_query_filter( self, trans, query, **kwd ): sample_id = kwd.get( 'sample_id', None ) @@ -158,6 +168,12 @@ class RequestsAdmin( BaseController, Use action='edit_basic_request_info', cntrller='requests_admin', **kwd ) ) + if operation == "edit_samples": + kwd[ 'editing_samples' ] = True + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='edit_samples', + cntrller='requests_admin', + **kwd ) ) if operation == "view_request": return trans.response.send_redirect( web.url_for( controller='requests_common', action='view_request', @@ -273,7 +289,7 @@ class RequestsAdmin( BaseController, Use break if no_datasets_transferred: status = 'error' - message = 'A dataset can be renamed only if it is in the "Not Started" state.' + message = 'A dataset can be renamed only if it has been transferred.' return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( selected_sample_datasets[0].sample.id ), @@ -282,7 +298,7 @@ class RequestsAdmin( BaseController, Use return trans.fill_template( '/admin/requests/rename_datasets.mako', sample=selected_sample_datasets[0].sample, id_list=id_list ) - elif operation == "start transfer": + elif operation == "transfer": self.__start_datatx( trans, selected_sample_datasets[0].sample, selected_sample_datasets ) # Render the grid view sample_id = params.get( 'sample_id', None ) @@ -292,7 +308,7 @@ class RequestsAdmin( BaseController, Use return invalid_id_redirect( trans, 'requests_admin', sample_id ) request_id = trans.security.encode_id( sample.request.id ) library_id = trans.security.encode_id( sample.library.id ) - self.datatx_grid.global_actions = [ grids.GridAction( "Refresh", + self.datatx_grid.global_actions = [ grids.GridAction( "Refresh page", dict( controller='requests_admin', action='manage_datasets', sample_id=sample_id ) ), @@ -302,11 +318,11 @@ class RequestsAdmin( BaseController, Use request_id=request_id, folder_path=sample.request.type.datatx_info[ 'data_dir' ], sample_id=sample_id ) ), - #grids.GridAction( 'Data library "%s"' % sample.library.name, - # dict( controller='library_common', - # action='browse_library', - # cntrller='library_admin', - # id=library_id ) ), + grids.GridAction( "Browse target data library", + dict( controller='library_common', + action='browse_library', + cntrller='library_admin', + id=library_id ) ), grids.GridAction( "Browse this request", dict( controller='requests_common', action='view_request', --- a/templates/requests/common/view_request.mako +++ b/templates/requests/common/view_request.mako @@ -18,15 +18,18 @@ from galaxy.web.framework.helpers import time_ago is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_complete = request.is_complete is_unsubmitted = request.is_unsubmitted can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted can_add_samples = is_unsubmitted + can_edit_or_delete_samples = request.samples and not is_complete + can_submit = request.samples and is_unsubmitted %><br/><br/><ul class="manage-table-actions"> - %if is_unsubmitted: + %if can_submit: <li><a class="action-button" confirm="More samples cannot be added to this request after it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit request</a></li> %endif <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request actions</a></li> @@ -66,13 +69,12 @@ </div><div class="form-row"><label>User:</label> - %if is_admin: - ${request.user.email} - %elif request.user.username: - ${request.user.username} - %else: - Unknown - %endif + ${request.user.email} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Sequencer configuration:</label> + ${request.type.name} <div style="clear: both"></div></div><div class="form-row"> @@ -129,11 +131,6 @@ ${states} <div style="clear: both"></div></div> - <div class="form-row"> - <label>Sequencer configuration:</label> - ${request.type.name} - <div style="clear: both"></div> - </div></div></div></div> @@ -141,7 +138,7 @@ <p/> %if current_samples: <% grid_header = '<h3>Samples</h3>' %> - ${render_samples_grid( cntrller, request, current_samples=current_samples, action='view_request', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=can_edit_request, grid_header=grid_header )} + ${render_samples_grid( cntrller, request, current_samples=current_samples, action='view_request', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=can_edit_or_delete_samples, grid_header=grid_header )} %else: There are no samples. %if can_add_samples: --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -752,11 +752,18 @@ %if grid.global_actions: <ul class="manage-table-actions"> - %for action in grid.global_actions: - <li> - <a class="action-button" href="${h.url_for( **action.url_args )}">${action.label}</a> - </li> - %endfor + %if len( grid.global_actions ) < 4: + %for action in grid.global_actions: + <li><a class="action-button" href="${h.url_for( **action.url_args )}">${action.label}</a></li> + %endfor + %else: + <li><a class="action-button" id="action-8675309-popup" class="menubutton">Actions</a></li> + <div popupmenu="action-8675309-popup"> + %for action in grid.global_actions: + <a class="action-button" href="${h.url_for( **action.url_args )}">${action.label}</a> + %endfor + </div> + %endif </ul> %endif --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -88,26 +88,26 @@ %if is_admin and is_submitted and editing_samples: <td><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" ${checked_str}/><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"/></td> %endif - <td> + <td valign="top"><input type="text" name="sample_${current_sample_index}_name" value="${current_sample['name']}" size="10"/><div class="toolParamHelp" style="clear: both;"><i>${' (required)' }</i></div></td> %if sample and is_submitted or is_complete: - <td><input type="text" name="sample_${current_sample_index}_barcode" value="${current_sample['barcode']}" size="10"/></td> + <td valign="top"><input type="text" name="sample_${current_sample_index}_barcode" value="${current_sample['barcode']}" size="10"/></td> %endif %if sample: %if is_unsubmitted: <td>Unsubmitted</td> %else: - <td><a href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a></td> + <td valign="top"><a href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a></td> %endif %else: <td></td> %endif - <td>${current_sample['library_select_field'].get_html()}</td> - <td>${current_sample['folder_select_field'].get_html()}</td> + <td valign="top">${current_sample['library_select_field'].get_html()}</td> + <td valign="top">${current_sample['folder_select_field'].get_html()}</td> %if is_submitted or is_complete: <% if sample: @@ -115,12 +115,12 @@ else: label = 'add' %> - <td><a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${label}</a></td> - <td><a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${label}</a></td> + <td valign="top"><a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${label}</a></td> + <td valign="top"><a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${label}</a></td> %endif %if sample and ( is_admin or is_unsubmitted ): ## Delete button - <td><a class="action-button" href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=current_sample_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td> + <td valign="top"><a class="action-button" href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=current_sample_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td> %endif </%def> @@ -132,7 +132,7 @@ is_submitted = request.is_submitted is_unsubmitted = request.is_unsubmitted can_add_samples = request.is_unsubmitted - can_edit_or_delete_samples = request.samples and ( is_admin or request.is_unsubmitted ) + can_edit_or_delete_samples = request.samples and not is_complete %> ${grid_header} %if render_buttons and ( can_add_samples or can_edit_or_delete_samples ):

1 0

galaxy-dist commit 667043341e81: Significant cleanup for the Sample Tracking UI. Things are more streamlined and Galaxy UI standards are now followed.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1288649810 14400 # Node ID 667043341e81261a7fe587daa475110486b15292 # Parent c4d8ffb3109e8cfb8143dc87c88dee3337bb7569 Significant cleanup for the Sample Tracking UI. Things are more streamlined and Galaxy UI standards are now followed. --- a/templates/requests/common/sample_events.mako +++ b/templates/requests/common/sample_events.mako @@ -5,10 +5,7 @@ <h2>Events for Sample "${sample.name}"</h2><ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}"> - <span>Browse this request</span></a> - </li> + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li></ul><h3>Sequencing Request "${sample.request.name}"</h3> --- /dev/null +++ b/templates/requests/common/edit_samples.mako @@ -0,0 +1,240 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/requests/common/common.mako" import="common_javascripts" /> +<%namespace file="/requests/common/common.mako" import="render_samples_grid" /> +<%namespace file="/requests/common/common.mako" import="render_request_type_sample_form_grids" /> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "library" )} +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${common_javascripts()} + ${local_javascripts()} +</%def> + +<%def name="local_javascripts()"> + <script type="text/javascript"> + // Looks for changes in sample states using an async request. Keeps + // calling itself (via setTimeout) until all samples are in a terminal + // state. + var updater = function ( sample_states ) { + // Check if there are any items left to track + var empty = true; + for ( i in sample_states ) { + empty = false; + break; + } + if ( ! empty ) { + setTimeout( function() { updater_callback( sample_states ) }, 1000 ); + } + }; + + var updater_callback = function ( sample_states ) { + // Build request data + var ids = [] + var states = [] + $.each( sample_states, function ( id, state ) { + ids.push( id ); + states.push( state ); + }); + // Make ajax call + $.ajax( { + type: "POST", + url: "${h.url_for( controller='requests_common', action='sample_state_updates' )}", + dataType: "json", + data: { ids: ids.join( "," ), states: states.join( "," ) }, + success : function ( data ) { + $.each( data, function( id, val ) { + // Replace HTML + var cell1 = $("#sampleState-" + id); + cell1.html( val.html_state ); + var cell2 = $("#sampleDatasets-" + id); + cell2.html( val.html_datasets ); + sample_states[ parseInt( id ) ] = val.state; + }); + updater( sample_states ); + }, + error: function() { + // Just retry, like the old method, should try to be smarter + updater( sample_states ); + } + }); + }; + </script> +</%def> + +<% + from galaxy.web.framework.helpers import time_ago + + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_complete = request.is_complete + is_unsubmitted = request.is_unsubmitted + can_add_samples = is_unsubmitted + can_edit_or_delete_samples = is_unsubmitted and request.samples + can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted + can_reject_or_transfer = is_admin and request.is_submitted +%> + +<br/><br/> + +<ul class="manage-table-actions"> + %if not editing_samples and can_edit_or_delete_samples: + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), editing_samples='True' )}">Edit samples</a></li> + %endif + %if editing_samples and can_add_samples: + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='add_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), add_sample_button='Add sample' )}">Add sample</a></li> + %endif + %if is_unsubmitted: + <li><a class="action-button" confirm="More samples cannot be added to this request after it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit request</a></li> + %endif + <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request actions</a></li> + <div popupmenu="request-${request.id}-popup"> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> + %if can_edit_request: + <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> + %endif + <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> + %if can_reject_or_transfer: + <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> + %endif + </div> +</ul> + +%if request.samples_without_library_destinations: + <br/> + <font color="red"><b><i>Select a target data library and folder for all samples before starting the sequence run</i></b></font> + <br/> +%endif + +%if request.is_rejected: + <br/> + <font color="red"><b><i>Reason for rejection: </i></b></font><b>${request.last_comment}</b> + <br/> +%endif + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolFormBody"> + <form id="edit_samples" name="edit_samples" action="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), editing_samples=editing_samples )}" method="post"> + %if current_samples: + <% + if editing_samples: + grid_header = '<h3>Edit Current Samples of Request "%s"</h3>' % request.name + else: + grid_header = '<h3>Add Samples to Request "%s"</h3>' % request.name + %> + ${render_samples_grid( cntrller, request, current_samples, action='edit_samples', editing_samples=editing_samples, encoded_selected_sample_ids=encoded_selected_sample_ids, render_buttons=False, grid_header=grid_header )} + %if editing_samples and len( sample_operation_select_field.options ) > 1 and not ( is_unsubmitted or is_complete ): + <div class="form-row" style="background-color:#FAFAFA;"> + For selected samples: + ${sample_operation_select_field.get_html()} + </div> + <% sample_operation_selected_value = sample_operation_select_field.get_selected( return_value=True ) %> + %if sample_operation_selected_value != 'none' and encoded_selected_sample_ids: + <div class="form-row" style="background-color:#FAFAFA;"> + %if sample_operation_selected_value == trans.model.Sample.bulk_operations.CHANGE_STATE: + ## sample_operation_selected_value == 'Change state' + <div class="form-row"> + <label>Change current state</label> + ${sample_state_id_select_field.get_html()} + <label>Comments</label> + <input type="text" name="sample_event_comment" value=""/> + <div class="toolParamHelp" style="clear: both;"> + Optional + </div> + </div> + %elif sample_operation_selected_value == trans.app.model.Sample.bulk_operations.SELECT_LIBRARY: + <% libraries_selected_value = libraries_select_field.get_selected( return_value=True ) %> + <div class="form-row"> + <label>Select data library:</label> + ${libraries_select_field.get_html()} + </div> + %if libraries_selected_value != 'none': + <div class="form-row"> + <label>Select folder:</label> + ${folders_select_field.get_html()} + </div> + %endif + %endif + </div> + %endif + %endif + ## Render the other grids + <% trans.sa_session.refresh( request.type.sample_form ) %> + %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), editing_samples=editing_samples )} + %endfor + %else: + <label>There are no samples.</label> + %endif + %if not editing_samples and is_unsubmitted: + ## The user is adding a new sample + %if current_samples: + <p/> + <div class="form-row"> + <label> Copy <input type="text" name="num_sample_to_copy" value="1" size="3"/> samples from sample ${sample_copy.get_html()}</label> + <div class="toolParamHelp" style="clear: both;"> + Select the sample from which the new sample should be copied or leave selection as <b>None</b> to add a new "generic" sample. + </div> + </div> + %endif + <p/> + <div class="form-row"> + %if ( request.samples or current_samples ) and ( editing_samples or len( current_samples ) > len( request.samples ) ): + <input type="submit" name="add_sample_button" value="Add sample"/> + <input type="submit" name="save_samples_button" value="Save"/> + <input type="submit" name="cancel_changes_button" value="Cancel"/> + <div class="toolParamHelp" style="clear: both;"> + Click the <b>Add sample</b> button for each new sample and click the <b>Save</b> button when you have finished adding samples. + </div> + %else: + <input type="submit" name="add_sample_button" value="Add sample"/> + <div class="toolParamHelp" style="clear: both;"> + Click the <b>Add sample</b> button for each new sample. + </div> + %endif + </div> + %elif editing_samples: + <p/> + <div class="form-row"> + <input type="submit" name="save_samples_button" value="Save"/> + <input type="submit" name="cancel_changes_button" value="Cancel"/> + <div class="toolParamHelp" style="clear: both;"> + Click the <b>Save</b> button when you have finished editing the samples + </div> + %endif + %if request.samples and request.is_submitted: + <script type="text/javascript"> + // Updater + updater( {${ ",".join( [ '"%s" : "%s"' % ( s.id, s.state.name ) for s in request.samples ] ) }}); + </script> + %endif + </form> +</div> +%if is_unsubmitted and not editing_samples: + <p/> + ##<div class="toolForm"> + ##<div class="toolFormTitle">Import samples from csv file</div> + <h4><img src="/static/images/fugue/toggle-expand.png" alt="Hide" onclick="showContent(this);" style="cursor:pointer;"/> Import samples from csv file</h4> + <div style="display:none;"> + <div class="toolFormBody"> + <form id="import" name="import" action="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), editing_samples=editing_samples )}" enctype="multipart/form-data" method="post" > + <div class="form-row"> + <input type="file" name="file_data" /> + <input type="submit" name="import_samples_button" value="Import samples"/> + <div class="toolParamHelp" style="clear: both;"> + The csv file must be in the following format:<br/> + SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2... + </div> + </div> + </form> + </div> + </div> + ##</div> +%endif --- a/test/functional/test_forms_and_requests.py +++ b/test/functional/test_forms_and_requests.py @@ -225,15 +225,12 @@ class TestFormsAndRequests( TwillTestCas strings_displayed_after_submit = [ 'Unsubmitted' ] for sample_name, field_values in sample_value_tuples: strings_displayed_after_submit.append( sample_name ) - for field_value in field_values: - strings_displayed_after_submit.append( field_value ) # Add samples to the request self.add_samples( cntrller='requests', request_id=self.security.encode_id( request_one.id ), request_name=request_one.name, sample_value_tuples=sample_value_tuples, - strings_displayed=[ 'Sequencing Request "%s"' % request_one.name, - 'There are no samples.' ], + strings_displayed=[ 'There are no samples.' ], strings_displayed_after_submit=strings_displayed_after_submit ) def test_030_edit_basic_request_info( self ): """Testing editing the basic information of a sequence run request""" @@ -277,11 +274,11 @@ class TestFormsAndRequests( TwillTestCas self.check_request_grid( cntrller='requests_admin', state=request_one.states.SUBMITTED, strings_displayed=[ request_one.name ] ) - self.visit_url( "%s/requests_common/manage_request?cntrller=requests&id=%s" % ( self.url, self.security.encode_id( request_one.id ) ) ) - self.check_page_for_string( 'Sequencing Request "%s"' % request_one.name ) + self.visit_url( "%s/requests_common/view_request?cntrller=requests&id=%s" % ( self.url, self.security.encode_id( request_one.id ) ) ) + # TODO: add some string for checking on the page above... # Set bar codes for the samples bar_codes = [ '1234567890', '0987654321' ] - strings_displayed_after_submit=[ 'Changes made to the samples are saved.' ] + strings_displayed_after_submit=[ 'Changes made to the samples have been saved.' ] for bar_code in bar_codes: strings_displayed_after_submit.append( bar_code ) self.add_bar_codes( request_id=self.security.encode_id( request_one.id ), @@ -333,7 +330,7 @@ class TestFormsAndRequests( TwillTestCas test_field_name1, test_field_name2, test_field_name3 ], - strings_displayed_after_submit=[ "The request has been created" ] ) + strings_displayed_after_submit=[ "The request has been created." ] ) global request_two request_two = get_request_by_name( name ) # Make sure the request is showing in the 'new' filter @@ -349,15 +346,12 @@ class TestFormsAndRequests( TwillTestCas strings_displayed_after_submit = [ 'Unsubmitted' ] for sample_name, field_values in sample_value_tuples: strings_displayed_after_submit.append( sample_name ) - for field_value in field_values: - strings_displayed_after_submit.append( field_value ) # Add samples to the request self.add_samples( cntrller='requests_admin', request_id=self.security.encode_id( request_two.id ), request_name=request_two.name, sample_value_tuples=sample_value_tuples, - strings_displayed=[ 'Sequencing Request "%s"' % request_two.name, - 'There are no samples.' ], + strings_displayed=[ 'There are no samples.' ], strings_displayed_after_submit=strings_displayed_after_submit ) # Submit the request self.submit_request( cntrller='requests_admin', @@ -394,6 +388,7 @@ class TestFormsAndRequests( TwillTestCas % ( request_two.name, request_two.states.REJECTED ) def test_055_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" + """ # Logged in as admin_user ################## # Delete request_type permissions @@ -438,3 +433,4 @@ class TestFormsAndRequests( TwillTestCas # Manually delete the group from the database refresh( group ) delete( group ) + """ --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -10,7 +10,7 @@ <a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a></li><li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller='requests_admin', id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller='requests_admin', id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li></ul> --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -158,9 +158,9 @@ class RequestsAdmin( BaseController, Use action='edit_basic_request_info', cntrller='requests_admin', **kwd ) ) - if operation == "manage_request": + if operation == "view_request": return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', + action='view_request', cntrller='requests_admin', **kwd ) ) if operation == "request_events": @@ -186,14 +186,14 @@ class RequestsAdmin( BaseController, Use return self.request_grid( trans, **kwd ) @web.expose @web.require_admin - def reject( self, trans, **kwd ): + def reject_request( self, trans, **kwd ): params = util.Params( kwd ) request_id = params.get( 'id', '' ) status = params.get( 'status', 'done' ) message = params.get( 'message', 'done' ) if params.get( 'cancel_reject_button', False ): return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', + action='view_request', cntrller='requests_admin', id=request_id ) ) try: @@ -292,7 +292,6 @@ class RequestsAdmin( BaseController, Use return invalid_id_redirect( trans, 'requests_admin', sample_id ) request_id = trans.security.encode_id( sample.request.id ) library_id = trans.security.encode_id( sample.library.id ) - self.datatx_grid.title = 'Datasets of sample "%s"' % sample.name self.datatx_grid.global_actions = [ grids.GridAction( "Refresh", dict( controller='requests_admin', action='manage_datasets', @@ -303,14 +302,14 @@ class RequestsAdmin( BaseController, Use request_id=request_id, folder_path=sample.request.type.datatx_info[ 'data_dir' ], sample_id=sample_id ) ), - grids.GridAction( 'Data library "%s"' % sample.library.name, - dict( controller='library_common', - action='browse_library', - cntrller='library_admin', - id=library_id ) ), + #grids.GridAction( 'Data library "%s"' % sample.library.name, + # dict( controller='library_common', + # action='browse_library', + # cntrller='library_admin', + # id=library_id ) ), grids.GridAction( "Browse this request", dict( controller='requests_common', - action='manage_request', + action='view_request', cntrller='requests_admin', id=request_id ) ) ] return self.datatx_grid( trans, **kwd ) --- a/templates/requests/common/edit_basic_request_info.mako +++ b/templates/requests/common/edit_basic_request_info.mako @@ -1,14 +1,25 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> +<% + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + can_add_samples = request.is_unsubmitted +%> + <br/><br/><ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> - </li> - <li> - <a class="action-button" href="${h.url_for( controller=cntrller, action='browse_requests' )}">Browse all requests</a> - </li> + <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li> + <div popupmenu="request-${request.id}-popup"> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> + %if can_add_samples: + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a> + %endif + <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> + %if is_admin and request.is_submitted: + <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> + %endif + </div></ul> %if message: --- /dev/null +++ b/templates/requests/common/view_request.mako @@ -0,0 +1,157 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/requests/common/common.mako" import="common_javascripts" /> +<%namespace file="/requests/common/common.mako" import="render_samples_grid" /> +<%namespace file="/requests/common/common.mako" import="render_request_type_sample_form_grids" /> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "library" )} +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${common_javascripts()} +</%def> + +<% + from galaxy.web.framework.helpers import time_ago + + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_unsubmitted = request.is_unsubmitted + can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted + can_add_samples = is_unsubmitted +%> + +<br/><br/> + +<ul class="manage-table-actions"> + %if is_unsubmitted: + <li><a class="action-button" confirm="More samples cannot be added to this request after it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit request</a></li> + %endif + <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request actions</a></li> + <div popupmenu="request-${request.id}-popup"> + %if can_edit_request: + <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> + %endif + <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> + %if is_admin and request.is_submitted: + <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> + %endif + </div> +</ul> + +%if request.is_rejected: + <font color="red"><b><i>Reason for rejection: </i></b></font><b>${request.last_comment}</b> + <br/><br/> +%endif + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Sequencing request "${request.name}"</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>Current state:</label> + ${request.state} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Description:</label> + ${request.desc} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>User:</label> + %if is_admin: + ${request.user.email} + %elif request.user.username: + ${request.user.username} + %else: + Unknown + %endif + <div style="clear: both"></div> + </div> + <div class="form-row"> + <h4><img src="/static/images/fugue/toggle-expand.png" alt="Show" onclick="showContent(this);" style="cursor:pointer;"/> More</h4> + <div style="display:none;"> + %for index, rd in enumerate( request_widgets ): + <% + field_label = rd[ 'label' ] + field_value = rd[ 'value' ] + %> + <div class="form-row"> + <label>${field_label}:</label> + %if field_label == 'State': + <a href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">${field_value}</a> + %else: + ${field_value} + %endif + </div> + <div style="clear: both"></div> + %endfor + <div class="form-row"> + <label>Date created:</label> + ${request.create_time} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Last updated:</label> + ${time_ago( request.update_time )} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Email recipients:</label> + <% + if request.notification: + emails = ', '.join( request.notification[ 'email' ] ) + else: + emails = '' + %> + ${emails} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Send email when state changes to:</label> + <% + if request.notification: + states = [] + for ss in request.type.states: + if ss.id in request.notification[ 'sample_states' ]: + states.append( ss.name ) + states = ', '.join( states ) + else: + states = '' + %> + ${states} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Sequencer configuration:</label> + ${request.type.name} + <div style="clear: both"></div> + </div> + </div> + </div> + </div> +</div> +<p/> +%if current_samples: + <% grid_header = '<h3>Samples</h3>' %> + ${render_samples_grid( cntrller, request, current_samples=current_samples, action='view_request', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=can_edit_request, grid_header=grid_header )} +%else: + There are no samples. + %if can_add_samples: + <ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='add_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), add_sample_button='Add sample' )}">Add sample</a></li> + </ul> + %endif +%endif +## Render the other grids +<% trans.sa_session.refresh( request.type.sample_form ) %> +%for grid_index, grid_name in enumerate( request.type.sample_form.layout ): + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), editing_samples=False )} +%endfor --- a/lib/galaxy/web/controllers/library.py +++ b/lib/galaxy/web/controllers/library.py @@ -24,13 +24,11 @@ class LibraryListGrid( grids.Grid ): columns = [ NameColumn( "Name", key="name", - model_class=model.Library, link=( lambda library: dict( operation="browse", id=library.id ) ), attach_popup=False, filterable="advanced" ), DescriptionColumn( "Description", key="description", - model_class=model.Library, attach_popup=False, filterable="advanced" ), ] --- a/templates/admin/forms/show_form_read_only.mako +++ b/templates/admin/forms/show_form_read_only.mako @@ -81,10 +81,10 @@ <form name="library" action="${h.url_for( controller='forms', action='manage' )}" method="post" > %if form_definition.type == trans.app.model.FormDefinition.types.SAMPLE: %if not len(form_definition.layout): - ${render_grid( 0, '', form_definition.fields_of_grid( None ) )} + ${render_grid( 0, '', form_definition.grid_fields( None ) )} %else: %for grid_index, grid_name in enumerate(form_definition.layout): - ${render_grid( grid_index, grid_name, form_definition.fields_of_grid( grid_index ) )} + ${render_grid( grid_index, grid_name, form_definition.grid_fields( grid_index ) )} %endfor %endif %else: --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -346,7 +346,6 @@ ><td style="padding-left: ${folder_pad}px;"><input type="checkbox" class="folderCheckbox"/> - %if folder.deleted: <span class="libraryItem-error"> %endif @@ -354,7 +353,6 @@ <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup"><a href="javascript:void(0);">${folder.name}</a></div> - %if folder.deleted: </span> %endif --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -8,16 +8,16 @@ <h2>Reject Sequencing Request "${request.name}"</h2><ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">Events</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">View history</a></li><li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">Browse this request</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">Browse this request</a></li></ul><div class="toolForm"><div class="toolFormTitle">Reject request</div> - <form name="event" action="${h.url_for( controller='requests_admin', action='reject', id=trans.security.encode_id( request.id ) )}" method="post" > + <form name="event" action="${h.url_for( controller='requests_admin', action='reject_request', id=trans.security.encode_id( request.id ) )}" method="post" ><div class="form-row"> Rejecting this request will move the request state to <b>Rejected</b>. </div> --- a/templates/admin/requests/get_data.mako +++ b/templates/admin/requests/get_data.mako @@ -75,7 +75,7 @@ <a class="action-button" href="${h.url_for( controller='requests_admin', action='view_request_type', id=trans.security.encode_id( request.type.id ) )}">Sequencer configuration "${request.type.name}"</a></li><li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a></li></ul> --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1488,25 +1488,23 @@ class MetadataFile( object ): return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) ) class FormDefinition( object ): - types = Bunch( REQUEST = 'Sequencing Request Form', - SAMPLE = 'Sequencing Sample Form', - LIBRARY_INFO_TEMPLATE = 'Library information template', - USER_INFO = 'User Information' ) - def __init__(self, name=None, desc=None, fields=[], - form_definition_current=None, form_type=None, layout=None): + types = Bunch( REQUEST = 'Sequencing Request Form', + SAMPLE = 'Sequencing Sample Form', + LIBRARY_INFO_TEMPLATE = 'Library information template', + USER_INFO = 'User Information' ) + def __init__( self, name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None ): self.name = name self.desc = desc self.fields = fields self.form_definition_current = form_definition_current self.type = form_type self.layout = layout - def fields_of_grid(self, grid_index): - ''' - This method returns the list of fields belonging to the given grid. - ''' + def grid_fields( self, grid_index ): + # Returns a dictionary whose keys are integers corresponding to field positions + # on the grid and whose values are the field. gridfields = {} - for i, f in enumerate(self.fields): - if str(f['layout']) == str(grid_index): + for i, f in enumerate( self.fields ): + if str( f[ 'layout' ] ) == str( grid_index ): gridfields[i] = f return gridfields def get_widgets( self, user, contents=[], **kwd ): --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -10,11 +10,10 @@ log = logging.getLogger( __name__ ) class UserRequestsGrid( RequestsGrid ): operations = [ operation for operation in RequestsGrid.operations ] - operations.append( grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted and item.is_unsubmitted ) ) ) - operations.append( grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: not item.deleted and item.is_new ) ) ) + operations.append( grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: item.is_unsubmitted and not item.deleted ) ) ) + operations.append( grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: item.is_new and not item.deleted ) ) ) operations.append( grids.GridOperation( "Undelete", allow_multiple=True, condition=( lambda item: item.deleted ) ) ) def apply_query_filter( self, trans, query, **kwd ): - # gvk ( 9/28/10 ) TODO: is this method needed? return query.filter_by( user=trans.user ) class Requests( BaseController ): @@ -37,9 +36,9 @@ class Requests( BaseController ): action='edit_basic_request_info', cntrller='requests', **kwd ) ) - if operation == "manage_request": + if operation == "view_request": return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', + action='view_request', cntrller='requests', **kwd ) ) if operation == "delete": @@ -70,12 +69,12 @@ class Requests( BaseController ): message = "%d requests (highlighted in red) were rejected. Click on the request name for details." % rejected kwd[ 'status' ] = status kwd[ 'message' ] = message - # show the create request button to the user, only when the user has permissions - # to at least one request_type (sequencer configuration) + # Allow the user to create a new request only if they have permission to access a + # (sequencer configuration) request type. if len( trans.user.accessible_request_types( trans ) ): self.request_grid.global_actions = [ grids.GridAction( "Create new request", dict( controller='requests_common', - action='create_request', - cntrller='requests' ) ) ] + action='create_request', + cntrller='requests' ) ) ] else: self.request_grid.global_actions = [] # Render the list view --- a/templates/requests/common/find_samples.mako +++ b/templates/requests/common/find_samples.mako @@ -76,7 +76,7 @@ <i>User: ${sample.request.user.email}</i> %endif <div class="toolParamHelp" style="clear: both;"> - <a href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a> + <a href="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a></div></div><br/> --- a/lib/galaxy/web/controllers/forms.py +++ b/lib/galaxy/web/controllers/forms.py @@ -86,7 +86,7 @@ class Forms( BaseController ): status='error', message="Invalid form ID") ) if operation == "view": - return self.__view( trans, **kwd ) + return self.view_form_definition( trans, **kwd ) elif operation == "delete": return self.__delete( trans, **kwd ) elif operation == "undelete": @@ -94,10 +94,12 @@ class Forms( BaseController ): elif operation == "edit": return self.edit( trans, **kwd ) return self.forms_grid( trans, **kwd ) - def __view(self, trans, **kwd): + @web.expose + def view_form_definition( self, trans, **kwd ): + form_definition_current_id = kwd.get( 'id', None ) try: - fdc = trans.sa_session.query( trans.app.model.FormDefinitionCurrent )\ - .get( trans.security.decode_id(kwd['id']) ) + fdc = trans.sa_session.query( trans.app.model.FormDefinitionCurrent ) \ + .get( trans.security.decode_id( form_definition_current_id ) ) except: return trans.response.send_redirect( web.url_for( controller='forms', action='manage', --- /dev/null +++ b/templates/requests/common/common.mako @@ -0,0 +1,332 @@ +<%namespace file="/requests/common/sample_state.mako" import="render_sample_state" /> + +<%def name="javascripts()"> + ${self.common_javascripts()} +</%def> + +<%def name="common_javascripts()"> + <script type="text/javascript"> + function showContent(vThis) + { + // http://www.javascriptjunkie.com + // alert(vSibling.className + " " + vDef_Key); + vParent = vThis.parentNode; + vSibling = vParent.nextSibling; + while (vSibling.nodeType==3) { + // Fix for Mozilla/FireFox Empty Space becomes a TextNode or Something + vSibling = vSibling.nextSibling; + }; + if(vSibling.style.display == "none") + { + vThis.src="/static/images/fugue/toggle.png"; + vThis.alt = "Hide"; + vSibling.style.display = "block"; + } else { + vSibling.style.display = "none"; + vThis.src="/static/images/fugue/toggle-expand.png"; + vThis.alt = "Show"; + } + return; + } + $(document).ready(function(){ + //hide the all of the element with class msg_body + $(".msg_body").hide(); + //toggle the component with class msg_body + $(".msg_head").click(function(){ + $(this).next(".msg_body").slideToggle(0); + }); + }); + + function checkAllFields() + { + var chkAll = document.getElementById('checkAll'); + var checks = document.getElementsByTagName('input'); + var boxLength = checks.length; + var allChecked = false; + var totalChecked = 0; + if ( chkAll.checked == true ) + { + for ( i=0; i < boxLength; i++ ) + { + if ( checks[i].name.indexOf( 'select_sample_' ) != -1) + { + checks[i].checked = true; + } + } + } + else + { + for ( i=0; i < boxLength; i++ ) + { + if ( checks[i].name.indexOf( 'select_sample_' ) != -1) + { + checks[i].checked = false + } + } + } + } + </script> +</%def> + +<%def name="render_editable_sample_row( is_admin, sample, current_sample_index, current_sample, encoded_selected_sample_ids )"> + <% + if sample: + is_complete = sample.request.is_complete + is_submitted = sample.request.is_submitted + is_unsubmitted = sample.request.is_unsubmitted + else: + is_complete = False + is_submitted = False + is_unsubmitted = False + %> + <% + if is_admin and is_submitted and editing_samples and trans.security.encode_id( sample.id ) in encoded_selected_sample_ids: + checked_str = "checked" + else: + checked_str = "" + %> + %if is_admin and is_submitted and editing_samples: + <td><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" ${checked_str}/><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"/></td> + %endif + <td> + <input type="text" name="sample_${current_sample_index}_name" value="${current_sample['name']}" size="10"/> + <div class="toolParamHelp" style="clear: both;"> + <i>${' (required)' }</i> + </div> + </td> + %if sample and is_submitted or is_complete: + <td><input type="text" name="sample_${current_sample_index}_barcode" value="${current_sample['barcode']}" size="10"/></td> + %endif + %if sample: + %if is_unsubmitted: + <td>Unsubmitted</td> + %else: + <td><a href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a></td> + %endif + %else: + <td></td> + %endif + <td>${current_sample['library_select_field'].get_html()}</td> + <td>${current_sample['folder_select_field'].get_html()}</td> + %if is_submitted or is_complete: + <% + if sample: + label = str( len( sample.datasets ) ) + else: + label = 'add' + %> + <td><a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${label}</a></td> + <td><a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${label}</a></td> + %endif + %if sample and ( is_admin or is_unsubmitted ): + ## Delete button + <td><a class="action-button" href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=current_sample_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td> + %endif +</%def> + +<%def name="render_samples_grid( cntrller, request, current_samples, action, editing_samples=False, encoded_selected_sample_ids=[], render_buttons=False, grid_header='<h3>Samples</h3>' )"> + ## Displays the "Samples" grid + <% + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_complete = request.is_complete + is_submitted = request.is_submitted + is_unsubmitted = request.is_unsubmitted + can_add_samples = request.is_unsubmitted + can_edit_or_delete_samples = request.samples and ( is_admin or request.is_unsubmitted ) + %> + ${grid_header} + %if render_buttons and ( can_add_samples or can_edit_or_delete_samples ): + <ul class="manage-table-actions"> + %if can_add_samples: + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='add_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), add_sample_button='Add sample' )}">Add sample</a></li> + %endif + %if can_edit_or_delete_samples: + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), editing_samples='True' )}">Edit samples</a></li> + %endif + </ul> + %endif + <table class="grid"> + <thead> + <tr> + %if is_admin and is_submitted and editing_samples: + <th><input type="checkbox" id="checkAll" name=select_all_samples_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_samples_checkbox value="true"/></th> + %endif + <th>Name</th> + %if is_submitted or is_complete: + <th>Barcode</th> + %endif + <th>State</th> + <th>Data Library</th> + <th>Folder</th> + %if is_submitted or is_complete: + <th>Datasets Selected</th> + <th>Datasets Transferred</th> + %endif + <th> + %if editing_samples: + Delete + %endif + </th> + </tr> + <thead> + <tbody> + <% trans.sa_session.refresh( request ) %> + ## current_samples is a dictionary whose keys are: + ## name, barcode, library, folder, field_values, library_select_field, folder_select_field + %for current_sample_index, current_sample in enumerate( current_samples ): + <% + current_sample_name = current_sample[ 'name' ] + current_sample_barcode = current_sample[ 'barcode' ] + current_sample_library = current_sample[ 'library' ] + if current_sample_library: + if cntrller == 'requests': + library_cntrller = 'library' + elif is_admin: + library_cntrller = 'library_admin' + else: + library_cntrller = None + current_sample_folder = current_sample[ 'folder' ] + try: + sample = request.samples[ current_sample_index ] + except: + sample = None + %> + %if editing_samples: + <tr>${render_editable_sample_row( is_admin, sample, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr> + %elif sample: + <tr> + <td>${current_sample_name}</td> + %if is_submitted or is_complete: + <td>${current_sample_barcode}</td> + %endif + %if is_unsubmitted: + <td>Unsubmitted</td> + %else: + <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> + %endif + %if current_sample_library and library_cntrller is not None: + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( current_sample_library.id ) )}">${current_sample_library.name}</a></td> + %else: + <td></td> + %endif + %if current_sample_folder: + <td>${current_sample_folder.name}</td> + %else: + <td></td> + %endif + %if is_submitted or is_complete: + <td><a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a></td> + <td><a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a></td> + %endif + </tr> + %else: + <tr>${render_editable_sample_row( is_admin, None, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr> + %endif + %endfor + </tbody> + </table> +</%def> + +<%def name="render_sample_form( index, sample_name, sample_values, fields_dict, display_only )"> + <tr> + <td>${sample_name}</td> + %for field_index, field in fields_dict.items(): + <% + field_type = field[ 'type' ] + %> + <td> + %if display_only: + %if sample_values[field_index]: + %if field_type == 'WorkflowField': + %if str(sample_values[field_index]) != 'none': + <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int( sample_values[ field_index ] ) ) %> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name}</a> + %endif + %else: + ${sample_values[ field_index ]} + %endif + %else: + <i>None</i> + %endif + %else: + %if field_type == 'TextField': + <input type="text" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/> + %elif field_type == 'SelectField': + <select name="sample_${index}_field_${field_index}" last_selected_value="2"> + %for option_index, option in enumerate(field['selectlist']): + %if option == sample_values[field_index]: + <option value="${option}" selected>${option}</option> + %else: + <option value="${option}">${option}</option> + %endif + %endfor + </select> + %elif field_type == 'WorkflowField': + <select name="sample_${index}_field_${field_index}"> + %if str(sample_values[field_index]) == 'none': + <option value="none" selected>Select one</option> + %else: + <option value="none">Select one</option> + %endif + %for option_index, option in enumerate(request.user.stored_workflows): + %if not option.deleted: + %if str(option.id) == str(sample_values[field_index]): + <option value="${option.id}" selected>${option.name}</option> + %else: + <option value="${option.id}">${option.name}</option> + %endif + %endif + %endfor + </select> + %elif field_type == 'CheckboxField': + <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/> + %endif + <div class="toolParamHelp" style="clear: both;"> + <i>${'('+field['required']+')' }</i> + </div> + %endif + </td> + %endfor + </tr> +</%def> + +<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, editing_samples )"> + <% + if not grid_name: + grid_name = "Sample form layout " + grid_index + %> + <h4><img src="/static/images/fugue/toggle-expand.png" alt="Hide" onclick="showContent(this);" style="cursor:pointer;"/> ${grid_name}</h4> + <div style="display:none;"> + <table class="grid"> + <thead> + <tr> + <th>Name</th> + %for index, field in fields_dict.items(): + <th> + ${field['label']} + ## TODO: help comments in the grid header are UGLY! + ## If they are needed display them more appropriately, + ## if they are not, delete this commented code. + ##<div class="toolParamHelp" style="clear: both;"> + ## <i>${field['helptext']}</i> + ##</div> + </th> + %endfor + <th></th> + </tr> + <thead> + <tbody> + <% trans.sa_session.refresh( request ) %> + %for sample_index, sample in enumerate( current_samples ): + <% + if editing_samples or sample_index >= len( request.samples ): + display_only = False + else: + display_only = True + %> + ${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict, display_only )} + %endfor + </tbody> + </table> + </div> +</%def> --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1489,17 +1489,17 @@ class TwillTestCase( unittest.TestCase ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) def add_samples( self, cntrller, request_id, request_name, sample_value_tuples, strings_displayed=[], strings_displayed_after_submit=[] ): - self.visit_url( "%s/requests_common/manage_request?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) + self.visit_url( "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=False" % ( self.url, cntrller, request_id ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) # Simulate clicking the add-sample_button on the form. (gvk: 9/21/10 - TODO : There must be a bug in the mako template # because twill cannot find any forms on the page, but I cannot find it although I've spent time cleaning up the # template code and looking for any problems. - url = "%s/requests_common/manage_request?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) + url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=False" % ( self.url, cntrller, request_id ) # This should work, but although twill does not thorw any exceptions, the button click never occurs - # There are multiple forms on this page, and we'll only be using the form named manage_request. + # There are multiple forms on this page, and we'll only be using the form named edit_samples. # for sample_index, sample_value_tuple in enumerate( sample_value_tuples ): - # # Add the following form value to the already populated hidden field so that the manage_request + # # Add the following form value to the already populated hidden field so that the edit_samples # # form is the current form # tc.fv( "1", "id", request_id ) # tc.submit( 'add_sample_button' ) @@ -1530,7 +1530,7 @@ class TwillTestCase( unittest.TestCase ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) def reject_request( self, request_id, request_name, comment, strings_displayed=[], strings_displayed_after_submit=[] ): - self.visit_url( "%s/requests_admin/reject?id=%s" % ( self.url, request_id ) ) + self.visit_url( "%s/requests_admin/reject_request?id=%s" % ( self.url, request_id ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) tc.fv( "1", "comment", comment ) @@ -1540,7 +1540,7 @@ class TwillTestCase( unittest.TestCase ) def add_bar_codes( self, request_id, request_name, bar_codes, samples, strings_displayed_after_submit=[] ): # We have to simulate the form submission here since twill barfs on the page # gvk - 9/22/10 - TODO: make sure the mako template produces valid html - url = "%s/requests_common/manage_request?cntrller=requests_admin&id=%s&managing_samples=True" % ( self.url, request_id ) + url = "%s/requests_common/edit_samples?cntrller=requests_admin&id=%s&editing_samples=True" % ( self.url, request_id ) for index, field_value in enumerate( bar_codes ): sample_field_name = "sample_%i_name" % index sample_field_value = samples[ index ].name.replace( ' ', '+' ) @@ -1555,15 +1555,15 @@ class TwillTestCase( unittest.TestCase ) strings_displayed=[], strings_displayed_after_submit=[] ): # We have to simulate the form submission here since twill barfs on the page # gvk - 9/22/10 - TODO: make sure the mako template produces valid html - url = "%s/requests_common/manage_request?cntrller=requests_admin&id=%s" % ( self.url, request_id ) + url = "%s/requests_common/edit_samples?cntrller=requests_admin&id=%s" % ( self.url, request_id ) url += "&comment=%s&sample_state_id=%s" % ( comment, self.security.encode_id( new_sample_state_id ) ) # select_sample_%i=true must be included twice for each sample to simulate a CheckboxField checked setting. for sample_id in sample_ids: url += "&select_sample_%i=true&select_sample_%i=true" % ( sample_id, sample_id ) url += "&sample_operation=Change%20state&refresh=true" - url += "&change_state_button=Save" + url += "&save_changes_button=Save&editing_samples=True" self.visit_url( url ) - self.check_page_for_string( 'Sequencing Request "%s"' % request_name ) + self.check_page_for_string( 'Edit Current Samples of Request "%s"' % request_name ) for sample_id, sample_name in zip( sample_ids, sample_names ): self.visit_url( "%s/requests_common/sample_events?cntrller=requests_admin&sample_id=%s" % ( self.url, self.security.encode_id( sample_id ) ) ) self.check_page_for_string( 'Events for Sample "%s"' % sample_name ) --- a/templates/requests/common/events.mako +++ b/templates/requests/common/events.mako @@ -1,20 +1,36 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<h2>History of Sequencing Request "${request.name}"</h2> +<% + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted + can_add_samples = request.is_unsubmitted +%> + +<br/><br/><ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> - </li> - <li> - <a class="action-button" href="${h.url_for( controller=cntrller, action='browse_requests' )}">Browse all requests</a> - </li> + <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li> + <div popupmenu="request-${request.id}-popup"> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> + %if can_edit_request: + <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> + %endif + %if can_add_samples: + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a> + %endif + %if is_admin and request.is_submitted: + <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> + %endif + </div></ul> %if message: ${render_msg( message, status )} %endif +<h2>History of Sequencing Request "${request.name}"</h2> + <div class="toolForm"><table class="grid"><thead> --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -70,14 +70,14 @@ class RequestsGrid( grids.Grid ): columns = [ NameColumn( "Name", key="name", - link=( lambda item: iff( item.deleted, None, dict( operation="manage_request", id=item.id ) ) ), + link=( lambda item: iff( item.deleted, None, dict( operation="view_request", id=item.id ) ) ), attach_popup=True, filterable="advanced" ), DescriptionColumn( "Description", key='desc', filterable="advanced" ), SamplesColumn( "Samples", - link=( lambda item: iff( item.deleted, None, dict( operation="manage_request", id=item.id ) ) ) ), + link=( lambda item: iff( item.deleted, None, dict( operation="edit_samples", id=item.id ) ) ) ), TypeColumn( "Sequencer", link=( lambda item: iff( item.deleted, None, dict( operation="view_type", id=item.type.id ) ) ) ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -148,7 +148,7 @@ class RequestsCommon( BaseController, Us except TypeError, e: # We must have an email address rather than an encoded user id # This is because the galaxy.base.js creates a search+select box - # when there are more than 20 items in a selectfield + # when there are more than 20 items in a SelectField. user = trans.sa_session.query( trans.model.User ) \ .filter( trans.model.User.table.c.email==util.restore_text( user_id ) ) \ .first() @@ -178,7 +178,8 @@ class RequestsCommon( BaseController, Us message=message , status='done' ) ) elif params.get( 'add_sample_button', False ): - return self.__add_sample( trans, cntrller, request, **kwd ) + request_id = trans.security.encode_id( request.id ) + return self.add_sample( trans, cntrller, request_id, **kwd ) request_type_select_field = self.__build_request_type_id_select_field( trans, selected_value=request_type_id ) # Widgets to be rendered on the request form widgets = [] @@ -194,7 +195,7 @@ class RequestsCommon( BaseController, Us widgets += request_type.request_form.get_widgets( user, **kwd ) # In case there is an error on the form, make sure to populate widget fields with anything the user # may have already entered. - self.populate_widgets_from_kwd( trans, widgets, **kwd ) + widgets = self.populate_widgets_from_kwd( trans, widgets, **kwd ) if request_type is not None or status == 'error': # Either the user selected a request_type or an error exists on the form. if is_admin: @@ -214,6 +215,29 @@ class RequestsCommon( BaseController, Us message=message, status=status ) @web.expose + @web.require_login( "view request" ) + def view_request( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + request_id = params.get( 'id', None ) + try: + request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) + except: + return invalid_id_redirect( trans, cntrller, request_id ) + sample_state_id = params.get( 'sample_state_id', None ) + # Get the user entered sample information + current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd ) + request_widgets = self.__get_request_widgets( trans, request.id ) + return trans.fill_template( '/requests/common/view_request.mako', + cntrller=cntrller, + request=request, + request_widgets=request_widgets, + current_samples=current_samples, + status=status, + message=message ) + @web.expose @web.require_login( "edit sequencing requests" ) def edit_basic_request_info( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -226,7 +250,7 @@ class RequestsCommon( BaseController, Us return invalid_id_redirect( trans, cntrller, request_id ) name = util.restore_text( params.get( 'name', '' ) ) desc = util.restore_text( params.get( 'desc', '' ) ) - if params.get( 'edit_basic_request_info_button', False ) or params.get( 'edit_samples_button', False ): + if params.get( 'edit_basic_request_info_button', False ): if not name: status = 'error' message = 'Enter the name of the request' @@ -244,7 +268,7 @@ class RequestsCommon( BaseController, Us widgets = widgets + request.type.request_form.get_widgets( request.user, request.values.content, **kwd ) # In case there is an error on the form, make sure to populate widget fields with anything the user # may have already entered. - self.populate_widgets_from_kwd( trans, widgets, **kwd ) + widgets = self.populate_widgets_from_kwd( trans, widgets, **kwd ) return trans.fill_template( 'requests/common/edit_basic_request_info.mako', cntrller=cntrller, request_type=request.type, @@ -371,8 +395,8 @@ class RequestsCommon( BaseController, Us status=status, message=message ) ) @web.expose - @web.require_login( "sequencing request page" ) - def manage_request( self, trans, cntrller, **kwd ): + @web.require_login( "manage samples" ) + def edit_samples( self, trans, cntrller, **kwd ): params = util.Params( kwd ) is_admin = cntrller == 'requests_admin' and trans.user_is_admin() message = util.restore_text( params.get( 'message', '' ) ) @@ -382,80 +406,64 @@ class RequestsCommon( BaseController, Us request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) except: return invalid_id_redirect( trans, cntrller, request_id ) - sample_state_id = params.get( 'sample_state_id', None ) + # This method is called when the user is adding new samples as well as + # editing existing samples, so we use the editing_samples flag to keep + # track of what's occurring. + # TODO: CRITICAL: We need another round of code fixes to abstract out + # adding samples vs editing samples. We need to eliminate the need for + # this editing_samples flag since it is not maintainable. Greg will do + # this work as soon as possible. + editing_samples = util.string_as_bool( params.get( 'editing_samples', False ) ) + if params.get( 'cancel_changes_button', False ): + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='edit_samples', + cntrller=cntrller, + id=request_id, + editing_samples=editing_samples ) ) + # Get all libraries for which the current user has permission to add items. + libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) # Get the user entered sample information - current_samples, managing_samples, libraries = self.__get_sample_info( trans, request, **kwd ) - selected_samples = self.__get_selected_samples( trans, request, **kwd ) - selected_value = params.get( 'sample_operation', 'none' ) - if selected_value != 'none' and not selected_samples: + current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd ) + encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) + sample_operation = params.get( 'sample_operation', 'none' ) + def handle_error( **kwd ): + kwd[ 'status' ] = 'error' + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='edit_samples', + cntrller=cntrller, + **kwd ) ) + if not encoded_selected_sample_ids and sample_operation != 'none': + # Probably occurred due to refresh_on_change...is there a better approach? + kwd[ 'sample_operation' ] = 'none' message = 'Select at least one sample before selecting an operation.' - status = 'error' - return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', - cntrller=cntrller, - id=request_id, - status=status, - message=message ) ) - sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, selected_value ) - sample_operation_selected_value = sample_operation_select_field.get_selected( return_value=True ) + kwd[ 'message' ] = message + handle_error( **kwd ) if params.get( 'import_samples_button', False ): # Import sample field values from a csv file return self.__import_samples( trans, cntrller, request, current_samples, libraries, **kwd ) elif params.get( 'add_sample_button', False ): - return self.__add_sample( trans, cntrller, request, **kwd ) + return self.add_sample( trans, cntrller, request_id, **kwd ) elif params.get( 'save_samples_button', False ): - return self.__save_sample( trans, cntrller, request, current_samples, **kwd ) - elif params.get( 'edit_samples_button', False ): - managing_samples = True - elif params.get( 'cancel_changes_button', False ): - return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', - cntrller=cntrller, - id=request_id ) ) - pass - elif params.get( 'change_state_button', False ): - sample_event_comment = util.restore_text( params.get( 'sample_event_comment', '' ) ) - new_state = trans.sa_session.query( trans.model.SampleState ).get( trans.security.decode_id( sample_state_id ) ) - self.update_sample_state(trans, cntrller, selected_samples, new_state, comment=sample_event_comment ) - return trans.response.send_redirect( web.url_for( controller='requests_common', - cntrller=cntrller, - action='update_request_state', - request_id=request_id ) ) - elif params.get( 'cancel_change_state_button', False ): - return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', - cntrller=cntrller, - id=request_id ) ) - elif params.get( 'change_lib_button', False ): - library_id = params.get( 'sample_0_library_id', None ) - try: - library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( library_id ) ) - except: - invalid_id_redirect( trans, cntrller, library_id ) - folder_id = params.get( 'sample_0_folder_id', None ) - try: - folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) ) - except: - invalid_id_redirect( trans, cntrller, folder_id ) - for sample_id in selected_samples: - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) - sample.library = library - sample.folder = folder - trans.sa_session.add( sample ) - trans.sa_session.flush() - trans.sa_session.refresh( request ) - message = 'Changes made to the selected samples have been saved. ' - return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', - cntrller=cntrller, - id=request_id, - status=status, - message=message ) ) - elif params.get( 'cancel_change_lib_button', False ): - return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', - cntrller=cntrller, - id=trans.security.encode_id( request.id ) ) ) + if encoded_selected_sample_ids: + # This gets tricky because we need the list of samples to include the same number + # of objects that that current_samples ( i.e., request.samples ) has. We'll first + # get the set of samples corresponding to the checked sample ids. + samples = [] + selected_samples = [] + for encoded_sample_id in encoded_selected_sample_ids: + sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( encoded_sample_id ) ) + selected_samples.append( sample ) + # Now build the list of samples, inserting None for samples that have not been checked. + for sample in request.samples: + if sample in selected_samples: + samples.append( sample ) + else: + samples.append( None ) + # The __save_samples method requires samples widgets, not sample objects + samples = self.__get_sample_widgets( trans, request, samples, **kwd ) + else: + samples = current_samples + return self.__save_samples( trans, cntrller, request, samples, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, @@ -464,12 +472,13 @@ class RequestsCommon( BaseController, Us libraries, None, **kwd ) - # Build the sample_state_id_select_field SelectField + sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, sample_operation ) + sample_state_id = params.get( 'sample_state_id', None ) sample_state_id_select_field = self.__build_sample_state_id_select_field( trans, request, sample_state_id ) - return trans.fill_template( '/requests/common/manage_request.mako', + return trans.fill_template( '/requests/common/edit_samples.mako', cntrller=cntrller, request=request, - selected_samples=selected_samples, + encoded_selected_sample_ids=encoded_selected_sample_ids, request_widgets=request_widgets, current_samples=current_samples, sample_copy=sample_copy, @@ -478,7 +487,7 @@ class RequestsCommon( BaseController, Us libraries_select_field=libraries_select_field, folders_select_field=folders_select_field, sample_state_id_select_field=sample_state_id_select_field, - managing_samples=managing_samples, + editing_samples=editing_samples, status=status, message=message ) @web.expose @@ -489,7 +498,7 @@ class RequestsCommon( BaseController, Us except: if cntrller == 'api': trans.response.status = 400 - return "Malformed sample id ( %s ) specified, unable to decode." % str( sample_id ) + return "Invalid sample id ( %s ) specified, unable to decode." % str( sample_id ) else: return invalid_id_redirect( trans, cntrller, sample_id ) event = trans.model.SampleEvent( sample, new_state, comment ) @@ -516,7 +525,7 @@ class RequestsCommon( BaseController, Us if ok_for_now: request.deleted = True trans.sa_session.add( request ) - # delete all the samples belonging to this request + # Delete all the samples belonging to this request for s in request.samples: s.deleted = True trans.sa_session.add( s ) @@ -546,7 +555,7 @@ class RequestsCommon( BaseController, Us if ok_for_now: request.deleted = False trans.sa_session.add( request ) - # undelete all the samples belonging to this request + # Undelete all the samples belonging to this request for s in request.samples: s.deleted = False trans.sa_session.add( s ) @@ -655,9 +664,10 @@ class RequestsCommon( BaseController, Us if cntrller == 'api': return 200, message return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', + action='edit_samples', cntrller=cntrller, id=request_id, + editing_samples=True, status=status, message=message ) ) final_state = False @@ -673,8 +683,8 @@ class RequestsCommon( BaseController, Us event = trans.model.RequestEvent( request, state, comments ) trans.sa_session.add( event ) trans.sa_session.flush() - # check if an email notification is configured to be sent when the samples - # are in this state + # See if an email notification is configured to be sent when the samples + # are in this state. retval = request.send_email_notification( trans, common_state, final_state ) if retval: message = comments + retval @@ -683,113 +693,10 @@ class RequestsCommon( BaseController, Us if cntrller == 'api': return 200, message return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', + action='edit_samples', cntrller=cntrller, - id=trans.security.encode_id(request.id), - status='done', - message=message ) ) - def __save_sample( self, trans, cntrller, request, current_samples, **kwd ): - # Save all the new/unsaved samples entered by the user - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - managing_samples = util.string_as_bool( params.get( 'managing_samples', False ) ) - is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - selected_value = params.get( 'sample_operation', 'none' ) - # Check for duplicate sample names - message = '' - for index in range( len( current_samples ) - len( request.samples ) ): - sample_index = index + len( request.samples ) - current_sample = current_samples[ sample_index ] - sample_name = current_sample[ 'name' ] - if not sample_name.strip(): - message = 'Enter the name of sample number %i' % sample_index - break - count = 0 - for i in range( len( current_samples ) ): - if sample_name == current_samples[ i ][ 'name' ]: - count += 1 - if count > 1: - message = "This request has %i samples with the name (%s). Samples belonging to a request must have unique names." % ( count, sample_name ) - break - if message: - selected_samples = self.__get_selected_samples( trans, request, **kwd ) - request_widgets = self.__get_request_widgets( trans, request.id ) - sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) - sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, selected_value ) - status = 'error' - return trans.fill_template( '/requests/common/manage_request.mako', - cntrller=cntrller, - request=request, - selected_samples=selected_samples, - request_widgets=request_widgets, - current_samples=current_samples, - sample_copy=sample_copy, - managing_samples=managing_samples, - sample_operation_select_field=sample_operation_select_field, - status=status, - message=message ) - if not managing_samples: - for index in range( len( current_samples ) - len( request.samples ) ): - sample_index = len( request.samples ) - current_sample = current_samples[ sample_index ] - form_values = trans.model.FormValues( request.type.sample_form, current_sample[ 'field_values' ] ) - trans.sa_session.add( form_values ) - trans.sa_session.flush() - s = trans.model.Sample( current_sample[ 'name' ], - '', - request, - form_values, - current_sample[ 'barcode' ], - current_sample[ 'library' ], - current_sample[ 'folder' ] ) - trans.sa_session.add( s ) - trans.sa_session.flush() - else: - message = 'Changes made to the samples are saved. ' - for sample_index in range( len( current_samples ) ): - sample = request.samples[ sample_index ] - current_sample = current_samples[ sample_index ] - sample.name = current_sample[ 'name' ] - sample.library = current_sample[ 'library' ] - sample.folder = current_sample[ 'folder' ] - if request.is_submitted: - bc_message = self.__validate_barcode( trans, sample, current_sample[ 'barcode' ] ) - if bc_message: - status = 'error' - message += bc_message - else: - if not sample.bar_code: - # If this is a 'new' (still in its first state) sample - # change the state to the next - if sample.state.id == request.type.states[0].id: - event = trans.model.SampleEvent( sample, - request.type.states[1], - 'Sample added to the system' ) - trans.sa_session.add( event ) - trans.sa_session.flush() - # Now check if all the samples' barcode has been entered. - # If yes then send notification email if configured - common_state = request.samples_have_common_state - if common_state: - if common_state.id == request.type.states[1].id: - event = trans.model.RequestEvent( request, - request.states.SUBMITTED, - "All samples are in %s state." % common_state.name ) - trans.sa_session.add( event ) - trans.sa_session.flush() - request.send_email_notification( trans, request.type.states[1] ) - sample.bar_code = current_samples[sample_index]['barcode'] - trans.sa_session.add( sample ) - trans.sa_session.flush() - form_values = trans.sa_session.query( trans.model.FormValues ).get( sample.values.id ) - form_values.content = current_sample[ 'field_values' ] - trans.sa_session.add( form_values ) - trans.sa_session.flush() - return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', - cntrller=cntrller, - id=trans.security.encode_id( request.id ), + id=request_id, + editing_samples=True, status=status, message=message ) ) @web.expose @@ -876,25 +783,33 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, events_list=events_list, sample=sample ) - def __add_sample( self, trans, cntrller, request, **kwd ): + @web.expose + @web.require_login( "add sample" ) + def add_sample( self, trans, cntrller, request_id, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - managing_samples = util.string_as_bool( params.get( 'managing_samples', False ) ) + try: + request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) + except: + return invalid_id_redirect( trans, cntrller, request_id ) is_admin = cntrller == 'requests_admin' and trans.user_is_admin() # Get the widgets for rendering the request form request_widgets = self.__get_request_widgets( trans, request.id ) - current_samples, managing_samples, libraries = self.__get_sample_info( trans, request, **kwd ) + current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd ) if not current_samples: # Form field names are zero-based. sample_index = 0 else: sample_index = len( current_samples ) if params.get( 'add_sample_button', False ): + # Get all libraries for which the current user has permission to add items + libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) num_samples_to_add = int( params.get( 'num_sample_to_copy', 1 ) ) # See if the user has selected a sample to copy. copy_sample_index = int( params.get( 'copy_sample_index', -1 ) ) for index in range( num_samples_to_add ): + id_index = len( current_samples ) + 1 if copy_sample_index != -1: # The user has selected a sample to copy. library_id = current_samples[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True ) @@ -902,7 +817,7 @@ class RequestsCommon( BaseController, Us name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( len( current_samples ) + 1 ) field_values = [ val for val in current_samples[ copy_sample_index ][ 'field_values' ] ] else: - # The user has not selected a sample to copy (may just be adding a sample). + # The user has not selected a sample to copy, just adding a new generic sample. library_id = None folder_id = None name = 'Sample_%i' % ( len( current_samples ) + 1 ) @@ -910,7 +825,7 @@ class RequestsCommon( BaseController, Us # Build the library_select_field and folder_select_field for the new sample being added. library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, user=request.user, - sample_index=len( current_samples ), + sample_index=id_index, libraries=libraries, sample=None, library_id=library_id, @@ -926,101 +841,21 @@ class RequestsCommon( BaseController, Us field_values=field_values, library_select_field=library_select_field, folder_select_field=folder_select_field ) ) - selected_samples = self.__get_selected_samples( trans, request, **kwd ) - selected_value = params.get( 'sample_operation', 'none' ) - sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, selected_value ) + encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) + sample_operation = params.get( 'sample_operation', 'none' ) + sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, sample_operation ) sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) - return trans.fill_template( '/requests/common/manage_request.mako', + return trans.fill_template( '/requests/common/edit_samples.mako', cntrller=cntrller, request=request, - selected_samples=selected_samples, + encoded_selected_sample_ids=encoded_selected_sample_ids, request_widgets=request_widgets, current_samples=current_samples, sample_operation_select_field=sample_operation_select_field, sample_copy=sample_copy, - managing_samples=managing_samples, + editing_samples=False, message=message, status=status ) - def __get_sample_info( self, trans, request, **kwd ): - """ - Retrieves all user entered sample information and returns a - list of all the samples and their field values. - """ - params = util.Params( kwd ) - managing_samples = util.string_as_bool( params.get( 'managing_samples', False ) ) - # Bet all data libraries accessible to this user - libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) - # Build the list of widgets which will be used to render each sample row on the request page - current_samples = [] - for index, sample in enumerate( request.samples ): - library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, - request.user, - index, - libraries, - sample, - **kwd ) - current_samples.append( dict( name=sample.name, - barcode=sample.bar_code, - library=sample.library, - folder=sample.folder, - field_values=sample.values.content, - library_select_field=library_select_field, - folder_select_field=folder_select_field ) ) - if not managing_samples: - sample_index = len( request.samples ) - else: - sample_index = 0 - while True: - library_id = params.get( 'sample_%i_library_id' % sample_index, None ) - folder_id = params.get( 'sample_%i_folder_id' % sample_index, None ) - if params.get( 'sample_%i_name' % sample_index, False ): - # Data library - try: - library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( library_id ) ) - #library_id = library.id - except: - library = None - if library is not None: - # Folder - try: - folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) ) - #folder_id = folder.id - except: - if library: - folder = library.root_folder - else: - folder = None - else: - folder = None - sample_info = dict( name=util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ), - barcode=util.restore_text( params.get( 'sample_%i_barcode' % sample_index, '' ) ), - library=library, - folder=folder) - sample_info[ 'field_values' ] = [] - for field_index in range( len( request.type.sample_form.fields ) ): - sample_info[ 'field_values' ].append( util.restore_text( params.get( 'sample_%i_field_%i' % ( sample_index, field_index ), '' ) ) ) - if not managing_samples: - sample_info[ 'library_select_field' ], sample_info[ 'folder_select_field' ] = self.__build_library_and_folder_select_fields( trans, - request.user, - sample_index, - libraries, - None, - library_id, - folder_id, - **kwd ) - current_samples.append( sample_info ) - else: - sample_info[ 'library_select_field' ], sample_info[ 'folder_select_field' ] = self.__build_library_and_folder_select_fields( trans, - request.user, - sample_index, - libraries, - request.samples[ sample_index ], - **kwd ) - current_samples[ sample_index ] = sample_info - sample_index += 1 - else: - break - return current_samples, managing_samples, libraries @web.expose @web.require_login( "delete sample from sequencing request" ) def delete_sample( self, trans, cntrller, **kwd ): @@ -1032,7 +867,7 @@ class RequestsCommon( BaseController, Us request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) except: return invalid_id_redirect( trans, cntrller, request_id ) - current_samples, managing_samples, libraries = self.__get_sample_info( trans, request, **kwd ) + current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd ) sample_index = int( params.get( 'sample_id', 0 ) ) sample_name = current_samples[sample_index]['name'] sample = request.has_sample( sample_name ) @@ -1042,9 +877,10 @@ class RequestsCommon( BaseController, Us trans.sa_session.flush() message = 'Sample (%s) has been deleted.' % sample_name return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', + action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), + editing_samples=True, status=status, message=message ) ) @web.expose @@ -1059,12 +895,12 @@ class RequestsCommon( BaseController, Us sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) except: return invalid_id_redirect( trans, cntrller, sample_id ) - # check if a library and folder has been set for this sample yet. + # See if a library and folder have been set for this sample. if not sample.library or not sample.folder: status = 'error' message = "Set a data library and folder for sequencing request (%s) to transfer datasets." % sample.name return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', + action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ), status=status, @@ -1101,7 +937,6 @@ class RequestsCommon( BaseController, Us SampleName,DataLibrary,DataLibraryFolder,Field1,Field2.... """ params = util.Params( kwd ) - managing_samples = util.string_as_bool( params.get( 'managing_samples', False ) ) file_obj = params.get( 'file_data', '' ) try: reader = csv.reader( file_obj.file ) @@ -1137,23 +972,211 @@ class RequestsCommon( BaseController, Us folder_select_field=folder_select_field, field_values=row[3:] ) ) except Exception, e: - status = 'error' - message = 'Error thrown when importing samples file: %s' % str( e ) + if str( e ) == "'unicode' object has no attribute 'file'": + message = "Select a file" + else: + message = 'Error attempting to create samples from selected file: %s.' % str( e ) + message += ' Make sure the selected csv file uses the format: SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...' return trans.response.send_redirect( web.url_for( controller='requests_common', - action='manage_request', + action='add_sample', cntrller=cntrller, - id=trans.security.encode_id( request.id ), - status=status, + request_id=trans.security.encode_id( request.id ), + add_sample_button='Add sample', + status='error', message=message ) ) request_widgets = self.__get_request_widgets( trans, request.id ) sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) - return trans.fill_template( '/requests/common/manage_request.mako', + return trans.fill_template( '/requests/common/edit_samples.mako', cntrller=cntrller, request=request, request_widgets=request_widgets, current_samples=current_samples, sample_copy=sample_copy, - managing_samples=managing_samples ) + editing_samples=False ) + def __save_samples( self, trans, cntrller, request, samples, **kwd ): + # Here we handle saving all new samples added by the user as well as saving + # changes to any subset of the request's samples. + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + editing_samples = util.string_as_bool( params.get( 'editing_samples', False ) ) + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + sample_operation = params.get( 'sample_operation', 'none' ) + # Check for duplicate sample names within the request + self.__validate_sample_names( trans, cntrller, request, samples, **kwd ) + if editing_samples: + library = None + folder = None + def handle_error( **kwd ): + kwd[ 'status' ] = 'error' + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='edit_samples', + cntrller=cntrller, + **kwd ) ) + # Here we handle saving changes to single samples as well as saving changes to + # selected sets of samples. If samples are selected, the sample_operation param + # will have a value other than 'none', and the samples param will be a list of + # encoded sample ids. There are currently only 2 multi-select operations; + # 'Change state' and 'Select data library and folder'. If sample_operation is + # 'none, then the samples param will be a list of sample objects. + if sample_operation == 'Change state': + sample_state_id = params.get( 'sample_state_id', None ) + if sample_state_id in [ None, 'none' ]: + message = "Select a new state from the <b>Change current state</b> list before clicking the <b>Save</b> button." + kwd[ 'message' ] = message + del kwd[ 'save_changes_button' ] + handle_error( **kwd ) + sample_event_comment = util.restore_text( params.get( 'sample_event_comment', '' ) ) + new_state = trans.sa_session.query( trans.model.SampleState ).get( trans.security.decode_id( sample_state_id ) ) + # Send the encoded sample_ids to update_sample_state. + # TODO: make changes necessary to just send the samples... + encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) + # Make sure all samples have a unique barcode if the state is changing + for sample_index in range( len( samples ) ): + current_sample = samples[ sample_index ] + if current_sample is None: + # We have a None value because the user did not select this sample + # on which to perform the action. + continue + request_sample = request.samples[ sample_index ] + bc_message = self.__validate_barcode( trans, request_sample, current_sample[ 'barcode' ] ) + if bc_message: + #status = 'error' + message += bc_message + kwd[ 'message' ] = message + del kwd[ 'save_samples_button' ] + handle_error( **kwd ) + self.update_sample_state( trans, cntrller, encoded_selected_sample_ids, new_state, comment=sample_event_comment ) + return trans.response.send_redirect( web.url_for( controller='requests_common', + cntrller=cntrller, + action='update_request_state', + request_id=trans.security.encode_id( request.id ) ) ) + elif sample_operation == 'Select data library and folder': + library_id = params.get( 'sample_0_library_id', 'none' ) + folder_id = params.get( 'sample_0_folder_id', 'none' ) + library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) + self.__update_samples( trans, request, samples, **kwd ) + # See if all the samples' barcodes are in the same state, + # and if so send email if configured to. + common_state = request.samples_have_common_state + if common_state and common_state.id == request.type.states[1].id: + event = trans.model.RequestEvent( request, + request.states.SUBMITTED, + "All samples are in %s state." % common_state.name ) + trans.sa_session.add( event ) + trans.sa_session.flush() + request.send_email_notification( trans, request.type.states[1] ) + message = 'Changes made to the samples have been saved. ' + else: + # Saving a newly created sample. + for index in range( len( samples ) - len( request.samples ) ): + sample_index = len( request.samples ) + current_sample = samples[ sample_index ] + form_values = trans.model.FormValues( request.type.sample_form, current_sample[ 'field_values' ] ) + trans.sa_session.add( form_values ) + trans.sa_session.flush() + s = trans.model.Sample( current_sample[ 'name' ], + '', + request, + form_values, + current_sample[ 'barcode' ], + current_sample[ 'library' ], + current_sample[ 'folder' ] ) + trans.sa_session.add( s ) + trans.sa_session.flush() + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='edit_samples', + cntrller=cntrller, + id=trans.security.encode_id( request.id ), + editing_samples=editing_samples, + status=status, + message=message ) ) + def __update_samples( self, trans, request, sample_widgets, **kwd ): + # Determine if the values in kwd require updating the request's samples. The list of + # sample_widgets must have the same number of objects as request.samples, but some of + # the objects can be None. Those that are not None correspond to samples selected by + # the user for performing an action on multiple samples simultaneously. + def handle_error( **kwd ): + kwd[ 'status' ] = 'error' + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='edit_samples', + cntrller=cntrller, + **kwd ) ) + params = util.Params( kwd ) + sample_operation = params.get( 'sample_operation', 'none' ) + if sample_operation != 'none': + # These values will be in kwd if the user checked 1 or more checkboxes for performing this action + # on a set of samples. + library_id = params.get( 'sample_0_library_id', 'none' ) + folder_id = params.get( 'sample_0_folder_id', 'none' ) + for index, obj in enumerate( sample_widgets ): + if obj is not None: + # obj will be None if the user checked sample check boxes and selected an action + # to perform on multiple samples, but did not select certain samples. + sample_updated = False + # If this sample has values in kwd, then kwd will include a + # key whose value is this sample's ( possibly changed ) name. An + # example of this key is 'sample_0_name'. + for k, v in kwd.items(): + name_key = 'sample_%i_name' % index + if k == name_key: + sample_updated = True + break + if sample_updated: + id_index = index + 1 + if sample_operation == 'none': + # We are handling changes to a single sample. + library_id = params.get( 'sample_%i_library_id' % id_index, 'none' ) + folder_id = params.get( 'sample_%i_folder_id' % id_index, 'none' ) + # Update the corresponding sample's values as well as the sample_widget. + sample = request.samples[ index ] + sample.name = util.restore_text( params.get( 'sample_%i_name' % index, '' ) ) + # The bar_code field requires special handling because after a request is submitted, the + # state of a sample cannot be changed without a bar_code assocaited with the sample. + bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, '' ) ) + if not bar_code and not sample.bar_code: + # If this is a 'new' (still in its first state) sample, create an event + if sample.state.id == request.states[0].id: + event = trans.model.SampleEvent( sample, + request.type.states[1], + 'Sample added to the system' ) + trans.sa_session.add( event ) + trans.sa_session.flush() + elif bar_code: + bc_message = self.__validate_barcode( trans, sample, bar_code ) + if bc_message: + kwd[ 'message' ] = bc_message + del kwd[ 'save_samples_button' ] + handle_error( **kwd ) + sample.bar_code = bar_code + library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) + sample.library = library + sample.folder = folder + field_values = [] + for field_index in range( len( request.type.sample_form.fields ) ): + field_values.append( util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) ) + form_values = trans.sa_session.query( trans.model.FormValues ).get( sample.values.id ) + form_values.content = field_values + trans.sa_session.add_all( ( sample, form_values ) ) + trans.sa_session.flush() + def __get_library_and_folder( self, trans, library_id, folder_id ): + try: + library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( library_id ) ) + except: + library = None + if library and folder_id == 'none': + folder = library.root_folder + elif library and folder_id != 'none': + try: + folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) ) + except: + if library: + folder = library.root_folder + else: + folder = None + else: + folder = None + return library, folder # ===== Methods for handling form definition widgets ===== def __get_request_widgets( self, trans, id ): """Get the widgets for the request""" @@ -1179,27 +1202,104 @@ class RequestsCommon( BaseController, Us value=request.values.content[ index ], helptext=field[ 'helptext' ] + ' (' + required_label + ')' ) ) return request_widgets - def __get_samples_widgets( self, trans, request, libraries, **kwd ): - """Get the widgets for all of the samples currently associated with the request""" - # The current_samples_widgets list is a list of dictionaries - current_samples_widgets = [] - for index, sample in enumerate( request.samples ): - # Build the library_select_field and folder_select_field for each existing sample - library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, + def __get_sample_widgets( self, trans, request, samples, **kwd ): + """ + Returns a list of dictionaries, each representing the widgets that define a sample on a form. + The widgets are populated from kwd based on the set of samples received. The set of samples + corresponds to a reques.samples list, but if the user checked specific check boxes on the form, + those samples that were not check will have None objects in the list of samples. In this case, + the corresponding sample_widget is populated from the db rather than kwd. + """ + params = util.Params( kwd ) + sample_operation = params.get( 'sample_operation', 'none' ) + # This method is called when the user is adding new samples as well as + # editing existing samples, so we use the editing_samples flag to keep + # track of what's occurring. + editing_samples = util.string_as_bool( params.get( 'editing_samples', False ) ) + sample_widgets = [] + if sample_operation != 'none': + # The sample_operatin param has a value other than 'none', and a specified + # set of samples was received. + library_id = util.restore_text( params.get( 'sample_0_library_id', 'none' ) ) + folder_id = util.restore_text( params.get( 'sample_0_folder_id', 'none' ) ) + # Build the list of widgets which will be used to render each sample row on the request page + if not request: + return sample_widgets + # Get the list of libraries for which the current user has permission to add items. + libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) + # Build the list if sample widgets, populating the values from kwd. + for index, sample in enumerate( samples ): + id_index = index + 1 + if sample is None: + # Id sample is None, then we'll use the sample from the request object since it will + # not have updated =values from kwd. + sample = request.samples[ index ] + name = sample.name + bar_code = sample.bar_code + library = sample.library + folder = sample.folder + field_values = sample.values.content, + else: + # Update the sample attributes from kwd + name = util.restore_text( params.get( 'sample_%i_name' % index, sample.name ) ) + bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, sample.bar_code ) ) + library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) ) + if not library_id and sample.library: + library_id = trans.security.encode_id( sample.library.id ) + folder_id = util.restore_text( params.get( 'sample_%i_folder_id' % id_index, '' ) ) + if not folder_id and sample.folder: + folder_id = trans.security.encode_id( sample.folder.id ) + library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) + field_values = [] + for field_index in range( len( request.type.sample_form.fields ) ): + field_values.append( util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) ) + library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans=trans, user=request.user, - sample_index=index, + sample_index=id_index, libraries=libraries, sample=sample, + library_id=library_id, + folder_id=folder_id, **kwd ) - # Append the dictionary for the current sample to the current_samples_widgets list - current_samples_widgets.append( dict( name=sample.name, - barcode=sample.bar_code, - library=sample.library, - folder=sample.folder, - field_values=sample.values.content, - library_select_field=library_select_field, - folder_select_field=folder_select_field ) ) - return current_samples_widgets + sample_widgets.append( dict( name=name, + barcode=bar_code, + library=library, + folder=folder, + field_values=field_values, + library_select_field=library_select_field, + folder_select_field=folder_select_field ) ) + # There may be additional new samples on the form that have not yet been associated with the request. + # TODO: factor this code so it is not duplicating what's above. + index = len( samples ) + while True: + name = util.restore_text( params.get( 'sample_%i_name' % index, '' ) ) + if not name: + break + id_index = index + 1 + bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, '' ) ) + library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) ) + folder_id = util.restore_text( params.get( 'sample_%i_folder_id' % id_index, '' ) ) + library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) + field_values = [] + for field_index in range( len( request.type.sample_form.fields ) ): + field_values.append( util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) ) + library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans=trans, + user=request.user, + sample_index=id_index, + libraries=libraries, + sample=None, + library_id=library_id, + folder_id=folder_id, + **kwd ) + sample_widgets.append( dict( name=name, + barcode=bar_code, + library=library, + folder=folder, + field_values=field_values, + library_select_field=library_select_field, + folder_select_field=folder_select_field ) ) + index += 1 + return sample_widgets # ===== Methods for building SelectFields used on various request forms ===== def __build_copy_sample_select_field( self, trans, current_samples ): copy_sample_index_select_field = SelectField( 'copy_sample_index' ) @@ -1240,26 +1340,30 @@ class RequestsCommon( BaseController, Us # The libraries dictionary looks like: { library : '1,2' }, library : '3' }. Its keys are the libraries that # should be displayed for the current user and its values are strings of comma-separated folder ids that should # NOT be displayed. - # - # TODO: all object ids received in the params must be encoded. params = util.Params( kwd ) library_select_field_name= "sample_%i_library_id" % sample_index folder_select_field_name = "sample_%i_folder_id" % sample_index if not library_id: - library_id = params.get( library_select_field_name, 'none' ) + library_id = params.get( library_select_field_name, None ) + if not folder_id: + folder_id = params.get( folder_select_field_name, None ) selected_library = None selected_hidden_folder_ids = [] showable_folders = [] - if sample and sample.library and library_id == 'none': - library_id = str( sample.library.id ) + if library_id not in [ None, 'none' ]: + # If we have a selected library, get the list of it's folders that are not accessible to the current user + for library, hidden_folder_ids in libraries.items(): + encoded_id = trans.security.encode_id( library.id ) + if encoded_id == str( library_id ): + selected_library = library + selected_hidden_folder_ids = hidden_folder_ids.split( ',' ) + break + elif sample and sample.library and library_id == 'none': + # The user previously selected a library but is now resetting the selection to 'none' + selected_library = None + elif sample and sample.library: + library_id = trans.security.encode_id( sample.library.id ) selected_library = sample.library - # If we have a selected library, get the list of it's folders that are not accessible to the current user - for library, hidden_folder_ids in libraries.items(): - encoded_id = trans.security.encode_id( library.id ) - if encoded_id == str( library_id ): - selected_library = library - selected_hidden_folder_ids = hidden_folder_ids.split( ',' ) - break # sample_%i_library_id SelectField with refresh on change enabled library_select_field = build_select_field( trans, libraries.keys(), @@ -1275,20 +1379,12 @@ class RequestsCommon( BaseController, Us selected_library, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ], selected_hidden_folder_ids ) - if sample: - # The user is editing the request, and may have previously selected a folder - if sample.folder: - selected_folder_id = sample.folder.id + if folder_id: + selected_folder_id = folder_id + elif sample and sample.folder: + selected_folder_id = trans.security.encode_id( sample.folder.id ) else: - # If a library is selected but not a folder, use the library's root folder - if sample.library: - selected_folder_id = sample.library.root_folder.id - else: - # The user just selected a folder - selected_folder_id = params.get( folder_select_field_name, 'none' ) - elif folder_id: - # TODO: not sure when this would be passed - selected_folder_id = folder_id + selected_folder_id = trans.security.encode_id( selected_library.root_folder.id ) else: selected_folder_id = 'none' # TODO: Change the name of the library root folder to "Library root" to clarify to the @@ -1328,9 +1424,35 @@ class RequestsCommon( BaseController, Us message += '<b>' + ef + '</b> ' return message return None + def __validate_sample_names( self, trans, cntrller, request, current_samples, **kwd ): + # Check for duplicate sample names for all samples of the request. + editing_samples = util.string_as_bool( kwd.get( 'editing_samples', False ) ) + message = '' + for index in range( len( current_samples ) - len( request.samples ) ): + sample_index = index + len( request.samples ) + current_sample = current_samples[ sample_index ] + sample_name = current_sample[ 'name' ] + if not sample_name.strip(): + message = 'Enter the name of sample number %i' % sample_index + break + count = 0 + for i in range( len( current_samples ) ): + if sample_name == current_samples[ i ][ 'name' ]: + count += 1 + if count > 1: + message = "You tried to add %i samples with the name (%s). Samples belonging to a request must have unique names." % ( count, sample_name ) + break + if message: + del kwd[ 'save_samples_button' ] + kwd[ 'message' ] = message + kwd[ 'status' ] = 'error' + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='edit_samples', + cntrller=cntrller, + **kwd ) ) def __validate_barcode( self, trans, sample, barcode ): """ - Makes sure that the barcode about to be assigned to a sample is gobally unique. + Makes sure that the barcode about to be assigned to a sample is globally unique. That is, barcodes must be unique across requests in Galaxy sample tracking. """ message = '' @@ -1338,13 +1460,18 @@ class RequestsCommon( BaseController, Us for index in range( len( sample.request.samples ) ): # Check for empty bar code if not barcode.strip(): - message = 'Fill in the barcode for sample (%s).' % sample.name - break + if sample.state.id == sample.request.type.states[0].id: + # The user has not yet filled in the barcode value, but the sample is + # 'new', so all is well. + break + else: + message = "Fill in the barcode for sample (%s) before changing it's state." % sample.name + break # TODO: Add a unique constraint to sample.bar_code table column # Make sure bar code is unique - for sample_has_bar_code in trans.sa_session.query( trans.model.Sample ) \ - .filter( trans.model.Sample.table.c.bar_code == barcode ): - if sample_has_bar_code and sample_has_bar_code.id != sample.id: + for sample_with_barcode in trans.sa_session.query( trans.model.Sample ) \ + .filter( trans.model.Sample.table.c.bar_code == barcode ): + if sample_with_barcode and sample_with_barcode.id != sample.id: message = '''The bar code (%s) associated with the sample (%s) belongs to another sample. Bar codes must be unique across all samples, so use a different bar code for this sample.''' % ( barcode, sample.name ) @@ -1360,15 +1487,15 @@ class RequestsCommon( BaseController, Us elif len( email ) > 255: error = "(%s) exceeds maximum allowable length. " % str( email ) return error - # ===== Other miscellaneoud utility methods ===== - def __get_selected_samples( self, trans, request, **kwd ): - selected_samples = [] + # ===== Other miscellaneous utility methods ===== + def __get_encoded_selected_sample_ids( self, trans, request, **kwd ): + encoded_selected_sample_ids = [] for sample in request.samples: if CheckboxField.is_checked( kwd.get( 'select_sample_%i' % sample.id, '' ) ): - selected_samples.append( trans.security.encode_id( sample.id ) ) - return selected_samples + encoded_selected_sample_ids.append( trans.security.encode_id( sample.id ) ) + return encoded_selected_sample_ids -# ===== Miscellaneoud utility methods outside of the RequestsCommon class ===== +# ===== Miscellaneous utility methods outside of the RequestsCommon class ===== def invalid_id_redirect( trans, cntrller, obj_id, action='browse_requests' ): status = 'error' message = "Invalid request id (%s)" % str( obj_id ) --- a/templates/requests/common/dataset_transfer.mako +++ b/templates/requests/common/dataset_transfer.mako @@ -1,47 +1,46 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> +<br/><br/> + +<ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Refresh</a></li> + <li><a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">Target Data Library</a></li> + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li> +</ul> + %if message: ${render_msg( message, status )} %endif -<h2>Datasets of Sample "${sample.name}"</h2> - -<ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Refresh</a> - </li> - <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${sample.library.name} Data Library</a> - </li> - <li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a> - </li> -</ul> - -%if dataset_files: - <div class="form-row"> - <table class="grid"> - <thead> - <tr> - <th>Name</th> - <th>Size</th> - <th>Status</th> - </tr> - <thead> - <tbody> - %for dataset_file in dataset_files: - <tr> - <td>${dataset_file.name}</td> - <td>${dataset_file.size}</td> - <td>${dataset_file.status}</td> - </tr> - %endfor - </tbody> - </table> +<div class="toolForm"> + <div class="toolFormTitle">Sample "${sample.name}"</div> + <div class="toolFormBody"> + %if dataset_files: + <div class="form-row"> + <table class="grid"> + <thead> + <tr> + <th>Name</th> + <th>Size</th> + <th>Status</th> + </tr> + <thead> + <tbody> + %for dataset_file in dataset_files: + <tr> + <td>${dataset_file.name}</td> + <td>${dataset_file.size}</td> + <td>${dataset_file.status}</td> + </tr> + %endfor + </tbody> + </table> + </div> + %else: + <div class="form-row"> + There are no datasets associated with this sample. + </div> + %endif </div> -%else: - <div class="form-row"> - There are no datasets associated with this sample. - </div> -%endif +</div> --- a/templates/requests/common/manage_request.mako +++ /dev/null @@ -1,615 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/requests/common/sample_state.mako" import="render_sample_state" /> -<%namespace file="/requests/common/sample_datasets.mako" import="render_sample_datasets" /> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "library" )} -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - function showContent(vThis) - { - // http://www.javascriptjunkie.com - // alert(vSibling.className + " " + vDef_Key); - vParent = vThis.parentNode; - vSibling = vParent.nextSibling; - while (vSibling.nodeType==3) { - // Fix for Mozilla/FireFox Empty Space becomes a TextNode or Something - vSibling = vSibling.nextSibling; - }; - if(vSibling.style.display == "none") - { - vThis.src="/static/images/fugue/toggle.png"; - vThis.alt = "Hide"; - vSibling.style.display = "block"; - } else { - vSibling.style.display = "none"; - vThis.src="/static/images/fugue/toggle-expand.png"; - vThis.alt = "Show"; - } - return; - } - - $(document).ready(function(){ - //hide the all of the element with class msg_body - $(".msg_body").hide(); - //toggle the component with class msg_body - $(".msg_head").click(function(){ - $(this).next(".msg_body").slideToggle(0); - }); - }); - - // Looks for changes in sample states using an async request. Keeps - // calling itself (via setTimeout) until all samples are in a terminal - // state. - var updater = function ( sample_states ) { - // Check if there are any items left to track - var empty = true; - for ( i in sample_states ) { - empty = false; - break; - } - if ( ! empty ) { - setTimeout( function() { updater_callback( sample_states ) }, 1000 ); - } - }; - - var updater_callback = function ( sample_states ) { - // Build request data - var ids = [] - var states = [] - $.each( sample_states, function ( id, state ) { - ids.push( id ); - states.push( state ); - }); - // Make ajax call - $.ajax( { - type: "POST", - url: "${h.url_for( controller='requests_common', action='sample_state_updates' )}", - dataType: "json", - data: { ids: ids.join( "," ), states: states.join( "," ) }, - success : function ( data ) { - $.each( data, function( id, val ) { - // Replace HTML - var cell1 = $("#sampleState-" + id); - cell1.html( val.html_state ); - var cell2 = $("#sampleDatasets-" + id); - cell2.html( val.html_datasets ); - sample_states[ parseInt( id ) ] = val.state; - }); - updater( sample_states ); - }, - error: function() { - // Just retry, like the old method, should try to be smarter - updater( sample_states ); - } - }); - }; - - function checkAllFields() - { - var chkAll = document.getElementById('checkAll'); - var checks = document.getElementsByTagName('input'); - var boxLength = checks.length; - var allChecked = false; - var totalChecked = 0; - if ( chkAll.checked == true ) - { - for ( i=0; i < boxLength; i++ ) - { - if ( checks[i].name.indexOf( 'select_sample_' ) != -1) - { - checks[i].checked = true; - } - } - } - else - { - for ( i=0; i < boxLength; i++ ) - { - if ( checks[i].name.indexOf( 'select_sample_' ) != -1) - { - checks[i].checked = false - } - } - } - } - - function stopRKey(evt) { - var evt = (evt) ? evt : ((event) ? event : null); - var node = (evt.target) ? evt.target : ((evt.srcElement) ? evt.srcElement : null); - if ((evt.keyCode == 13) && (node.type=="text")) {return false;} - } - document.onkeypress = stopRKey - </script> -</%def> - -<% is_admin = cntrller == 'requests_admin' and trans.user_is_admin() %> - -<div class="grid-header"> - <h2>Sequencing Request "${request.name}"</h2> - - <ul class="manage-table-actions"> - <li><a class="action-button" id="seqreq-${request.id}-popup" class="menubutton">Sequencing Request Actions</a></li> - <div popupmenu="seqreq-${request.id}-popup"> - %if request.is_unsubmitted and request.samples: - <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a> - %endif - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">History</a> - %if is_admin: - %if request.is_submitted: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> - %endif - %endif - </div> - <li><a class="action-button" href="${h.url_for( controller=cntrller, action='browse_requests' )}">Browse requests</a></li> - </ul> - - <div class="toolParamHelp" style="clear: both;"> - <b>Sequencer</b>: ${request.type.name} - %if is_admin: - | <b>User</b>: ${request.user.email} - %endif - %if request.is_submitted: - | <b>State</b>: <i>${request.state}</i> - %else: - | <b>State</b>: ${request.state} - %endif - </div> -</div> - -%if request.samples_without_library_destinations: - ${render_msg( "Select a target data library and folder for all the samples before starting the sequence run", "warning" )} -%endif - -%if request.is_rejected: - ${render_msg( "Reason for rejection: " + request.last_comment, "warning" )} -%endif - -%if message: - ${render_msg( message, status )} -%endif - -<h4><img src="/static/images/fugue/toggle-expand.png" alt="Show" onclick="showContent(this);" style="cursor:pointer;"/> Request Information</h4> -<div style="display:none;"> - <div class="form-row"> - <ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit request informaton</a> - </li> - </ul> - </div> - <table class="grid" border="0"> - <tbody> - <tr> - <td valign="top" width="50%"> - <div class="form-row"> - <label>Description:</label> - ${request.desc} - </div> - <div style="clear: both"></div> - %for index, rd in enumerate( request_widgets ): - <% - field_label = rd[ 'label' ] - field_value = rd[ 'value' ] - %> - <div class="form-row"> - <label>${field_label}:</label> - %if field_label == 'State': - <a href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">${field_value}</a> - %else: - ${field_value} - %endif - </div> - <div style="clear: both"></div> - %endfor - </td> - <td valign="top" width="50%"> - <div class="form-row"> - <label>Date created:</label> - ${request.create_time} - </div> - <div class="form-row"> - <label>Date updated:</label> - ${request.update_time} - </div> - <div class="form-row"> - <label>Email notification recipients:</label> - <% - if request.notification: - emails = ', '.join( request.notification[ 'email' ] ) - else: - emails = '' - %> - ${emails} - </div> - <div style="clear: both"></div> - <div class="form-row"> - <label>Email notification on sample states:</label> - <% - if request.notification: - states = [] - for ss in request.type.states: - if ss.id in request.notification[ 'sample_states' ]: - states.append( ss.name ) - states = ', '.join( states ) - else: - states = '' - %> - ${states} - </div> - <div style="clear: both"></div> - </td> - </tr> - </tbody> - </table> -</div> -<br/> -<form id="manage_request" name="manage_request" action="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( request.id ), managing_samples=managing_samples )}" method="post"> - %if current_samples: - <% sample_operation_selected_value = sample_operation_select_field.get_selected( return_value=True ) %> - ## first render the basic info grid - ${render_basic_info_grid()} - %if not request.is_new and not managing_samples and len( sample_operation_select_field.options ) > 1: - <div class="form-row" style="background-color:#FAFAFA;"> - For selected samples: - ${sample_operation_select_field.get_html()} - </div> - %if sample_operation_selected_value != 'none' and selected_samples: - <div class="form-row" style="background-color:#FAFAFA;"> - %if sample_operation_selected_value == trans.model.Sample.bulk_operations.CHANGE_STATE: - ## sample_operation_selected_value == 'Change state' - <div class="form-row"> - <label>Change current state</label> - ${sample_state_id_select_field.get_html()} - <label>Comments</label> - <input type="text" name="sample_event_comment" value=""/> - <div class="toolParamHelp" style="clear: both;"> - Optional - </div> - </div> - <div class="form-row"> - <input type="submit" name="change_state_button" value="Save"/> - <input type="submit" name="cancel_change_state_button" value="Cancel"/> - </div> - %elif sample_operation_selected_value == trans.app.model.Sample.bulk_operations.SELECT_LIBRARY: - <% libraries_selected_value = libraries_select_field.get_selected( return_value=True ) %> - <div class="form-row"> - <label>Select data library:</label> - ${libraries_select_field.get_html()} - </div> - %if libraries_selected_value != 'none': - <div class="form-row"> - <label>Select folder:</label> - ${folders_select_field.get_html()} - </div> - <div class="form-row"> - <input type="submit" name="change_lib_button" value="Save"/> - <input type="submit" name="cancel_change_lib_button" value="Cancel"/> - </div> - %endif - %endif - </div> - %endif - %endif - ## Render the other grids - <% trans.sa_session.refresh( request.type.sample_form ) %> - %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_index ) )} - %endfor - %else: - <label>There are no samples.</label> - %endif - %if request.samples and request.is_submitted: - <script type="text/javascript"> - // Updater - updater({${ ",".join( [ '"%s" : "%s"' % ( s.id, s.state.name ) for s in request.samples ] ) }}); - </script> - %endif - %if not managing_samples: - <table class="grid"> - <tbody> - <tr> - <div class="form-row"> - %if request.is_unsubmitted: - <td> - %if current_samples: - <label>Copy </label> - <input type="integer" name="num_sample_to_copy" value="1" size="3"/> - <label>samples from sample</label> - ${sample_copy.get_html()} - %endif - <input type="submit" name="add_sample_button" value="Add New"/> - </td> - %endif - <td> - %if current_samples and len( current_samples ) <= len( request.samples ): - <input type="submit" name="edit_samples_button" value="Edit samples"/> - %endif - </td> - </div> - </tr> - </tbody> - </table> - %endif - %if request.samples or current_samples: - %if managing_samples: - <div class="form-row"> - <input type="submit" name="save_samples_button" value="Save"/> - <input type="submit" name="cancel_changes_button" value="Cancel"/> - </div> - %elif len( current_samples ) > len( request.samples ): - <div class="form-row"> - <input type="submit" name="save_samples_button" value="Save"/> - <input type="submit" name="cancel_changes_button" value="Cancel"/> - </div> - %endif - %endif -</form> -<br/> -%if request.is_unsubmitted: - <form id="import" name="import" action="${h.url_for( controller='requests_common', action='manage_request', managing_samples=managing_samples, id=trans.security.encode_id( request.id ) )}" enctype="multipart/form-data" method="post" > - <h4><img src="/static/images/fugue/toggle-expand.png" alt="Show" onclick="showContent(this);" style="cursor:pointer;"/> Import samples</h4> - <div style="display:none;"> - <input type="file" name="file_data" /> - <input type="submit" name="import_samples_button" value="Import samples"/> - <br/> - <div class="toolParamHelp" style="clear: both;"> - The csv file must be in the following format:<br/> - SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2... - </div> - </div> - </form> -%endif - -<%def name="render_grid( grid_index, grid_name, fields_dict )"> - <br/> - <% if not grid_name: - grid_name = "Grid "+ grid_index - %> - <div> - %if managing_samples or len( current_samples ) > len( request.samples ): - <h4><img src="/static/images/fugue/toggle.png" alt="Show" onclick="showContent(this);" style="cursor:pointer;"/> ${grid_name}</h4> - <div> - %else: - <h4><img src="/static/images/fugue/toggle-expand.png" alt="Hide" onclick="showContent(this);" style="cursor:pointer;"/> ${grid_name}</h4> - <div style="display:none;"> - %endif - <table class="grid"> - <thead> - <tr> - <th>Name</th> - %for index, field in fields_dict.items(): - <th> - ${field['label']} - <div class="toolParamHelp" style="clear: both;"> - <i>${field['helptext']}</i> - </div> - </th> - %endfor - <th></th> - </tr> - <thead> - <tbody> - <% trans.sa_session.refresh( request ) %> - %for sample_index, sample in enumerate( current_samples ): - %if managing_samples: - <tr>${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}</tr> - %else: - <tr> - %if sample_index in range( len( request.samples ) ): - ${render_sample( sample_index, sample['name'], sample['field_values'], fields_dict )} - %else: - ${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)} - %endif - </tr> - %endif - %endfor - </tbody> - </table> - </div> - </div> -</%def> - -## This function displays the "Basic Information" grid -<%def name="render_basic_info_grid()"> - <h3>Sample Information</h3> - <table class="grid"> - <thead> - <tr> - <th><input type="checkbox" id="checkAll" name=select_all_samples_checkbox value="true" onclick='checkAllFields(1);'><input type="hidden" name=select_all_samples_checkbox value="true"></th> - <th>Name</th> - <th>Barcode</th> - <th>State</th> - <th>Data Library</th> - <th>Folder</th> - %if request.is_submitted or request.is_complete: - <th>Datasets Transferred</th> - %endif - <th></th> - </tr> - <thead> - <tbody> - <% trans.sa_session.refresh( request ) %> - %for sample_index, info in enumerate( current_samples ): - <% - if sample_index in range( len(request.samples ) ): - sample = request.samples[sample_index] - else: - sample = None - %> - %if managing_samples: - <tr>${show_basic_info_form( sample_index, sample, info )}</tr> - %else: - <tr> - %if sample_index in range( len( request.samples ) ): - %if trans.security.encode_id( sample.id ) in selected_samples: - <td><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" checked><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"></td> - %else: - <td><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true"><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"></td> - %endif - <td>${info['name']}</td> - <td>${info['barcode']}</td> - %if sample.request.is_unsubmitted: - <td>Unsubmitted</td> - %else: - <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> - %endif - %if info['library']: - %if cntrller == 'requests': - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td> - %elif is_admin: - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td> - %endif - %else: - <td></td> - %endif - %if info['folder']: - <td>${info['folder'].name}</td> - %else: - <td></td> - %endif - %if request.is_submitted or request.is_complete: - <td><a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}"> - ${render_sample_datasets( sample )} - </a></td> - %endif - %else: - ${show_basic_info_form( sample_index, sample, info )} - %endif - %if request.is_unsubmitted or request.is_rejected: - <td> - %if sample: - %if sample.request.is_unsubmitted: - <a class="action-button" href="${h.url_for( controller='requests_common', cntrller=cntrller, action='delete_sample', request_id=trans.security.encode_id( request.id ), sample_id=sample_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a> - %endif - %endif - </td> - %endif - </tr> - %endif - %endfor - </tbody> - </table> -</%def> - -<%def name="show_basic_info_form( sample_index, sample, info )"> - <td></td> - <td> - <input type="text" name="sample_${sample_index}_name" value="${info['name']}" size="10"/> - <div class="toolParamHelp" style="clear: both;"> - <i>${' (required)' }</i> - </div> - </td> - %if cntrller == 'requests': - %if sample: - %if sample.request.is_unsubmitted: - <td></td> - %else: - <td><input type="text" name="sample_${sample_index}_barcode" value="${info['barcode']}" size="10"/></td> - %endif - %else: - <td></td> - %endif - %elif is_admin: - %if sample: - %if sample.request.is_unsubmitted: - <td></td> - %else: - <td><input type="text" name="sample_${sample_index}_barcode" value="${info['barcode']}" size="10"/></td> - %endif - %else: - <td></td> - %endif - %endif - %if sample: - %if sample.request.is_unsubmitted: - <td>Unsubmitted</td> - %else: - <td><a href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a></td> - %endif - %else: - <td></td> - %endif - <td>${info['library_select_field'].get_html()}</td> - <td>${info['folder_select_field'].get_html()}</td> - %if request.is_submitted or request.is_complete: - <% - if sample: - label = str( len( sample.datasets ) ) - else: - label = 'Add' - %> - <td><a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${label}</a></td> - %endif -</%def> - -<%def name="render_sample( index, sample_name, sample_values, fields_dict )"> - <td> - ${sample_name} - </td> - %for field_index, field in fields_dict.items(): - <td> - %if sample_values[field_index]: - %if field['type'] == 'WorkflowField': - %if str(sample_values[field_index]) != 'none': - <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> - %endif - %else: - ${sample_values[field_index]} - %endif - %else: - <i>None</i> - %endif - </td> - %endfor -</%def> - -<%def name="render_sample_form( index, sample_name, sample_values, fields_dict )"> - <td>${sample_name}</td> - %for field_index, field in fields_dict.items(): - <td> - %if field['type'] == 'TextField': - <input type="text" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/> - %elif field['type'] == 'SelectField': - <select name="sample_${index}_field_${field_index}" last_selected_value="2"> - %for option_index, option in enumerate(field['selectlist']): - %if option == sample_values[field_index]: - <option value="${option}" selected>${option}</option> - %else: - <option value="${option}">${option}</option> - %endif - %endfor - </select> - %elif field['type'] == 'WorkflowField': - <select name="sample_${index}_field_${field_index}"> - %if str(sample_values[field_index]) == 'none': - <option value="none" selected>Select one</option> - %else: - <option value="none">Select one</option> - %endif - %for option_index, option in enumerate(request.user.stored_workflows): - %if not option.deleted: - %if str(option.id) == str(sample_values[field_index]): - <option value="${option.id}" selected>${option.name}</option> - %else: - <option value="${option.id}">${option.name}</option> - %endif - %endif - %endfor - </select> - %elif field['type'] == 'CheckboxField': - <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/> - %endif - <div class="toolParamHelp" style="clear: both;"> - <i>${'('+field['required']+')' }</i> - </div> - </td> - %endfor -</%def>

1 0

galaxy-dist commit 9285b39ae2f3: Packing editor.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1288646507 14400 # Node ID 9285b39ae2f3dfd5017808b4d9b657094fec802b # Parent 695c89309bcb2f5d31bfb8b9d8b0124ff3abf90f Packing editor. Tweak to reload. --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.act ion_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(t his.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind ("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){workflow.check_changes_in_active_form();v ar i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");return i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:fun ction(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions;if(h.workflow_outputs){this.workflow_outputs=h.workflow_outputs}else{this.workflow_outputs=[]}if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div >").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});$("body").remove(b);i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/ fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tipsy({delayIn:500,fallback:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)==-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}m.bind("hover",function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small-yellow.png")});m.bind("mouseleave",function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small.png");if($.inArray(b.name,d.workf low_outputs)==-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});$("body").remove(m);a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;this.post_job_actions=$.parseJSON(f.post_job_actions);if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.n ame,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);th is.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={job_id:h.id,action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job _actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_no de!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30 ;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math .max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",image_path+"/delete_icon.png").c lick(function(b){g.destroy()}).hover(function(){$(this).attr("src",image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];retur n(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){thi s.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes ();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("hei ght",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.act ion_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(t his.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind ("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){workflow.check_changes_in_active_form();v ar i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");return i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:fun ction(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions;if(h.workflow_outputs){this.workflow_outputs=h.workflow_outputs}else{this.workflow_outputs=[]}if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div >").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});$("body").remove(b);i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/ fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tipsy({delayIn:500,fallback:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)==-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}m.bind("hover",function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small-yellow.png")});m.bind("mouseleave",function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small.png");if($.inArray(b.name,d.workf low_outputs)==-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});$("body").remove(m);a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;this.post_job_actions=$.parseJSON(f.post_job_actions);if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.n ame,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);th is.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var a=false;$.each(this.nodes,function(b,c){if(c.workflow_outputs&&c.workflow_outputs.length>0){a=true}});if(a==false){return true}wf=this;$.each(this.nodes,function(b,f){if(f.type=="tool"){var d=false;if(f.post_job_actions==null){f.post_job_actions={}}var c=[];$.each(f.post_job_actions,function(h,g){if(g.action_type=="HideDatasetAction"){c.push(h)}});if(c.length>0&&f==workflow.active_node){$.each(c,function(g,h){d=true;delete f.post_job_actions[h]})}$.each(f.output_terminals,function(h,i){var g=true;$.each(f.workflow_outputs,function(k,l){if(i.name==l){g=false}});if(g==true){d=true;var j={action_type:"HideDatasetAction",output_name:i.name,action_arguments :{}};f.post_job_actions["HideDatasetAction"+i.name]=null;f.post_job_actions["HideDatasetAction"+i.name]=j}});if(wf.active_node==f&&d==true){wf.reload_active_node()}}})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b= 0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){th is.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h; $.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g +i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",image_path+"/delete_icon.png").click(func tion(b){g.destroy()}).hover(function(){$(this).attr("src",image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to _type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;th is.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw _overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$ .each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -614,8 +614,11 @@ function Workflow( canvas_container ) { } }, reload_active_node : function() { - this.clear_active_node(); - this.activate_node(node); + if (this.active_node){ + var node = this.active_node; + this.clear_active_node(); + this.activate_node(node); + } }, clear_active_node : function() { if ( this.active_node ) {

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galaxy-dist commit c4d8ffb3109e: Increment js version to get around cached editors.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1288647270 14400 # Node ID c4d8ffb3109e8cfb8143dc87c88dee3337bb7569 # Parent 9285b39ae2f3dfd5017808b4d9b657094fec802b Increment js version to get around cached editors. --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -44,7 +44,7 @@ def js( *args ): TODO: This has a hardcoded "?v=X" to defeat caching. This should be done in a better way. """ - return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=7" ) for name in args ] ) + return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=8" ) for name in args ] ) # Hashes

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galaxy-dist commit 695c89309bcb: Cleanup of debug info.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1288645775 14400 # Node ID 695c89309bcb2f5d31bfb8b9d8b0124ff3abf90f # Parent cf7ec71c561323940ce95c8148d2008508920092 Cleanup of debug info. --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -476,7 +476,6 @@ function Workflow( canvas_container ) { }); }, rectify_workflow_outputs : function() { - console.log("RECTIFICATION!"); // Find out if we're using workflow_outputs or not. var using_workflow_outputs = false; $.each( this.nodes, function ( k, node ) { @@ -493,7 +492,6 @@ function Workflow( canvas_container ) { if (node.type == 'tool'){ var node_changed = false; if (node.post_job_actions == null){ - console.log("CREATED FOR NEW NODE"); node.post_job_actions = {}; } var pjas_to_rem = [];

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galaxy-dist commit 2c934a168af9: More tweaking of lines_diff for cuffdiff test.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288633591 14400 # Node ID 2c934a168af968dc84300412220c2f2cb74bf676 # Parent 9415f380f2e7d4aca44f74923b6984ab3bcc1dfb More tweaking of lines_diff for cuffdiff test. --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -78,11 +78,11 @@ TODO: can we find datasets that lead to deterministic behavior? --><output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="14"/> - <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="4"/> + <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="10"/><output name="tss_groups_exp" file="cuffdiff_out3.txt"/><output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> - <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="8"/> - <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="4"/> + <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="16"/> + <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="8"/><output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/><output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/><output name="splicing_diff" file="cuffdiff_out9.txt"/>

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galaxy-dist commit cbb895e2b272: If a job's input fails to set metadata, fail the job rather than leaving it in the 'new' state indefinitely.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1288376593 14400 # Node ID cbb895e2b2729d324c1693882de7939360e683a4 # Parent 23844e86e6167c79737a7e0396c39e350e95d1c4 If a job's input fails to set metadata, fail the job rather than leaving it in the 'new' state indefinitely. --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -241,6 +241,9 @@ class JobQueue( object ): elif idata.state == idata.states.ERROR: JobWrapper( job, self ).fail( "input data %d is in error state" % ( idata.hid ) ) return JOB_INPUT_ERROR + elif idata.state == idata.states.FAILED_METADATA: + JobWrapper( job, self ).fail( "input data %d failed to properly set metadata" % ( idata.hid ) ) + return JOB_INPUT_ERROR elif idata.state != idata.states.OK and not ( idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id ): # need to requeue return JOB_WAIT

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