November 2010 - galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 0185bb614c77: Fix condition used to check if tiles have been loaded/drawn in trackster.
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 1288186007 14400 # Node ID 0185bb614c7721d6edf6822ad973e589620b91f5 # Parent e5f90080a2db9c16bad2300c5ef0b5c49a558638 Fix condition used to check if tiles have been loaded/drawn in trackster. --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -772,7 +772,8 @@ var TiledTrack = function() { this.max_height = 0; // Index of first tile that overlaps visible region var tile_index = Math.floor( low / resolution / DENSITY ); - // A list of setTimeout() ids used when drawing tiles. + // A list of setTimeout() ids used when drawing tiles. Each ID indicates + // a tile has been requested to be drawn or is being drawn. var draw_tile_ids = {}; while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache @@ -800,8 +801,9 @@ var TiledTrack = function() { // var track = this; var intervalId = setInterval(function() { - if ( draw_tile_ids.length !== 0 ) { - // Add drawing has finished; if there is more than one child in the content div, + // Only do stuff if all tile drawing is complete: + if (obj_length(draw_tile_ids) === 0) { + // All drawing has finished; if there is more than one child in the content div, // remove the first one, which is the oldest. if ( track.content_div.children().length > 1 ) { track.content_div.children( ":first" ).remove(); --- 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(j.length!==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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.appen d(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.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}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_r ange=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#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=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*D ENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.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=$(b);if(this.data_cache.get(w)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(w);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(d-(h-k)/m*d);n.fillRect(u,h,f,d-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,d)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<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></input>") .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);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_px=0;thi s.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true}};$.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.resol ution,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_offse t,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_slot s[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.fillStyle= "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_o ptions: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};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=50,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPa ttern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.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,{});

1 0

galaxy-dist commit 677bcc65f74f: 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 rc # Date 1288101623 14400 # Node ID 677bcc65f74f5a460277f089d0cdebf170f02831 # Parent 9e27a8ad881dc4451add6d518468a73dbc9028bc sample_tracking: - added web api methods to update requests, samples using restful api - removed the old ad-doc web api - modified the data transfer code to use this api - code cleanup --- a/scripts/galaxy_messaging/server/galaxyweb_interface.py +++ /dev/null @@ -1,122 +0,0 @@ -import ConfigParser -import sys, os -import array -import time -import optparse,array -import shutil, traceback -import urllib,urllib2, cookielib - -assert sys.version_info[:2] >= ( 2, 4 ) -new_path = [ os.path.join( os.getcwd(), "lib" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path -sys.path = new_path - -from galaxy import eggs -import pkg_resources - -import pkg_resources -pkg_resources.require( "pycrypto" ) - -from Crypto.Cipher import Blowfish -from Crypto.Util.randpool import RandomPool -from Crypto.Util import number - - -class GalaxyWebInterface(object): - def __init__(self, server_host, server_port, datatx_email, datatx_password, config_id_secret): - self.server_host = server_host - self.server_port = server_port - self.datatx_email = datatx_email - self.datatx_password = datatx_password - self.config_id_secret = config_id_secret - # create url - self.base_url = "http://%s:%s" % (self.server_host, self.server_port) - # login - url = "%s/user/login?email=%s&password=%s&login_button=Login" % (self.base_url, self.datatx_email, self.datatx_password) - cj = cookielib.CookieJar() - self.opener = urllib2.build_opener(urllib2.HTTPCookieProcessor(cj)) - #print url - f = self.opener.open(url) - if f.read().find("ogged in as "+self.datatx_email) == -1: - # if the user doesnt exist, create the user - url = "%s/user/create?email=%s&username=%s&password=%s&confirm=%s&create_user_button=Submit" % ( self.base_url, self.datatx_email, self.datatx_email, self.datatx_password, self.datatx_password ) - f = self.opener.open(url) - if f.read().find("ogged in as "+self.datatx_email) == -1: - raise Exception("The "+self.datatx_email+" user could not login to Galaxy") - - def add_to_library(self, server_dir, library_id, folder_id, dbkey=''): - ''' - This method adds the dataset file to the target data library & folder - by opening the corresponding url in Galaxy server running. - ''' - params = urllib.urlencode(dict( cntrller='library_admin', - tool_id='upload1', - tool_state='None', - library_id=self.encode_id(library_id), - folder_id=self.encode_id(folder_id), - upload_option='upload_directory', - file_type='auto', - server_dir=os.path.basename(server_dir), - dbkey=dbkey, - show_dataset_id='True', - runtool_btn='Upload to library')) - url = self.base_url+"/library_common/upload_library_dataset" - print url - print params - try: - f = self.opener.open(url, params) - if f.read().find("Data Library") == -1: - raise Exception("Dataset could not be uploaded to the data library. URL: %s, PARAMS=%s" % (url, params)) - except: - return 'ERROR', url, params - - def import_to_history(self, ldda_id, library_id, folder_id): - params = urllib.urlencode(dict( cntrller='library_admin', - show_deleted='False', - library_id=self.encode_id(library_id), - folder_id=self.encode_id(folder_id), - ldda_ids=self.encode_id(ldda_id), - do_action='import_to_history', - use_panels='False')) - #url = "http://lion.bx.psu.edu:8080/library_common/act_on_multiple_datasets?library…" - url = self.base_url+"/library_common/act_on_multiple_datasets" - f = self.opener.open(url, params) - x = f.read() - if x.find("1 dataset(s) have been imported into your history.") == -1: - raise Exception("Dataset could not be imported into history") - - def run_workflow(self, workflow_id, hid, workflow_step): - input = str(workflow_step)+'|input' - params = urllib.urlencode({'id':self.encode_id(workflow_id), - 'run_workflow': 'Run workflow', - input: hid}) - url = self.base_url+"/workflow/run" - f = self.opener.open(url, params) - - def logout(self): - # finally logout - f = self.opener.open(self.base_url+'/user/logout') - - def encode_id(self, obj_id ): - id_cipher = Blowfish.new( self.config_id_secret ) - # Convert to string - s = str( obj_id ) - # Pad to a multiple of 8 with leading "!" - s = ( "!" * ( 8 - len(s) % 8 ) ) + s - # Encrypt - return id_cipher.encrypt( s ).encode( 'hex' ) - - def update_request_state(self, request_id): - params = urllib.urlencode(dict( cntrller='requests_admin', - request_id=request_id)) - url = self.base_url + "/requests_common/update_request_state" - f = self.opener.open(url, params) - print url - print params - x = f.read() - - - - - - --- /dev/null +++ b/scripts/api/requests_update_state.py @@ -0,0 +1,16 @@ +#!/usr/bin/env python + + +import os, sys, traceback +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import update + +try: + data = {} + data[ 'update_type' ] = 'request_state' +except IndexError: + print 'usage: %s key url' % os.path.basename( sys.argv[0] ) + sys.exit( 1 ) + +update( sys.argv[1], sys.argv[2], data, return_formatted=True ) + --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -106,6 +106,7 @@ def app_factory( global_conf, **kwargs ) add_api_controllers( webapp, app ) webapp.api_mapper.resource( 'content', 'contents', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.api_mapper.resource( 'library', 'libraries', path_prefix='/api' ) + webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): --- /dev/null +++ b/scripts/api/sample_dataset_update_status.py @@ -0,0 +1,22 @@ +#!/usr/bin/env python + + +import os, sys, traceback +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import display +from common import submit +from common import update +try: + data = {} + data[ 'update_type' ] = 'sample_dataset_transfer_status' + data[ 'sample_dataset_ids' ] = sys.argv[3].split(',') + data[ 'new_status' ] = sys.argv[4] +except IndexError: + print 'usage: %s key url sample_dataset_ids new_state [error msg]' % os.path.basename( sys.argv[0] ) + sys.exit( 1 ) +try: + data[ 'error_msg' ] = sys.argv[5] +except IndexError: + data[ 'error_msg' ] = '' +print data +update( sys.argv[1], sys.argv[2], data, return_formatted=True ) --- a/scripts/galaxy_messaging/server/amqp_consumer.py +++ b/scripts/galaxy_messaging/server/amqp_consumer.py @@ -14,24 +14,22 @@ import sys, os import optparse import xml.dom.minidom import subprocess +import urllib2 from galaxydb_interface import GalaxyDbInterface -new_path = [ os.path.join( os.getcwd(), "scripts/galaxy_messaging/server" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path -sys.path = new_path -from galaxyweb_interface import GalaxyWebInterface +api_path = [ os.path.join( os.getcwd(), "scripts/api" ) ] +sys.path.extend( api_path ) +import common as api assert sys.version_info[:2] >= ( 2, 4 ) new_path = [ os.path.join( os.getcwd(), "lib" ) ] new_path.extend( sys.path[1:] ) # remove scripts/ from the path sys.path = new_path - - from galaxy import eggs +from galaxy.web.api.requests import RequestsController import pkg_resources pkg_resources.require( "amqplib" ) - from amqplib import client_0_8 as amqp import logging @@ -43,7 +41,12 @@ formatter = logging.Formatter("%(asctime fh.setFormatter(formatter) log.addHandler(fh) +# data transfer script +data_transfer_script = os.path.join( os.getcwd(), + "scripts/galaxy_messaging/server/data_transfer.py" ) + global dbconnstr +global webconfig global config def get_value(dom, tag_name): @@ -71,84 +74,98 @@ def get_value_index(dom, tag_name, index rc = rc + node.data return rc -def recv_callback(msg): - global config - global webconfig +def start_data_transfer(message): + # fork a new process to transfer datasets + cmd = '%s "%s" "%s" "%s"' % ( "python", + data_transfer_script, + message.body, + sys.argv[1] ) # Galaxy config file name + pid = subprocess.Popen(cmd, shell=True).pid + log.debug('Started process (%i): %s' % (pid, str(cmd))) + +def update_sample_state(message): + dom = xml.dom.minidom.parseString(message.body) + barcode = get_value(dom, 'barcode') + state = get_value(dom, 'state') + log.debug('Barcode: ' + barcode) + log.debug('State: ' + state) + # update the sample state in Galaxy db + galaxydb = GalaxyDbInterface(dbconnstr) + sample_id = galaxydb.get_sample_id(field_name='bar_code', value=barcode) + if sample_id == -1: + log.debug('Invalid barcode.') + return + galaxydb.change_state(sample_id, state) + # after updating the sample state, update request status + request_id = galaxydb.get_request_id(sample_id) + update_request( request_id ) + +def update_request( request_id ): + http_server_section = webconfig.get( "universe_wsgi_config", "http_server_section" ) + encoded_request_id = api.encode_id( config.get( "app:main", "id_secret" ), request_id ) + api_key = webconfig.get( "data_transfer_user_login_info", "api_key" ) + data = dict( update_type=RequestsController.update_types.REQUEST ) + url = "http://%s:%s/api/requests/%s" % ( config.get(http_server_section, "host"), + config.get(http_server_section, "port"), + encoded_request_id ) + log.debug( 'Updating request %i' % request_id ) + try: + api.update( api_key, url, data, return_formatted=False ) + except urllib2.URLError, e: + log.debug( 'ERROR(update_request (%s)): %s' % ( str((self.api_key, url, data)), str(e) ) ) + +def recv_callback(message): # check the meesage type. - msg_type = msg.properties['application_headers'].get('msg_type') - log.debug('\nMESSAGE RECVD: '+str(msg_type)) + msg_type = message.properties['application_headers'].get('msg_type') + log.debug( 'MESSAGE RECVD: ' + str( msg_type ) ) if msg_type == 'data_transfer': - log.debug('DATA TRANSFER') - # fork a new process to transfer datasets - transfer_script = os.path.join(os.getcwd(), - "scripts/galaxy_messaging/server/data_transfer.py") - cmd = '%s "%s" "%s" "%s"' % ("python", - transfer_script, - msg.body, - config.get("app:main", "id_secret") ) - pid = subprocess.Popen(cmd, shell=True).pid - log.debug('Started process (%i): %s' % (pid, str(cmd))) + log.debug( 'DATA TRANSFER' ) + start_data_transfer( message ) elif msg_type == 'sample_state_update': - log.debug('SAMPLE STATE UPDATE') - dom = xml.dom.minidom.parseString(msg.body) - barcode = get_value(dom, 'barcode') - state = get_value(dom, 'state') - log.debug('Barcode: '+barcode) - log.debug('State: '+state) - # update the galaxy db - galaxydb = GalaxyDbInterface(dbconnstr) - sample_id = galaxydb.get_sample_id(field_name='bar_code', value=barcode) - if sample_id == -1: - log.debug('Invalid barcode.') - return - galaxydb.change_state(sample_id, state) - # update the request state - galaxyweb = GalaxyWebInterface(webconfig.get("universe_wsgi_config", "host"), - webconfig.get("universe_wsgi_config", "port"), - webconfig.get("data_transfer_user_login_info", "email"), - webconfig.get("data_transfer_user_login_info", "password"), - config.get("app:main", "id_secret")) - galaxyweb.update_request_state(galaxydb.get_request_id(sample_id)) - galaxyweb.logout() + log.debug( 'SAMPLE STATE UPDATE' ) + update_sample_state( message ) def main(): if len(sys.argv) < 2: - print 'Usage: python amqp_consumer.py <Galaxy config file>' + print 'Usage: python amqp_consumer.py <Galaxy configuration file>' return global config config = ConfigParser.ConfigParser() - config.read(sys.argv[1]) + config.read( sys.argv[1] ) global dbconnstr dbconnstr = config.get("app:main", "database_connection") amqp_config = {} for option in config.options("galaxy_amqp"): amqp_config[option] = config.get("galaxy_amqp", option) - log.debug(str(amqp_config)) + log.debug("PID: " + str(os.getpid()) + ", " + str(amqp_config)) # web server config global webconfig webconfig = ConfigParser.ConfigParser() webconfig.read('transfer_datasets.ini') - - - - - + # connect conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], userid=amqp_config['userid'], password=amqp_config['password'], virtual_host=amqp_config['virtual_host'], insist=False) chan = conn.channel() - chan.queue_declare(queue=amqp_config['queue'], durable=True, exclusive=True, auto_delete=False) - chan.exchange_declare(exchange=amqp_config['exchange'], type="direct", durable=True, auto_delete=False,) - chan.queue_bind(queue=amqp_config['queue'], - exchange=amqp_config['exchange'], - routing_key=amqp_config['routing_key']) + chan.queue_declare( queue=amqp_config['queue'], + durable=True, + exclusive=True, + auto_delete=False) + chan.exchange_declare( exchange=amqp_config['exchange'], + type="direct", + durable=True, + auto_delete=False,) + chan.queue_bind( queue=amqp_config['queue'], + exchange=amqp_config['exchange'], + routing_key=amqp_config['routing_key']) - chan.basic_consume(queue=amqp_config['queue'], - no_ack=True, - callback=recv_callback, - consumer_tag="testtag") + chan.basic_consume( queue=amqp_config['queue'], + no_ack=True, + callback=recv_callback, + consumer_tag="testtag") + log.debug('Connected to rabbitmq server - '+amqp_config['host']+":"+amqp_config['port']) while True: chan.wait() chan.basic_cancel("testtag") @@ -157,3 +174,5 @@ def main(): if __name__ == '__main__': main() + + --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1584,6 +1584,7 @@ class Request( object ): SUBMITTED = 'In Progress', REJECTED = 'Rejected', COMPLETE = 'Complete' ) + api_collection_visible_keys = ( 'id', 'name', 'state' ) def __init__( self, name=None, desc=None, request_type=None, user=None, form_values=None, notification=None ): self.name = name self.desc = desc @@ -1663,7 +1664,7 @@ class Request( object ): # Send email if trans.app.config.smtp_server is not None and self.notification and self.notification[ 'email' ]: host = trans.request.host.split( ':' )[0] - if host in [ 'localhost', '127.0.0.1' ]: + if host in [ 'localhost', '127.0.0.1', '0.0.0.0' ]: host = socket.getfqdn() body = """ Galaxy Sample Tracking Notification @@ -1704,8 +1705,8 @@ All samples in state: %(sample_state s.sendmail( frm, to, message ) s.quit() comments = "Email notification sent to %s." % ", ".join( to ).strip().strip( ',' ) - except: - comments = "Email notification failed." + except Exception,e: + comments = "Email notification failed. (%s)" % str(e) # update the request history with the email notification event elif not trans.app.config.smtp_server: comments = "Email notification failed as SMTP server not set in config file" @@ -1714,6 +1715,18 @@ All samples in state: %(sample_state trans.sa_session.add( event ) trans.sa_session.flush() return comments + def get_api_value( self, view='collection' ): + rval = {} + try: + visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' ) + except AttributeError: + raise Exception( 'Unknown API view: %s' % view ) + for key in visible_keys: + try: + rval[key] = self.__getattribute__( key ) + except AttributeError: + rval[key] = None + return rval class RequestEvent( object ): def __init__(self, request=None, request_state=None, comment=''): @@ -1734,7 +1747,7 @@ class RequestType( object ): self.sample_form = sample_form self.datatx_info = datatx_info @property - def state( self ): + def final_sample_state( self ): # The states mapper for this object orders ascending return self.states[-1] @@ -1747,12 +1760,6 @@ class RequestTypePermissions( object ): class Sample( object ): bulk_operations = Bunch( CHANGE_STATE = 'Change state', SELECT_LIBRARY = 'Select data library and folder' ) - transfer_status = Bunch( NOT_STARTED = 'Not started', - IN_QUEUE = 'In queue', - TRANSFERRING = 'Transferring dataset', - ADD_TO_LIBRARY = 'Adding to data library', - COMPLETE = 'Complete', - ERROR = 'Error' ) def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None): self.name = name self.desc = desc @@ -1776,21 +1783,21 @@ class Sample( object ): def untransferred_dataset_files( self ): untransferred_datasets = [] for dataset in self.datasets: - if dataset.status == self.transfer_status.NOT_STARTED: + if dataset.status == SampleDataset.transfer_status.NOT_STARTED: untransferred_datasets.append( dataset ) return untransferred_datasets @property def inprogress_dataset_files( self ): inprogress_datasets = [] for dataset in self.datasets: - if dataset.status not in [ self.transfer_status.NOT_STARTED, self.transfer_status.COMPLETE ]: + if dataset.status not in [ SampleDataset.transfer_status.NOT_STARTED, SampleDataset.transfer_status.COMPLETE ]: inprogress_datasets.append( dataset ) return inprogress_datasets @property def transferred_dataset_files( self ): transferred_datasets = [] for dataset in self.datasets: - if dataset.status == self.transfer_status.COMPLETE: + if dataset.status == SampleDataset.transfer_status.COMPLETE: transferred_datasets.append( dataset ) return transferred_datasets def dataset_size( self, filepath ): @@ -1818,6 +1825,12 @@ class SampleEvent( object ): self.comment = comment class SampleDataset( object ): + transfer_status = Bunch( NOT_STARTED = 'Not started', + IN_QUEUE = 'In queue', + TRANSFERRING = 'Transferring dataset', + ADD_TO_LIBRARY = 'Adding to data library', + COMPLETE = 'Complete', + ERROR = 'Error' ) def __init__(self, sample=None, name=None, file_path=None, status=None, error_msg=None, size=None): self.sample = sample --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -275,7 +275,7 @@ class RequestsCommon( BaseController, Us request_type = request.type name = util.restore_text( params.get( 'name', '' ) ) desc = util.restore_text( params.get( 'desc', '' ) ) - notification = dict( email=[ user.email ], sample_states=[ request_type.state.id ], body='', subject='' ) + notification = dict( email=[ user.email ], sample_states=[ request_type.final_sample_state.id ], body='', subject='' ) values = [] for index, field in enumerate( request_type.request_form.fields ): field_type = field[ 'type' ] @@ -416,11 +416,7 @@ class RequestsCommon( BaseController, Us 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 ) ) - for sample_id in selected_samples: - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) - event = trans.model.SampleEvent( sample, new_state, sample_event_comment ) - trans.sa_session.add( event ) - trans.sa_session.flush() + 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', @@ -486,6 +482,22 @@ class RequestsCommon( BaseController, Us status=status, message=message ) @web.expose + def update_sample_state(self, trans, cntrller, sample_ids, new_state, comment=None ): + for sample_id in sample_ids: + try: + sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) + except: + if cntrller == 'api': + trans.response.status = 400 + return "Malformed 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 ) + trans.sa_session.add( event ) + trans.sa_session.flush() + if cntrller == 'api': + return 200, 'Done' + @web.expose @web.require_login( "delete sequencing requests" ) def delete_request( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -640,6 +652,8 @@ class RequestsCommon( BaseController, Us event = trans.model.RequestEvent( request, request.states.SUBMITTED, message ) trans.sa_session.add( event ) trans.sa_session.flush() + if cntrller == 'api': + return 200, message return trans.response.send_redirect( web.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, @@ -647,7 +661,7 @@ class RequestsCommon( BaseController, Us status=status, message=message ) ) final_state = False - request_type_state = request.type.state + request_type_state = request.type.final_sample_state if common_state.id == request_type_state.id: # since all the samples are in the final state, change the request state to 'Complete' comments = "All samples of this request are in the last sample state (%s). " % request_type_state.name @@ -656,7 +670,7 @@ class RequestsCommon( BaseController, Us else: comments = "All samples are in %s state. " % common_state.name state = request.states.SUBMITTED - event = trans.model.RequestEvent(request, state, comments) + 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 @@ -666,6 +680,8 @@ class RequestsCommon( BaseController, Us message = comments + retval else: message = comments + if cntrller == 'api': + return 200, message return trans.response.send_redirect( web.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, --- a/scripts/galaxy_messaging/server/data_transfer.py +++ b/scripts/galaxy_messaging/server/data_transfer.py @@ -19,25 +19,26 @@ import urllib,urllib2, cookielib, shutil import logging, time, datetime import xml.dom.minidom -sp = sys.path[0] +log = logging.getLogger("datatx_"+str(os.getpid())) +log.setLevel(logging.DEBUG) +fh = logging.FileHandler("data_transfer.log") +fh.setLevel(logging.DEBUG) +formatter = logging.Formatter("%(asctime)s - %(name)s - %(message)s") +fh.setFormatter(formatter) +log.addHandler(fh) -from galaxydb_interface import GalaxyDbInterface - -assert sys.version_info[:2] >= ( 2, 4 ) -new_path = [ sp ] -new_path.extend( sys.path ) -sys.path = new_path - -from galaxyweb_interface import GalaxyWebInterface +api_path = [ os.path.join( os.getcwd(), "scripts/api" ) ] +sys.path.extend( api_path ) +import common as api assert sys.version_info[:2] >= ( 2, 4 ) new_path = [ os.path.join( os.getcwd(), "lib" ) ] new_path.extend( sys.path[1:] ) # remove scripts/ from the path sys.path = new_path - from galaxy.util.json import from_json_string, to_json_string -from galaxy.model import Sample +from galaxy.model import SampleDataset +from galaxy.web.api.requests import RequestsController from galaxy import eggs import pkg_resources pkg_resources.require( "pexpect" ) @@ -46,28 +47,19 @@ import pexpect pkg_resources.require( "simplejson" ) import simplejson -log = logging.getLogger("datatx_"+str(os.getpid())) -log.setLevel(logging.DEBUG) -fh = logging.FileHandler("data_transfer.log") -fh.setLevel(logging.DEBUG) -formatter = logging.Formatter("%(asctime)s - %(name)s - %(message)s") -fh.setFormatter(formatter) -log.addHandler(fh) - - class DataTransfer(object): - def __init__(self, msg, config_id_secret): + def __init__(self, msg, config_file): log.info(msg) self.dom = xml.dom.minidom.parseString(msg) - self.host = self.get_value(self.dom, 'data_host') - self.username = self.get_value(self.dom, 'data_user') - self.password = self.get_value(self.dom, 'data_password') + self.sequencer_host = self.get_value(self.dom, 'data_host') + self.sequencer_username = self.get_value(self.dom, 'data_user') + self.sequencer_password = self.get_value(self.dom, 'data_password') + self.request_id = self.get_value(self.dom, 'request_id') self.sample_id = self.get_value(self.dom, 'sample_id') self.library_id = self.get_value(self.dom, 'library_id') self.folder_id = self.get_value(self.dom, 'folder_id') self.dataset_files = [] - self.config_id_secret = config_id_secret count=0 while True: dataset_id = self.get_value_index(self.dom, 'dataset_id', count) @@ -82,21 +74,25 @@ class DataTransfer(object): count=count+1 try: # Retrieve the upload user login information from the config file + transfer_datasets_config = ConfigParser.ConfigParser() + transfer_datasets_config.read('transfer_datasets.ini') + self.data_transfer_user_email = transfer_datasets_config.get("data_transfer_user_login_info", "email") + self.data_transfer_user_password = transfer_datasets_config.get("data_transfer_user_login_info", "password") + self.api_key = transfer_datasets_config.get("data_transfer_user_login_info", "api_key") + self.http_server_section = transfer_datasets_config.get("universe_wsgi_config", "http_server_section") config = ConfigParser.ConfigParser() - config.read('transfer_datasets.ini') - self.datatx_email = config.get("data_transfer_user_login_info", "email") - self.datatx_password = config.get("data_transfer_user_login_info", "password") - self.server_host = config.get("universe_wsgi_config", "host") - self.server_port = config.get("universe_wsgi_config", "port") - self.database_connection = config.get("universe_wsgi_config", "database_connection") - self.import_dir = config.get("universe_wsgi_config", "library_import_dir") + config.read( config_file ) + self.server_host = config.get(self.http_server_section, "host") + self.server_port = config.get(self.http_server_section, "port") + self.database_connection = config.get("app:main", "database_connection") + self.import_dir = config.get("app:main", "library_import_dir") + self.config_id_secret = config.get("app:main", "id_secret") + # create the destination directory within the import directory self.server_dir = os.path.join( self.import_dir, 'datatx_'+str(os.getpid())+'_'+datetime.date.today().strftime("%d%b%Y") ) os.mkdir(self.server_dir) if not os.path.exists(self.server_dir): raise Exception - # connect to db - self.galaxydb = GalaxyDbInterface(self.database_connection) except: log.error(traceback.format_exc()) log.error('FATAL ERROR') @@ -114,7 +110,7 @@ class DataTransfer(object): # add the dataset to the given library self.add_to_library() # update the data transfer status in the db - self.update_status(Sample.transfer_status.COMPLETE) + self.update_status(SampleDataset.transfer_status.COMPLETE) # cleanup #self.cleanup() sys.exit(0) @@ -149,15 +145,15 @@ class DataTransfer(object): def print_ticks(d): pass for i, df in enumerate(self.dataset_files): - self.update_status(Sample.transfer_status.TRANSFERRING, df['dataset_id']) + self.update_status(SampleDataset.transfer_status.TRANSFERRING, df['dataset_id']) try: - cmd = "scp %s@%s:'%s' '%s/%s'" % ( self.username, - self.host, - df['file'].replace(' ', '\ '), - self.server_dir.replace(' ', '\ '), - df['name'].replace(' ', '\ ')) + cmd = "scp %s@%s:'%s' '%s/%s'" % ( self.sequencer_username, + self.sequencer_host, + df['file'].replace(' ', '\ '), + self.server_dir.replace(' ', '\ '), + df['name'].replace(' ', '\ ') ) log.debug(cmd) - output = pexpect.run(cmd, events={'.ssword:*': self.password+'\r\n', + output = pexpect.run(cmd, events={'.ssword:*': self.sequencer_password+'\r\n', pexpect.TIMEOUT:print_ticks}, timeout=10) log.debug(output) @@ -176,17 +172,21 @@ class DataTransfer(object): This method adds the dataset file to the target data library & folder by opening the corresponding url in Galaxy server running. ''' + self.update_status(SampleDataset.transfer_status.ADD_TO_LIBRARY) try: - self.update_status(Sample.transfer_status.ADD_TO_LIBRARY) - log.debug("dir:%s, lib:%s, folder:%s" % (self.server_dir, str(self.library_id), str(self.folder_id))) - galaxyweb = GalaxyWebInterface(self.server_host, self.server_port, - self.datatx_email, self.datatx_password, - self.config_id_secret) - retval = galaxyweb.add_to_library(self.server_dir, self.library_id, self.folder_id) - log.debug(str(retval)) - galaxyweb.logout() - except Exception, e: - log.debug(e) + data = {} + data[ 'folder_id' ] = api.encode_id( self.config_id_secret, '%s.%s' % ( 'folder', self.folder_id ) ) + data[ 'file_type' ] = 'auto' + data[ 'server_dir' ] = self.server_dir + data[ 'dbkey' ] = '' + data[ 'upload_option' ] = 'upload_directory' + data[ 'create_type' ] = 'file' + url = "http://%s:%s/api/libraries/%s/contents" % ( self.server_host, + self.server_port, + api.encode_id( self.config_id_secret, self.library_id ) ) + log.debug(str((self.api_key, url, data))) + retval = api.submit( self.api_key, url, data, return_formatted=False ) + except: self.error_and_exit(str(e)) def update_status(self, status, dataset_id='All', msg=''): @@ -195,12 +195,27 @@ class DataTransfer(object): ''' try: log.debug('Setting status "%s" for dataset "%s" of sample "%s"' % ( status, str(dataset_id), str(self.sample_id) ) ) + sample_dataset_ids = [] if dataset_id == 'All': for dataset in self.dataset_files: - self.galaxydb.set_sample_dataset_status(dataset['dataset_id'], status, msg) + sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset['dataset_id'] ) ) else: - self.galaxydb.set_sample_dataset_status(dataset_id, status, msg) + sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset_id ) ) + # update the transfer status + data = {} + data[ 'update_type' ] = RequestsController.update_types.SAMPLE_DATASET + data[ 'sample_dataset_ids' ] = sample_dataset_ids + data[ 'new_status' ] = status + data[ 'error_msg' ] = msg + url = "http://%s:%s/api/requests/%s" % ( self.server_host, + self.server_port, + api.encode_id( self.config_id_secret, self.request_id ) ) + log.debug(str((self.api_key, url, data))) + retval = api.update( self.api_key, url, data, return_formatted=False ) log.debug('done.') + except urllib2.URLError, e: + log.debug( 'ERROR(sample_dataset_transfer_status (%s)): %s' % ( url, str(e) ) ) + log.error(traceback.format_exc()) except: log.error(traceback.format_exc()) log.error('FATAL ERROR') --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -32,7 +32,7 @@ <tbody> %for id in id_list: <% sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( id ) ) %> - %if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED: + %if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.NOT_STARTED: <tr><td><% rename_datasets_for_sample_select_field = build_rename_datasets_for_sample_select_field( trans, sample_dataset ) %> --- a/scripts/api/common.py +++ b/scripts/api/common.py @@ -10,6 +10,11 @@ import pkg_resources pkg_resources.require( "simplejson" ) import simplejson +pkg_resources.require( "pycrypto" ) +from Crypto.Cipher import Blowfish +from Crypto.Util.randpool import RandomPool +from Crypto.Util import number + def make_url( api_key, url, args=None ): # Adds the API Key to the URL if it's not already there. if args is None: @@ -36,7 +41,15 @@ def post( api_key, url, data ): req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ) ) return simplejson.loads( urllib2.urlopen( req ).read() ) -def display( api_key, url ): +def put( api_key, url, data ): + # Do the actual PUT + url = make_url( api_key, url ) + req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data )) + req.get_method = lambda: 'PUT' + return simplejson.loads( urllib2.urlopen( req ).read() ) + + +def display( api_key, url, return_formatted=True ): # Sends an API GET request and acts as a generic formatter for the JSON response. try: r = get( api_key, url ) @@ -47,6 +60,8 @@ def display( api_key, url ): if type( r ) == unicode: print 'error: %s' % r return None + if not return_formatted: + return r elif type( r ) == list: # Response is a collection as defined in the REST style. print 'Collection Members' @@ -68,7 +83,7 @@ def display( api_key, url ): else: print 'response is unknown type: %s' % type( r ) -def submit( api_key, url, data ): +def submit( api_key, url, data, return_formatted=True ): # Sends an API POST request and acts as a generic formatter for the JSON response. # 'data' will become the JSON payload read by Galaxy. try: @@ -77,6 +92,8 @@ def submit( api_key, url, data ): print e print e.read( 1024 ) sys.exit( 1 ) + if not return_formatted: + return r print 'Response' print '--------' if type( r ) == list: @@ -96,3 +113,45 @@ def submit( api_key, url, data ): print i else: print r + +def update( api_key, url, data, return_formatted=True ): + # Sends an API PUT request and acts as a generic formatter for the JSON response. + # 'data' will become the JSON payload read by Galaxy. + try: + r = put( api_key, url, data ) + except urllib2.HTTPError, e: + print e + print e.read( 1024 ) + sys.exit( 1 ) + if not return_formatted: + return r + print 'Response' + print '--------' + if type( r ) == list: + # Currently the only implemented responses are lists of dicts, because + # submission creates some number of collection elements. + for i in r: + if type( i ) == dict: + if 'url' in i: + print i.pop( 'url' ) + else: + print '----' + if 'name' in i: + print ' name: %s' % i.pop( 'name' ) + for k, v in i.items(): + print ' %s: %s' % ( k, v ) + else: + print i + else: + print r + +# utility method to encode ID's +def encode_id( config_id_secret, obj_id ): + id_cipher = Blowfish.new( config_id_secret ) + # Convert to string + s = str( obj_id ) + # Pad to a multiple of 8 with leading "!" + s = ( "!" * ( 8 - len(s) % 8 ) ) + s + # Encrypt + return id_cipher.encrypt( s ).encode( 'hex' ) + --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -129,9 +129,9 @@ class DataTransferGrid( grids.Grid ): visible=False, filterable="standard" ) ) operations = [ - grids.GridOperation( "Start Transfer", allow_multiple=True, condition=( lambda item: item.status in [ model.Sample.transfer_status.NOT_STARTED ] ) ), - grids.GridOperation( "Rename", allow_multiple=True, allow_popup=False, condition=( lambda item: item.status in [ model.Sample.transfer_status.NOT_STARTED ] ) ), - grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: item.status in [ model.Sample.transfer_status.NOT_STARTED ] ) ), + 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 ] ) ), ] def apply_query_filter( self, trans, query, **kwd ): sample_id = kwd.get( 'sample_id', None ) @@ -506,7 +506,7 @@ class RequestsAdmin( BaseController, Use name = self.__dataset_name( sample, filepath.split( '/' )[-1] ) sample_dataset = trans.model.SampleDataset( sample=sample, file_path=filepath, - status=sample.transfer_status.NOT_STARTED, + status=trans.app.model.SampleDataset.transfer_status.NOT_STARTED, name=name, error_msg='', size=sample.dataset_size( filepath ) ) @@ -575,6 +575,7 @@ class RequestsAdmin( BaseController, Use <data_host>%(DATA_HOST)s</data_host><data_user>%(DATA_USER)s</data_user><data_password>%(DATA_PASSWORD)s</data_password> + <request_id>%(REQUEST_ID)s</request_id><sample_id>%(SAMPLE_ID)s</sample_id><library_id>%(LIBRARY_ID)s</library_id><folder_id>%(FOLDER_ID)s</folder_id> @@ -588,16 +589,17 @@ class RequestsAdmin( BaseController, Use </dataset>''' datasets = '' for sample_dataset in selected_sample_datasets: - if sample_dataset.status == sample.transfer_status.NOT_STARTED: + if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.NOT_STARTED: datasets = datasets + dataset_xml % dict( ID=str( sample_dataset.id ), NAME=sample_dataset.name, FILE=sample_dataset.file_path ) - sample_dataset.status = sample.transfer_status.IN_QUEUE + sample_dataset.status = trans.app.model.SampleDataset.transfer_status.IN_QUEUE trans.sa_session.add( sample_dataset ) trans.sa_session.flush() data = xml % dict( DATA_HOST=datatx_info['host'], DATA_USER=datatx_info['username'], DATA_PASSWORD=datatx_info['password'], + REQUEST_ID=str(sample.request.id), SAMPLE_ID=str(sample.id), LIBRARY_ID=str(sample.library.id), FOLDER_ID=str(sample.folder.id), @@ -644,6 +646,25 @@ class RequestsAdmin( BaseController, Use sample_id=trans.security.encode_id( sample.id ), status=status, message=message) ) + @web.expose + def update_sample_dataset_status(self, trans, cntrller, sample_dataset_ids, new_status, error_msg=None ): + # check if the new status is a valid transfer status + possible_status_list = [v[1] for v in trans.app.model.SampleDataset.transfer_status.items()] + if new_status not in possible_status_list: + trans.response.status = 400 + return "The requested transfer status ( %s ) is not a valid transfer status." % new_status + for id in util.listify( sample_dataset_ids ): + try: + sd_id = trans.security.decode_id( id ) + sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( sd_id ) + except: + trans.response.status = 400 + return "Invalid sample dataset id ( %s ) specified." % str( id ) + sample_dataset.status = new_status + sample_dataset.error_msg = error_msg + trans.sa_session.add( sample_dataset ) + trans.sa_session.flush() + return 200, 'Done' # Request Type Stuff @web.expose @web.require_admin --- a/scripts/galaxy_messaging/server/galaxydb_interface.py +++ b/scripts/galaxy_messaging/server/galaxydb_interface.py @@ -28,7 +28,7 @@ class GalaxyDbInterface(object): def __init__(self, dbstr): self.dbstr = dbstr self.db_engine = create_engine(self.dbstr) - self.db_engine.echo = True + self.db_engine.echo = False self.metadata = MetaData(self.db_engine) self.session = sessionmaker(bind=self.db_engine) self.event_table = Table('sample_event', self.metadata, autoload=True ) --- /dev/null +++ b/scripts/api/sample_update_state.py @@ -0,0 +1,23 @@ +#!/usr/bin/env python + + +import os, sys, traceback +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import display +from common import submit +from common import update + +try: + data = {} + data[ 'update_type' ] = 'sample_state' + data[ 'sample_ids' ] = sys.argv[3].split(',') + data[ 'new_state' ] = sys.argv[4] +except IndexError: + print 'usage: %s key url sample_ids new_state [comment]' % os.path.basename( sys.argv[0] ) + sys.exit( 1 ) +try: + data[ 'comment' ] = sys.argv[5] +except IndexError: + data[ 'comment' ] = '' + +update( sys.argv[1], sys.argv[2], data, return_formatted=True ) --- /dev/null +++ b/lib/galaxy/web/api/requests.py @@ -0,0 +1,130 @@ +""" +API operations on a sample tracking system. +""" +import logging, os, string, shutil, urllib, re, socket +from cgi import escape, FieldStorage +from galaxy import util, datatypes, jobs, web, util +from galaxy.web.base.controller import * +from galaxy.util.sanitize_html import sanitize_html +from galaxy.model.orm import * +from galaxy.util.bunch import Bunch + +log = logging.getLogger( __name__ ) + +class RequestsController( BaseController ): + update_types = Bunch( REQUEST = 'request_state', + SAMPLE = 'sample_state', + SAMPLE_DATASET = 'sample_dataset_transfer_status' ) + update_type_values = [v[1] for v in update_types.items()] + @web.expose_api + def index( self, trans, **kwd ): + """ + GET /api/requests + Displays a collection (list) of sequencing requests. + """ + query = trans.sa_session.query( trans.app.model.Request )\ + .filter( and_( trans.app.model.Request.table.c.user_id == trans.user.id \ + and trans.app.model.Request.table.c.deleted == False ) ) \ + .all() + rval = [] + for request in query: + item = request.get_api_value() + item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) ) + item['id'] = trans.security.encode_id( item['id'] ) + rval.append( item ) + return rval + + @web.expose_api + def update( self, trans, id, key, payload, **kwd ): + """ + PUT /api/requests/{encoded_request_id} + Displays information about a sequencing request. + """ + params = util.Params( kwd ) + update_type = None + if 'update_type' not in payload: + trans.response.status = 400 + return "Missing required 'update_type' parameter. Please consult the API documentation for help." + else: + update_type = payload.pop( 'update_type' ) + if update_type not in self.update_type_values: + trans.response.status = 400 + return "Invalid value for 'update_type' parameter ( %s ) specified. Please consult the API documentation for help." % update_type + try: + request_id = trans.security.decode_id( id ) + except TypeError: + trans.response.status = 400 + return "Malformed %s id ( %s ) specified, unable to decode." % ( update_type, str( id ) ) + try: + request = trans.sa_session.query( trans.app.model.Request ).get( request_id ) + except: + request = None + if not request or not ( trans.user_is_admin() or request.user.id == trans.user.id ): + trans.response.status = 400 + return "Invalid request id ( %s ) specified." % str( request_id ) + # check update type + if update_type == 'request_state': + return self.__update_request_state( trans, encoded_request_id=id ) + elif update_type == 'sample_state': + return self.__update_sample_state( trans, request.type, **payload ) + elif update_type == 'sample_dataset_transfer_status': + # update sample_dataset transfer status + return self.__update_sample_dataset_status( trans, **payload ) + + + def __update_request_state( self, trans, encoded_request_id ): + requests_common_cntrller = trans.webapp.controllers['requests_common'] + status, output = requests_common_cntrller.update_request_state( trans, + cntrller='api', + request_id=encoded_request_id ) + return status, output + def __update_sample_state( self, trans, request_type, **payload ): + # only admin user may update sample state in Galaxy sample tracking + if not trans.user_is_admin(): + trans.response.status = 400 + return "only an admin user may update sample state in Galaxy sample tracking." + if 'sample_ids' not in payload or 'new_state' not in payload: + trans.response.status = 400 + return "Missing one or more required parameters: 'sample_ids' and 'new_state'." + sample_ids = payload.pop( 'sample_ids' ) + new_state_name = payload.pop( 'new_state' ) + comment = payload.get( 'comment', '' ) + # check if the new state is a valid sample state + possible_states = request_type.states + new_state = None + for state in possible_states: + if state.name == new_state_name: + new_state = state + if not new_state: + trans.response.status = 400 + return "Invalid sample state requested ( %s )." % new_state + requests_common_cntrller = trans.webapp.controllers['requests_common'] + status, output = requests_common_cntrller.update_sample_state( trans, + cntrller='api', + sample_ids=sample_ids, + new_state=new_state, + comment=comment ) + return status, output + + def __update_sample_dataset_status( self, trans, **payload ): + # only admin user may transfer sample datasets in Galaxy sample tracking + if not trans.user_is_admin(): + trans.response.status = 400 + return "Only an admin user may transfer sample datasets in Galaxy sample tracking and thus update transfer status." + if 'sample_dataset_ids' not in payload or 'new_status' not in payload: + trans.response.status = 400 + return "Missing one or more required parameters: 'sample_dataset_ids' and 'new_status'." + sample_dataset_ids = payload.pop( 'sample_dataset_ids' ) + new_status = payload.pop( 'new_status' ) + error_msg = payload.get( 'error_msg', '' ) + requests_admin_cntrller = trans.webapp.controllers['requests_admin'] + status, output = requests_admin_cntrller.update_sample_dataset_status( trans, + cntrller='api', + sample_dataset_ids=sample_dataset_ids, + new_status=new_status, + error_msg=error_msg ) + return status, output + + + + --- a/templates/admin/requests/dataset.mako +++ b/templates/admin/requests/dataset.mako @@ -58,7 +58,7 @@ <label>Transfer status:</label><div style="float: left; width: 250px; margin-right: 10px;"> ${sample_dataset.status} - %if sample_dataset.status == sample.transfer_status.ERROR: + %if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.ERROR: <br/> ${sample_dataset.error_msg} %endif --- a/scripts/api/display.py +++ b/scripts/api/display.py @@ -1,6 +1,6 @@ #!/usr/bin/env python -import os, sys +import os, sys, urllib2 sys.path.insert( 0, os.path.dirname( __file__ ) ) from common import display @@ -9,3 +9,6 @@ try: except TypeError: print 'usage: %s key url' % os.path.basename( sys.argv[0] ) sys.exit( 1 ) +except urllib2.URLError, e: + print str(e) + sys.exit( 1 )

1 0

galaxy-dist commit 87a6d4a29eee: fixed mutation viz functional tests
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 rc # Date 1288111817 14400 # Node ID 87a6d4a29eeea038c669f086d254aaa4140a15bb # Parent e6e68c67dd9759154876546662f59ee280b78a34 fixed mutation viz functional tests --- a/test-data/mutation_data1_zoom3x.svg +++ b/test-data/mutation_data1_zoom3x.svg @@ -5,21 +5,21 @@ <g id="viewport"> -<text y="4" x="12" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">A</tspan></text> +<text y="3" x="12" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">A</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="14" fill="blue" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="14" fill="blue" /> -<text y="4" x="22" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">C</tspan></text> +<text y="3" x="22" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">C</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="24" fill="green" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="24" fill="green" /> -<text y="4" x="32" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">G</tspan></text> +<text y="3" x="32" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">G</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="34" fill="orange" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="34" fill="orange" /> -<text y="4" x="42" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">T</tspan></text> +<text y="3" x="42" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">T</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="44" fill="red" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="44" fill="red" /><text y="25" x="23" stroke="none" transform="rotate(-90 23,25)" fill="black"><tspan style="font-family:Verdana;font-size:25%">s1</tspan></text> --- a/test-data/mutation_data1_interactive.svg +++ b/test-data/mutation_data1_interactive.svg @@ -234,21 +234,21 @@ function handleMouseUp(evt) { <g id="viewport"> -<text y="4" x="12" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">A</tspan></text> +<text y="3" x="12" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">A</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="14" fill="blue" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="14" fill="blue" /> -<text y="4" x="22" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">C</tspan></text> +<text y="3" x="22" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">C</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="24" fill="green" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="24" fill="green" /> -<text y="4" x="32" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">G</tspan></text> +<text y="3" x="32" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">G</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="34" fill="orange" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="34" fill="orange" /> -<text y="4" x="42" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">T</tspan></text> +<text y="3" x="42" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">T</tspan></text> -<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="1" x="44" fill="red" /> +<rect fill-opacity="0.5" height="3" width="4" stroke="none" y="0" x="44" fill="red" /><text y="35" x="23" stroke="none" transform="rotate(-90 23,35)" fill="black"><tspan style="font-family:Verdana;font-size:25%">s1</tspan></text>

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galaxy-dist commit 379d0701f198: added select all checkbox to grid framework
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 rc # Date 1288119695 14400 # Node ID 379d0701f198964fb964c3834cce7414cbc8f888 # Parent 262c91e3a2ea7d11d65875ec2af42526c92b7123 added select all checkbox to grid framework --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -610,6 +610,36 @@ } }); } + + function check_all_items() + { + var chk_all = document.getElementById('check_all'); + var checks = document.getElementsByTagName('input'); + //var boxLength = checks.length; + var total = 0; + if ( chk_all.checked == true ) + { + for ( i=0; i < checks.length; i++ ) + { + if ( checks[i].name.indexOf( 'id' ) != -1) + { + checks[i].checked = true; + total++; + } + } + } + else + { + for ( i=0; i < checks.length; i++ ) + { + if ( checks[i].name.indexOf( 'id' ) != -1) + { + checks[i].checked = false + } + } + } + + } </script></%def> @@ -761,7 +791,11 @@ <thead id="grid-table-header"><tr> %if show_item_checkboxes: - <th></th> + <th> + %if query.count() > 0: + <input type="checkbox" id="check_all" name=select_all_checkbox value="true" onclick='check_all_items(1);'><input type="hidden" name=select_all_checkbox value="true"> + %endif + </th> %endif %for column in grid.columns: %if column.visible:

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galaxy-dist commit e6e68c67dd97: Use a job to import a history from an archive. This makes it possible to move a history from one Galaxy instance to another, subject to the limitations below. The job itself unpacks the archive, and the job's cleanup creates a history from the archive. A history imported via an archive is only visible to the user when it has finished being imported.
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 1288106620 14400 # Node ID e6e68c67dd9759154876546662f59ee280b78a34 # Parent 677bcc65f74f5a460277f089d0cdebf170f02831 Use a job to import a history from an archive. This makes it possible to move a history from one Galaxy instance to another, subject to the limitations below. The job itself unpacks the archive, and the job's cleanup creates a history from the archive. A history imported via an archive is only visible to the user when it has finished being imported. Currently, there are limitations to this functionality; these will be fixed going forward. These limitations are: -history archives can be imported only via URL, not file; -histories must be shared in order for them to be importable via archive; -tags are not currently imported; -reproducibility is limited as parameters for imported jobs are not always recovered and set. --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -79,7 +79,7 @@ class HistoryListGrid( grids.Grid ): def get_current_item( self, trans, **kwargs ): return trans.get_history() def apply_query_filter( self, trans, query, **kwargs ): - return query.filter_by( user=trans.user, purged=False ) + return query.filter_by( user=trans.user, purged=False, importing=False ) class SharedHistoryListGrid( grids.Grid ): # Custom column types @@ -465,212 +465,40 @@ class HistoryController( BaseController, trans.sa_session.flush() return new_annotation - def import_archive( self, trans, archived_history=None, gzip=True ): - """ Import a history. """ + @web.expose + # TODO: Remove require_login when users are warned that, if they are not + # logged in, this will remove their current history. + @web.require_login( "use Galaxy histories" ) + def import_archive( self, trans, **kwargs ): + """ Import a history from a file archive. """ - def file_in_dir( file_path, a_dir ): - """ Returns true if file is in directory. """ - abs_file_path = os.path.abspath( file_path ) - return os.path.split( abs_file_path )[0] == a_dir + # Set archive source and type. + archive_file = kwargs.get( 'archive_file', None ) + archive_url = kwargs.get( 'archive_url', None ) + archive_source = None + if archive_file: + archive_source = archive_file + archive_type = 'file' + elif archive_url: + archive_source = archive_url + archive_type = 'url' - if archived_history is not None: - try: - history_archive_file = tarfile.open( archived_history.file.name ) - - # Unpack archive in temporary directory. - temp_output_dir = tempfile.mkdtemp() - history_archive_file.extractall( path=temp_output_dir ) - history_archive_file.close() - - # - # Create history. - # - history_attr_file_name = os.path.join( temp_output_dir, 'history_attrs.txt') - if not file_in_dir( history_attr_file_name, temp_output_dir ): - raise Exception( "Invalid location for history attributes file: %s" % history_attr_file_name ) - history_attr_in = open( history_attr_file_name, 'rb' ) - history_attr_str = '' - buffsize = 1048576 - try: - while True: - history_attr_str += history_attr_in.read( buffsize ) - if not history_attr_str or len( history_attr_str ) % buffsize != 0: - break - except OverflowError: - pass - history_attr_in.close() - history_attrs = from_json_string( history_attr_str ) - - # Create history. - new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), user=trans.user ) - trans.sa_session.add( new_history ) - - new_history.hid_counter = history_attrs['hid_counter'] - new_history.genome_build = history_attrs['genome_build'] - trans.sa_session.flush() - - # Builds a tag string for a tag, value pair. - def get_tag_str( tag, value ): - if not value: - return tag - else: - return tag + ":" + value - - # Add annotation, tags. - if trans.user: - self.add_item_annotation( trans.sa_session, trans.get_user(), new_history, history_attrs[ 'annotation' ] ) - for tag, value in history_attrs[ 'tags' ].items(): - trans.app.tag_handler.apply_item_tags( trans, trans.user, new_history, get_tag_str( tag, value ) ) - - # - # Create datasets. - # - datasets_attrs_file_name = os.path.join( temp_output_dir, 'datasets_attrs.txt') - if not file_in_dir( datasets_attrs_file_name, temp_output_dir ): - raise Exception( "Invalid location for dataset attributes file: %s" % datasets_attrs_file_name ) - datasets_attr_in = open( datasets_attrs_file_name, 'rb' ) - datasets_attr_str = '' - buffsize = 1048576 - try: - while True: - datasets_attr_str += datasets_attr_in.read( buffsize ) - if not datasets_attr_str or len( datasets_attr_str ) % buffsize != 0: - break - except OverflowError: - pass - datasets_attr_in.close() - datasets_attrs = from_json_string( datasets_attr_str ) - - # Create datasets. - for dataset_attrs in datasets_attrs: - metadata = dataset_attrs['metadata'] - - # Create dataset and HDA. - hda = model.HistoryDatasetAssociation( name = dataset_attrs['name'].encode( 'utf-8' ), - extension = dataset_attrs['extension'], - info = dataset_attrs['info'].encode( 'utf-8' ), - blurb = dataset_attrs['blurb'], - peek = dataset_attrs['peek'], - designation = dataset_attrs['designation'], - visible = dataset_attrs['visible'], - dbkey = metadata['dbkey'], - metadata = metadata, - history = new_history, - create_dataset = True, - sa_session = trans.sa_session ) - hda.state = hda.states.OK - trans.sa_session.add( hda ) - trans.sa_session.flush() - new_history.add_dataset( hda, genome_build = None ) - hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. - permissions = trans.app.security_agent.history_get_default_permissions( new_history ) - trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) - trans.sa_session.flush() - - # Do security check and copy dataset data. - temp_dataset_file_name = os.path.join( temp_output_dir, dataset_attrs['file_name'] ) - if not file_in_dir( temp_dataset_file_name, os.path.join( temp_output_dir, "datasets" ) ): - raise Exception( "Invalid dataset path: %s" % temp_dataset_file_name ) - shutil.move( temp_dataset_file_name, hda.file_name ) - - # Set tags, annotations. - if trans.user: - self.add_item_annotation( trans.sa_session, trans.get_user(), hda, dataset_attrs[ 'annotation' ] ) - for tag, value in dataset_attrs[ 'tags' ].items(): - trans.app.tag_handler.apply_item_tags( trans, trans.user, hda, get_tag_str( tag, value ) ) - trans.sa_session.flush() - - # - # Create jobs. - # - - # Read jobs attributes. - jobs_attr_file_name = os.path.join( temp_output_dir, 'jobs_attrs.txt') - if not file_in_dir( jobs_attr_file_name, temp_output_dir ): - raise Exception( "Invalid location for jobs' attributes file: %s" % jobs_attr_file_name ) - jobs_attr_in = open( jobs_attr_file_name, 'rb' ) - jobs_attr_str = '' - buffsize = 1048576 - try: - while True: - jobs_attr_str += jobs_attr_in.read( buffsize ) - if not jobs_attr_str or len( jobs_attr_str ) % buffsize != 0: - break - except OverflowError: - pass - jobs_attr_in.close() - - # Decode jobs attributes. - def as_hda( obj_dct ): - """ Hook to 'decode' an HDA; method uses history and HID to get the HDA represented by - the encoded object. This only works because HDAs are created above. """ - if obj_dct.get( '__HistoryDatasetAssociation__', False ): - return trans.sa_session.query( model.HistoryDatasetAssociation ) \ - .filter_by( history=new_history, hid=obj_dct['hid'] ).first() - return obj_dct - jobs_attrs = from_json_string( jobs_attr_str, object_hook=as_hda ) - - # Create each job. - for job_attrs in jobs_attrs: - imported_job = model.Job() - imported_job.user = trans.user - imported_job.session = trans.get_galaxy_session().id - imported_job.history = new_history - imported_job.tool_id = job_attrs[ 'tool_id' ] - imported_job.tool_version = job_attrs[ 'tool_version' ] - imported_job.set_state( job_attrs[ 'state' ] ) - imported_job.imported = True - trans.sa_session.add( imported_job ) - trans.sa_session.flush() - - class HistoryDatasetAssociationIDEncoder( simplejson.JSONEncoder ): - """ Custom JSONEncoder for a HistoryDatasetAssociation that encodes an HDA as its ID. """ - def default( self, obj ): - """ Encode an HDA, default encoding for everything else. """ - if isinstance( obj, model.HistoryDatasetAssociation ): - return obj.id - return simplejson.JSONEncoder.default( self, obj ) + # If no source to create archive from, show form to upload archive or specify URL. + if not archive_source: + return trans.show_form( + web.FormBuilder( web.url_for(), "Import a History from an Archive", submit_text="Submit" ) \ + .add_input( "text", "Archived History URL", "archive_url", value="", error=None ) + # TODO: add support for importing via a file. + #.add_input( "file", "Archived History File", "archive_file", value=None, error=None ) + ) - # Set parameters. May be useful to look at metadata.py for creating parameters. - # TODO: there may be a better way to set parameters, e.g.: - # for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): - # job.add_parameter( name, value ) - # to make this work, we'd need to flesh out the HDA objects. The code below is - # relatively similar. - for name, value in job_attrs[ 'params' ].items(): - # Transform parameter values when necessary. - if isinstance( value, model.HistoryDatasetAssociation ): - # HDA input: use hid to find input. - input_hda = trans.sa_session.query( model.HistoryDatasetAssociation ) \ - .filter_by( history=new_history, hid=value.hid ).first() - value = input_hda.id - #print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id ) - imported_job.add_parameter( name, to_json_string( value, cls=HistoryDatasetAssociationIDEncoder ) ) - - # TODO: Connect jobs to input datasets. - - # Connect jobs to output datasets. - for output_hid in job_attrs[ 'output_datasets' ]: - #print "%s job has output dataset %i" % (imported_job.id, output_hid) - output_hda = trans.sa_session.query( model.HistoryDatasetAssociation ) \ - .filter_by( history=new_history, hid=output_hid ).first() - if output_hda: - imported_job.add_output_dataset( output_hda.name, output_hda ) - trans.sa_session.flush() - - # Cleanup. - if os.path.exists( temp_output_dir ): - shutil.rmtree( temp_output_dir ) - - return trans.show_ok_message( message="History '%s' has been imported. " % history_attrs['name'] ) - except Exception, e: - return trans.show_error_message( 'Error importing history archive. ' + str( e ) ) - - return trans.show_form( - web.FormBuilder( web.url_for(), "Import a History from an Archive", submit_text="Submit" ) - .add_input( "file", "Archived History File", "archived_history", value=None, error=None ) - ) - + # Run job to do import. + history_imp_tool = trans.app.toolbox.tools_by_id[ '__IMPORT_HISTORY__' ] + incoming = { '__ARCHIVE_SOURCE__' : archive_source, '__ARCHIVE_TYPE__' : archive_type } + history_imp_tool.execute( trans, incoming=incoming ) + return trans.show_message( "Importing history from '%s'. \ + This history will be visible when the import is complete" % archive_source ) + @web.expose def export_archive( self, trans, id=None, gzip=True, include_hidden=False, include_deleted=False ): """ Export a history to an archive. """ --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -608,6 +608,7 @@ class JobWrapper( object ): if self.app.config.set_metadata_externally: self.external_output_metadata.cleanup_external_metadata( self.sa_session ) galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) + galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) except: log.exception( "Unable to cleanup job %d" % self.job_id ) --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -227,7 +227,13 @@ class JobExportHistoryArchive( object ): self.history_attrs_filename = history_attrs_filename self.datasets_attrs_filename = datasets_attrs_filename self.jobs_attrs_filename = jobs_attrs_filename - + +class JobImportHistoryArchive( object ): + def __init__( self, job=None, history=None, archive_dir=None ): + self.job = job + self.history = history + self.archive_dir=archive_dir + class Group( object ): def __init__( self, name = None ): self.name = name @@ -244,6 +250,7 @@ class History( object, UsesAnnotations ) self.name = name or "Unnamed history" self.deleted = False self.purged = False + self.importing = False self.genome_build = None self.published = False # Relationships --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -2,7 +2,7 @@ import os, shutil, logging, tempfile, si from galaxy import model from galaxy.web.framework.helpers import to_unicode from galaxy.model.item_attrs import UsesAnnotations -from galaxy.util.json import to_json_string +from galaxy.util.json import * from galaxy.web.base.controller import UsesHistory log = logging.getLogger(__name__) @@ -26,21 +26,252 @@ def load_history_imp_exp_tools( toolbox </outputs></tool> """ + + # Load export tool. tmp_name = tempfile.NamedTemporaryFile() tmp_name.write( tool_xml_text ) tmp_name.flush() history_exp_tool = toolbox.load_tool( tmp_name.name ) toolbox.tools_by_id[ history_exp_tool.id ] = history_exp_tool log.debug( "Loaded history export tool: %s", history_exp_tool.id ) + + # Load import tool. + tool_xml = os.path.join( os.getcwd(), "lib/galaxy/tools/imp_exp/imp_history_from_archive.xml" ) + history_imp_tool = toolbox.load_tool( tool_xml ) + toolbox.tools_by_id[ history_imp_tool.id ] = history_imp_tool + log.debug( "Loaded history import tool: %s", history_imp_tool.id ) + +class JobImportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ): + """ + Class provides support for performing jobs that import a history from + an archive. + """ + def __init__( self, job_id ): + self.job_id = job_id + + def cleanup_after_job( self, db_session ): + """ Set history, datasets, and jobs' attributes and clean up archive directory. """ + + # + # Helper methods. + # + + def file_in_dir( file_path, a_dir ): + """ Returns true if file is in directory. """ + abs_file_path = os.path.abspath( file_path ) + return os.path.split( abs_file_path )[0] == a_dir + + def read_file_contents( file_path ): + """ Read contents of a file. """ + fp = open( file_path, 'rb' ) + buffsize = 1048576 + file_contents = '' + try: + while True: + file_contents += fp.read( buffsize ) + if not file_contents or len( file_contents ) % buffsize != 0: + break + except OverflowError: + pass + fp.close() + return file_contents + + def get_tag_str( tag, value ): + """ Builds a tag string for a tag, value pair. """ + if not value: + return tag + else: + return tag + ":" + value + + # + # Import history. + # + + jiha = db_session.query( model.JobImportHistoryArchive ).filter_by( job_id=self.job_id ).first() + if jiha: + try: + archive_dir = jiha.archive_dir + user = jiha.job.user + + # + # Create history. + # + history_attr_file_name = os.path.join( archive_dir, 'history_attrs.txt') + history_attr_str = read_file_contents( history_attr_file_name ) + history_attrs = from_json_string( history_attr_str ) + + # Create history. + new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), \ + user=user ) + new_history.importing = True + new_history.hid_counter = history_attrs['hid_counter'] + new_history.genome_build = history_attrs['genome_build'] + db_session.add( new_history ) + jiha.history = new_history + db_session.flush() + + # Add annotation, tags. + if user: + self.add_item_annotation( db_session, user, new_history, history_attrs[ 'annotation' ] ) + """ + TODO: figure out to how add tags to item. + for tag, value in history_attrs[ 'tags' ].items(): + trans.app.tag_handler.apply_item_tags( trans, trans.user, new_history, get_tag_str( tag, value ) ) + """ + + # + # Create datasets. + # + datasets_attrs_file_name = os.path.join( archive_dir, 'datasets_attrs.txt') + datasets_attr_str = read_file_contents( datasets_attrs_file_name ) + datasets_attrs = from_json_string( datasets_attr_str ) + + # Get counts of how often each dataset file is used; a file can + # be linked to multiple dataset objects (HDAs). + datasets_usage_counts = {} + for dataset_attrs in datasets_attrs: + temp_dataset_file_name = \ + os.path.abspath( os.path.join( archive_dir, dataset_attrs['file_name'] ) ) + if ( temp_dataset_file_name not in datasets_usage_counts ): + datasets_usage_counts[ temp_dataset_file_name ] = 0 + datasets_usage_counts[ temp_dataset_file_name ] += 1 + + # Create datasets. + for dataset_attrs in datasets_attrs: + metadata = dataset_attrs['metadata'] + + # Create dataset and HDA. + hda = model.HistoryDatasetAssociation( name = dataset_attrs['name'].encode( 'utf-8' ), + extension = dataset_attrs['extension'], + info = dataset_attrs['info'].encode( 'utf-8' ), + blurb = dataset_attrs['blurb'], + peek = dataset_attrs['peek'], + designation = dataset_attrs['designation'], + visible = dataset_attrs['visible'], + dbkey = metadata['dbkey'], + metadata = metadata, + history = new_history, + create_dataset = True, + sa_session = db_session ) + hda.state = hda.states.OK + db_session.add( hda ) + db_session.flush() + new_history.add_dataset( hda, genome_build = None ) + hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. + # TODO: Is there a way to recover permissions? Is this needed? + #permissions = trans.app.security_agent.history_get_default_permissions( new_history ) + #trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) + db_session.flush() + + # Do security check and move/copy dataset data. + temp_dataset_file_name = \ + os.path.abspath( os.path.join( archive_dir, dataset_attrs['file_name'] ) ) + if not file_in_dir( temp_dataset_file_name, os.path.join( archive_dir, "datasets" ) ): + raise Exception( "Invalid dataset path: %s" % temp_dataset_file_name ) + if datasets_usage_counts[ temp_dataset_file_name ] == 1: + shutil.move( temp_dataset_file_name, hda.file_name ) + else: + datasets_usage_counts[ temp_dataset_file_name ] -= 1 + shutil.copyfile( temp_dataset_file_name, hda.file_name ) + + # Set tags, annotations. + if user: + self.add_item_annotation( db_session, user, hda, dataset_attrs[ 'annotation' ] ) + # TODO: Set tags. + """ + for tag, value in dataset_attrs[ 'tags' ].items(): + trans.app.tag_handler.apply_item_tags( trans, trans.user, hda, get_tag_str( tag, value ) ) + db_session.flush() + """ + + # + # Create jobs. + # + + # Read jobs attributes. + jobs_attr_file_name = os.path.join( archive_dir, 'jobs_attrs.txt') + jobs_attr_str = read_file_contents( jobs_attr_file_name ) + + # Decode jobs attributes. + def as_hda( obj_dct ): + """ Hook to 'decode' an HDA; method uses history and HID to get the HDA represented by + the encoded object. This only works because HDAs are created above. """ + if obj_dct.get( '__HistoryDatasetAssociation__', False ): + return db_session.query( model.HistoryDatasetAssociation ) \ + .filter_by( history=new_history, hid=obj_dct['hid'] ).first() + return obj_dct + jobs_attrs = from_json_string( jobs_attr_str, object_hook=as_hda ) + + # Create each job. + for job_attrs in jobs_attrs: + imported_job = model.Job() + imported_job.user = user + # TODO: set session? + # imported_job.session = trans.get_galaxy_session().id + imported_job.history = new_history + imported_job.tool_id = job_attrs[ 'tool_id' ] + imported_job.tool_version = job_attrs[ 'tool_version' ] + imported_job.set_state( job_attrs[ 'state' ] ) + imported_job.imported = True + db_session.add( imported_job ) + db_session.flush() + + class HistoryDatasetAssociationIDEncoder( simplejson.JSONEncoder ): + """ Custom JSONEncoder for a HistoryDatasetAssociation that encodes an HDA as its ID. """ + def default( self, obj ): + """ Encode an HDA, default encoding for everything else. """ + if isinstance( obj, model.HistoryDatasetAssociation ): + return obj.id + return simplejson.JSONEncoder.default( self, obj ) + + # Set parameters. May be useful to look at metadata.py for creating parameters. + # TODO: there may be a better way to set parameters, e.g.: + # for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): + # job.add_parameter( name, value ) + # to make this work, we'd need to flesh out the HDA objects. The code below is + # relatively similar. + for name, value in job_attrs[ 'params' ].items(): + # Transform parameter values when necessary. + if isinstance( value, model.HistoryDatasetAssociation ): + # HDA input: use hid to find input. + input_hda = db_session.query( model.HistoryDatasetAssociation ) \ + .filter_by( history=new_history, hid=value.hid ).first() + value = input_hda.id + #print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id ) + imported_job.add_parameter( name, to_json_string( value, cls=HistoryDatasetAssociationIDEncoder ) ) + + # TODO: Connect jobs to input datasets. + + # Connect jobs to output datasets. + for output_hid in job_attrs[ 'output_datasets' ]: + #print "%s job has output dataset %i" % (imported_job.id, output_hid) + output_hda = db_session.query( model.HistoryDatasetAssociation ) \ + .filter_by( history=new_history, hid=output_hid ).first() + if output_hda: + imported_job.add_output_dataset( output_hda.name, output_hda ) + + # Done importing. + new_history.importing = False + + db_session.flush() + + # Cleanup. + if os.path.exists( archive_dir ): + shutil.rmtree( archive_dir ) + except Exception, e: + jiha.job.stderr += "Error cleaning up history import job: %s" % e + db_session.flush() class JobExportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ): - """ Class provides support for performing jobs that export a history to an archive. """ + """ + Class provides support for performing jobs that export a history to an + archive. + """ def __init__( self, job_id ): self.job_id = job_id # TODO: should use db_session rather than trans in this method. def setup_job( self, trans, jeha, include_hidden=False, include_deleted=False ): - # jeha = job_export_history_archive for the job. """ Perform setup for job to export a history into an archive. Method generates attribute files for export, sets the corresponding attributes in the jeha object, and returns a command line for running the job. The command line --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1904,6 +1904,9 @@ class SetMetadataTool( Tool ): class ExportHistoryTool( Tool ): tool_type = 'export_history' + +class ImportHistoryTool( Tool ): + tool_type = 'import_history' # Populate tool_type to ToolClass mappings tool_types = {} --- a/lib/galaxy/tools/actions/history_imp_exp.py +++ b/lib/galaxy/tools/actions/history_imp_exp.py @@ -1,10 +1,56 @@ +import tempfile from __init__ import ToolAction from galaxy.util.odict import odict -from galaxy.tools.imp_exp import JobExportHistoryArchiveWrapper +from galaxy.tools.imp_exp import * import logging log = logging.getLogger( __name__ ) +class ImportHistoryToolAction( ToolAction ): + """Tool action used for importing a history to an archive. """ + + def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True ): + # + # Create job. + # + job = trans.app.model.Job() + job.session_id = trans.get_galaxy_session().id + job.history_id = trans.history.id + job.tool_id = tool.id + job.user_id = trans.user.id + start_job_state = job.state #should be job.states.NEW + job.state = job.states.WAITING #we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters + trans.sa_session.add( job ) + trans.sa_session.flush() #ensure job.id are available + + # + # Setup job and job wrapper. + # + + # Add association for keeping track of job, history relationship. + archive_dir = tempfile.mkdtemp() + jiha = trans.app.model.JobImportHistoryArchive( job=job, archive_dir=archive_dir ) + trans.sa_session.add( jiha ) + job_wrapper = JobImportHistoryArchiveWrapper( job ) + + # + # Add parameters to job_parameter table. + # + + # Set additional parameters. + incoming[ '__DEST_DIR__' ] = jiha.archive_dir + for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): + job.add_parameter( name, value ) + + job.state = start_job_state #job inputs have been configured, restore initial job state + trans.sa_session.flush() + + # Queue the job for execution + trans.app.job_queue.put( job.id, tool ) + trans.log_event( "Added import history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) + + return job, odict() + class ExportHistoryToolAction( ToolAction ): """Tool action used for exporting a history to an archive. """ @@ -30,6 +76,7 @@ class ExportHistoryToolAction( ToolActio job.session_id = trans.get_galaxy_session().id job.history_id = trans.history.id job.tool_id = tool.id + job.user_id = trans.user.id start_job_state = job.state #should be job.states.NEW job.state = job.states.WAITING #we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters trans.sa_session.add( job ) --- /dev/null +++ b/lib/galaxy/tools/imp_exp/imp_history_from_archive.xml @@ -0,0 +1,10 @@ +<tool id="__IMPORT_HISTORY__" name="Import History" version="0.1" tool_type="import_history"> + <type class="ImportHistoryTool" module="galaxy.tools"/> + <action module="galaxy.tools.actions.history_imp_exp" class="ImportHistoryToolAction"/> + <command interpreter="python">unpack_tar_gz_archive.py $__ARCHIVE_SOURCE__ $__DEST_DIR__ --$__ARCHIVE_TYPE__</command> + <inputs> + <param name="__ARCHIVE_SOURCE__" type="text"/> + <param name="__ARCHIVE_TYPE__" type="text"/> + <param name="__DEST_DIR__" type="text"/> + </inputs> +</tool> --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -53,10 +53,10 @@ galaxy_main.location = "${h.url_for( controller='history', action='delete_current' )}"; } }, - ##"Other Actions": null, - ##"Import from File": function() { - ## galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}"; - ##} + "Other Actions": null, + "Import from File": function() { + galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}"; + } }); // Init tool options. --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -77,6 +77,7 @@ History.table = Table( "history", metada Column( "hid_counter", Integer, default=1 ), Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ), + Column( "importing", Boolean, index=True, default=False ), Column( "genome_build", TrimmedString( 40 ) ), Column( "importable", Boolean, default=False ), Column( "slug", TEXT, index=True ), @@ -384,6 +385,13 @@ JobExportHistoryArchive.table = Table( " Column( "jobs_attrs_filename", TEXT ) ) +JobImportHistoryArchive.table = Table( "job_import_history_archive", metadata, + Column( "id", Integer, primary_key=True ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), + Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), + Column( "archive_dir", TEXT ) + ) + PostJobAction.table = Table("post_job_action", metadata, Column("id", Integer, primary_key=True), Column("workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False), @@ -1220,6 +1228,9 @@ assign_mapper( context, JobExportHistory properties=dict( job = relation( Job ), history = relation( History ), dataset = relation( Dataset ) ) ) + +assign_mapper( context, JobImportHistoryArchive, JobImportHistoryArchive.table, + properties=dict( job = relation( Job ), history = relation( History ) ) ) assign_mapper( context, PostJobAction, PostJobAction.table, properties=dict(workflow_step = relation( WorkflowStep, backref='post_job_actions', primaryjoin=(WorkflowStep.table.c.id == PostJobAction.table.c.workflow_step_id)))) --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0060_history_archive_import.py @@ -0,0 +1,72 @@ +""" +Migration script to create column and table for importing histories from +file archives. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +# Columns to add. + +importing_col = Column( "importing", Boolean, index=True, default=False ) +ldda_parent_col = Column( "ldda_parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ) + +# Table to add. + +JobImportHistoryArchive_table = Table( "job_import_history_archive", metadata, + Column( "id", Integer, primary_key=True ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), + Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), + Column( "archive_dir", TEXT ) + ) + +def upgrade(): + print __doc__ + metadata.reflect() + + # Add column to history table and initialize. + try: + History_table = Table( "history", metadata, autoload=True ) + importing_col.create( History_table ) + assert importing_col is History_table.c.importing + + # Initialize column to false. + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + default_false = "0" + elif migrate_engine.name == 'postgres': + default_false = "false" + db_session.execute( "UPDATE history SET importing=%s" % default_false ) + except Exception, e: + print str(e) + log.debug( "Adding column 'importing' to history table failed: %s" % str( e ) ) + + # Create job_import_history_archive table. + try: + JobImportHistoryArchive_table.create() + except Exception, e: + log.debug( "Creating job_import_history_archive table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + + # Drop 'importing' column from history table. + try: + History_table = Table( "history", metadata, autoload=True ) + importing_col = History_table.c.importing + importing_col.drop() + except Exception, e: + log.debug( "Dropping column 'importing' from history table failed: %s" % ( str( e ) ) ) + + # Drop job_import_history_archive table. + try: + JobImportHistoryArchive_table.drop() + except Exception, e: + log.debug( "Dropping job_import_history_archive table failed: %s" % str( e ) ) --- /dev/null +++ b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py @@ -0,0 +1,66 @@ +#!/usr/bin/env python +""" +Unpack a tar or tar.gz archive into a directory. + +usage: %prog archive_source dest_dir + --[url|file] source type, either a URL or a file. +""" + +import sys, optparse, tarfile, tempfile, urllib2, math + +# Set max size of archive/file that will be handled to be 100 GB. This is +# arbitrary and should be adjusted as needed. +MAX_SIZE = 100 * math.pow( 2, 30 ) + +def url_to_file( url, dest_file ): + """ + Transfer a file from a remote URL to a temporary file. + """ + try: + url_reader = urllib2.urlopen( url ) + CHUNK = 10 * 1024 # 10k + total = 0 + fp = open( dest_file, 'wb') + while True: + chunk = url_reader.read( CHUNK ) + if not chunk: + break + fp.write( chunk ) + total += CHUNK + if total > MAX_SIZE: + break + fp.close() + return dest_file + except Exception, e: + print "Exception getting file from URL: %s" % e, sys.stderr + return None + +def unpack_archive( archive_file, dest_dir ): + """ + Unpack a tar and/or gzipped archive into a destination directory. + """ + archive_fp = tarfile.open( archive_file, mode='r:gz' ) + archive_fp.extractall( path=dest_dir ) + archive_fp.close() + +if __name__ == "__main__": + # Parse command line. + parser = optparse.OptionParser() + parser.add_option( '-U', '--url', dest='is_url', action="store_true", help='Source is a URL.' ) + parser.add_option( '-F', '--file', dest='is_file', action="store_true", help='Source is a URL.' ) + (options, args) = parser.parse_args() + is_url = bool( options.is_url ) + is_file = bool( options.is_file ) + archive_source, dest_dir = args + + try: + # Get archive from URL. + if is_url: + archive_file = url_to_file( archive_source, tempfile.NamedTemporaryFile( dir=dest_dir ).name ) + elif is_file: + archive_file = archive_source + + # Unpack archive. + unpack_archive( archive_file, dest_dir ) + except Exception, e: + print "Error unpacking tar/gz archive: %s" % e, sys.stderr

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galaxy-dist commit bdcbd7ab6e7f: Fix solid_qual_stats tool when value is 0 or not a valid int. Fixes #405
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 1288115163 14400 # Node ID bdcbd7ab6e7fe0a6ed869d8a682660c0cebb7658 # Parent 87a6d4a29eeea038c669f086d254aaa4140a15bb Fix solid_qual_stats tool when value is 0 or not a valid int. Fixes #405 --- a/tools/solid_tools/solid_qual_stats.py +++ b/tools/solid_tools/solid_qual_stats.py @@ -31,6 +31,7 @@ def __main__(): infile_name = infile_score_name readlen = None + invalid_lines = 0 j = 0 for line in file( infile_name ): line = line.strip() @@ -39,18 +40,17 @@ def __main__(): elems = line.split() try: for item in elems: - assert int(item) - if not(readlen): + int(item) + if not readlen: readlen = len(elems) if len(elems) != readlen: print "Note: Reads in the input dataset are of variable lengths." j += 1 - except: + except ValueError: invalid_lines += 1 if j > 10: break - invalid_lines = 0 position_dict = {} print >>fout, "column\tcount\tmin\tmax\tsum\tmean\tQ1\tmed\tQ3\tIQR\tlW\trW" for k,line in enumerate(file( infile_name )): @@ -132,7 +132,7 @@ def __main__(): if invalid_lines: print "Skipped %d reads as invalid." %invalid_lines if invalid_positions: - print "Skipped stats computation for %d read postions." %invalid_positions + print "Skipped stats computation for %d read positions." %invalid_positions if __name__=="__main__": __main__()

1 0

galaxy-dist commit 262c91e3a2ea: Fix 'Select All' button in tool form due to a typo. Values next to checkboxes can now be clicked to check the corresponding box.
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 1288117861 14400 # Node ID 262c91e3a2ea7d11d65875ec2af42526c92b7123 # Parent bdcbd7ab6e7fe0a6ed869d8a682660c0cebb7658 Fix 'Select All' button in tool form due to a typo. Values next to checkboxes can now be clicked to check the corresponding box. --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -41,6 +41,7 @@ div.form-row-error{background:#FFCCCC;} div.form-row label{font-weight:bold;display:block;margin-bottom:.2em;} div.form-row-input{float:left;width:300px;} div.form-row-input > input{max-width:300px;} +div.form-row-input label{font-weight:normal;display:inline;} div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0 0 1em;} select,input,textarea{font:inherit;font-size:115%;} select,textarea,input[type="text"],input[type="file"],input[type="password"]{-webkit-box-sizing:border-box;max-width:300px;} --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -24,7 +24,7 @@ from galaxy.util.expressions import Expr file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); // create a new hidden field which stores the filename and has the original name of the file input var new_file_input = $(document.createElement('input')); - new_file_input.attr( { "type", "hidden", "value": file_value, "name": file_name } ); + new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } ); file.after(new_file_input); } }); @@ -36,14 +36,10 @@ from galaxy.util.expressions import Expr location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); } %endif -function checkUncheckAll( name, check ) -{ - if ( check == 0 ) - { +function checkUncheckAll( name, check ) { + if (!check) { $("input[name=" + name + "][type='checkbox']").attr('checked', false); - } - else - { + } else { $("input[name=" + name + "][type='checkbox']").attr('checked', true ); } } @@ -260,7 +256,7 @@ function checkUncheckAll( name, check ) ##inserts the Select All / Unselect All buttons for checkboxes $( function() { $("div.checkUncheckAllPlaceholder").each( function( i ) { - $( this )[0].innerHTML = '<a class="action-button" onclick="checkUncheckAll( \'' + this.attributes.getNamedItem( 'checkbox_name' ).value + '\', 1 );"><span>Select All</span></a><a class="action-button" onclick="checkUncheckAll( \'' + this.attributes.getNamedItem( 'checkbox_name' ).value + '\', 0 );"><span>Unselect All</span></a>'; + $( this )[0].innerHTML = '<a class="action-button" onclick="checkUncheckAll( \'' + this.attributes.getNamedItem( 'checkbox_name' ).value + '\', true );"><span>Select All</span></a><a class="action-button" onclick="checkUncheckAll( \'' + this.attributes.getNamedItem( 'checkbox_name' ).value + '\', false );"><span>Unselect All</span></a>'; }); }); --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -231,14 +231,14 @@ class SelectField(BaseField): rval.append ( '<div class="checkUncheckAllPlaceholder" checkbox_name="%s%s"></div>' % ( prefix, self.name ) ) #placeholder for the insertion of the Select All/Unselect All buttons for text, value, selected in self.options: style = "" + escaped_value = escape( str( value ), quote=True ) if len(self.options) > 2 and ctr % 2 == 1: style = " class=\"odd_row\"" + selected_text = "" if selected: - rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" checked%s>%s</div>' % \ - ( style, prefix, self.name, escape( str( value ), quote=True ), self.get_disabled_str( disabled ), text ) ) - else: - rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s"%s>%s</div>' % \ - ( style, prefix, self.name, escape( str( value ), quote=True ), self.get_disabled_str( disabled ), text ) ) + selected_text = "checked='checked'" + rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" id="%s" %s%s><label for="%s">%s</label></div>' % \ + ( style, prefix, self.name, escaped_value, escaped_value, selected_text, self.get_disabled_str( disabled ), escaped_value, text ) ) ctr += 1 return "\n".join( rval ) def get_html_radio( self, prefix="", disabled=False ): --- a/static/june_2007_style/base.css.tmpl +++ b/static/june_2007_style/base.css.tmpl @@ -219,6 +219,11 @@ div.form-row-input > input { max-width: 300px; } +div.form-row-input label { + font-weight: normal; + display: inline; +} + div.form-row-error-message { width: 300px; float: left;

1 0

galaxy-dist commit d73fa5f14b01: fixed select all checkbox in grid. the footer now updates when all items are selected
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 rc # Date 1288121253 14400 # Node ID d73fa5f14b013333b2e49bfbf775db8dd0197e2b # Parent 314f8a5d38237c3f1fafccb522ee45aebfa8464f fixed select all checkbox in grid. the footer now updates when all items are selected --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -611,34 +611,27 @@ }); } - function check_all_items() - { + function check_all_items() { var chk_all = document.getElementById('check_all'); var checks = document.getElementsByTagName('input'); //var boxLength = checks.length; var total = 0; - if ( chk_all.checked == true ) - { - for ( i=0; i < checks.length; i++ ) - { - if ( checks[i].name.indexOf( 'id' ) != -1) - { + if ( chk_all.checked == true ) { + for ( i=0; i < checks.length; i++ ) { + if ( checks[i].name.indexOf( 'id' ) != -1) { checks[i].checked = true; total++; } } } - else - { - for ( i=0; i < checks.length; i++ ) - { - if ( checks[i].name.indexOf( 'id' ) != -1) - { + else { + for ( i=0; i < checks.length; i++ ) { + if ( checks[i].name.indexOf( 'id' ) != -1) { checks[i].checked = false } } } - + init_grid_elements(); } </script></%def>

1 0

galaxy-dist commit 314f8a5d3823: Complete functional test for cuffcompare.
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 1288119881 14400 # Node ID 314f8a5d38237c3f1fafccb522ee45aebfa8464f # Parent 379d0701f198964fb964c3834cce7414cbc8f888 Complete functional test for cuffcompare. --- /dev/null +++ b/test-data/cuffcompare_out1.tmap @@ -0,0 +1,51 @@ +ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id +- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 +- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 +- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 +- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 +- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 +- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 +Xkr4 Xkr4 c CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 +Xkr4 Xkr4 i CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 +Xkr4 Xkr4 i CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 +Xkr4 Xkr4 i CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 +Xkr4 Xkr4 i CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 +Xkr4 Xkr4 i CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 +Xkr4 Xkr4 i CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 +Xkr4 Xkr4 i CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 +- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 +- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 +- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 +- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 +- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 +- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 +- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 +- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 +- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 +- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 +- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 +- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 +- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 +- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 +- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 +- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 +Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 +Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 +Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 +Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 +Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 +Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 +Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 +Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 +Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 +Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 +Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 +Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 +Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 +Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 +Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 +Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 +Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 +Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 +Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 +Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 --- /dev/null +++ b/test-data/cuffcompare_out2.refmap @@ -0,0 +1,2 @@ +ref_gene_id ref_id class_code cuff_id_list +Xkr4 Xkr4 c CUFF.13|CUFF.13.1 --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -81,16 +81,15 @@ <param name="use_ref_annotation" value="Yes"/><param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/><param name="ignore_nonoverlapping_reference" value="Yes"/> - ## HACK: need to specify output name and it needs to work (right now it uses the final output file) - <output name="XXXX" file="cuffcompare_out6.tracking"/> -  + <output name="transcripts_accuracy" file="cuffcompare_out7.txt" lines_diff="6"/><output name="input1_tmap" file="cuffcompare_out1.tmap"/><output name="input1_refmap" file="cuffcompare_out2.refmap"/><output name="input2_tmap" file="cuffcompare_out3.tmap"/><output name="input2_refmap" file="cuffcompare_out4.refmap"/> - <output name="transcripts_accuracy" file="cuffcompare_out7.txt"/> - --> + <output name="transcripts_combined" file="cuffcompare_out5.gtf"/> + <output name="transcripts_tracking" file="cuffcompare_out6.tracking"/></test></tests> --- /dev/null +++ b/test-data/cuffcompare_out4.refmap @@ -0,0 +1,1 @@ +ref_gene_id ref_id class_code cuff_id_list --- /dev/null +++ b/test-data/cuffcompare_out3.tmap @@ -0,0 +1,51 @@ +ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id +- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 +- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 +- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 +- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 +- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 +- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 +- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 +- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 +- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 +- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 +- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 +- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 +- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 +- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 +- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 +- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 +Xkr4 Xkr4 i CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 +Xkr4 Xkr4 i CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 +Xkr4 Xkr4 i CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 +Xkr4 Xkr4 i CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 +Xkr4 Xkr4 i CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 +Xkr4 Xkr4 i CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 +Xkr4 Xkr4 i CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 +Xkr4 Xkr4 i CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 +Xkr4 Xkr4 i CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 +Xkr4 Xkr4 i CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 +Xkr4 Xkr4 i CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 +Xkr4 Xkr4 i CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 +Xkr4 Xkr4 i CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 +Xkr4 Xkr4 i CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 +Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 +Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 +Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 +Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 +Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 +Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 +Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 +Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 +Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 +Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 +Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 +Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 +Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 +Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 +Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 +Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 +Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 +Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 +Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 +Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 --- /dev/null +++ b/test-data/cuffcompare_out7.txt @@ -0,0 +1,50 @@ +# Cuffcompare v0.9.1 | Command line was: +#cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf +# +#> Genomic sequence: chr1 +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 1 in 1 loci (1 multi-exon) +# Corresponding super-loci: 1 +#--------------------| Sn | Sp | fSn | fSp + Base level: 2.2 2.3 - - + Exon level: 0.0 0.0 0.0 0.0 + Intron level: 0.0 nan 0.0 100.0 +Intron chain level: 0.0 100.0 0.0 100.0 + Transcript level: 0.0 0.0 0.0 0.0 + Locus level: 0.0 0.0 0.0 0.0 + Missed exons: 2/3 ( 66.7%) + Wrong exons: 49/50 ( 98.0%) + Missed introns: 2/2 (100.0%) + Missed loci: 0/1 ( 0.0%) + Wrong loci: 49/50 ( 98.0%) + +#= Summary for dataset: cuffcompare_in1.gtf : +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 1 in 1 loci (1 multi-exon) +# Corresponding super-loci: 1 +#--------------------| Sn | Sp | fSn | fSp + Base level: 2.2 2.3 - - + Exon level: 0.0 0.0 0.0 0.0 + Intron level: 0.0 nan 0.0 100.0 +Intron chain level: 0.0 100.0 0.0 100.0 + Transcript level: 0.0 0.0 0.0 0.0 + Locus level: 0.0 0.0 0.0 0.0 + Missed exons: 2/3 ( 66.7%) + Wrong exons: 49/50 ( 98.0%) + Missed introns: 2/2 (100.0%) + Missed loci: 0/1 ( 0.0%) + Wrong loci: 49/50 ( 98.0%) +#> Genomic sequence: chr1 +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 0 in 0 loci (0 multi-exon) + +#= Summary for dataset: cuffcompare_in2.gtf : +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 0 in 0 loci (0 multi-exon) + + Total union super-loci across all input datasets: 87 + (0 multi-transcript, ~1.1 transcripts per locus)

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galaxy-dist commit 7114d0f8d487: Fix for a bug I introduced in NoseHTML changes.
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 1287858470 14400 # Node ID 7114d0f8d487536853cf25cf30bb86636bf0b24c # Parent bb93b5da724b8f0420ed5cb2371075b08947d0db Fix for a bug I introduced in NoseHTML changes. --- a/eggs.ini +++ b/eggs.ini @@ -38,7 +38,7 @@ GeneTrack = 2.0.0_beta_1 lrucache = 0.2 Mako = 0.2.5 nose = 0.11.1 -NoseHTML = 0.4 +NoseHTML = 0.4.1 NoseTestDiff = 0.1 Paste = 1.6 PasteDeploy = 1.3.3

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