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galaxy-dist commit c22562b86d0f: Make the production buildbot use Main's tool conf
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 1288123416 14400 # Node ID c22562b86d0f62d361fd2531d22d42cfd6bf07c1 # Parent 49c7938d582799125a89f0d6ba38be0ddc6f4b4f Make the production buildbot use Main's tool conf --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -54,6 +54,7 @@ def main(): galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ tool_path = os.environ.get( 'GALAXY_TEST_TOOL_PATH', 'tools' ) + tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml.sample' ) if start_server: psu_production = False galaxy_test_proxy_port = None @@ -75,6 +76,7 @@ def main(): nginx_upload_store = os.environ.get( 'GALAXY_TEST_NGINX_UPLOAD_STORE', None ) if not nginx_upload_store: raise Exception( 'Please set GALAXY_TEST_NGINX_UPLOAD_STORE to the path where the nginx upload module places uploaded files' ) + tool_config_file = 'tool_conf.xml.main' default_cluster_job_runner = os.environ.get( 'GALAXY_TEST_DEFAULT_CLUSTER_JOB_RUNNER', 'pbs:///' ) file_path = tempfile.mkdtemp( dir=base_file_path ) new_file_path = tempfile.mkdtemp( dir=base_new_file_path ) @@ -142,7 +144,7 @@ def main(): file_path = file_path, new_file_path = new_file_path, tool_path = tool_path, - tool_config_file = "tool_conf.xml.sample", + tool_config_file = tool_config_file, datatype_converters_config_file = "datatype_converters_conf.xml.sample", tool_parse_help = False, test_conf = "test.conf",

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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 29157e97e954: Added setup script to configure RabbitMQ
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 1288148662 14400 # Node ID 29157e97e95453c5f9022d9c571527a6de4032e1 # Parent af2d04e3568078d8d7ad94e229a17983f8282e20 Added setup script to configure RabbitMQ --- a/transfer_datasets.ini.sample +++ b/transfer_datasets.ini.sample @@ -3,13 +3,8 @@ [data_transfer_user_login_info] #email = datatx(a)bx.psu.edu #password = datatx - -# The following section contains 4 config variables neede for the data transfer. -# Please copy the exact values for each of these variables from the universe_wsgi.ini -# configuration file for this installation +#api_key = Generate it from the User menu in Galaxy [universe_wsgi_config] -#host = 127.0.0.1 -#port = -#database_connection = -#library_import_dir = +# The http server section name in the Galaxy config file (universe_wsgi.ini) +#http_server_section = server:main --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -420,4 +420,4 @@ upload1 = local:/// #queue = galaxy_queue #exchange = galaxy_exchange #routing_key = bar_code_scanner - +#rabbitmqctl_path = /path/to/rabbitmqctl --- /dev/null +++ b/scripts/galaxy_messaging/server/setup_rabbitmq.py @@ -0,0 +1,34 @@ +# +# Configuration script for RabbitMQ in Galaxy +# +# Requirements: +# - set the rabbitmqctl_path variable in the 'galaxy_amqp' section in Galaxy config file +# +# Usage: +# $ python setup_rabbitmq.py <Galaxy config file> +# + +import os, sys, csv, ConfigParser + +def main( config_file ): + config = ConfigParser.ConfigParser() + config.read( config_file ) + rabbitmqctl_path = config.get( 'galaxy_amqp', 'rabbitmqctl_path' ) + username = config.get( 'galaxy_amqp', 'userid' ) + password = config.get( 'galaxy_amqp', 'password' ) + virtual_host = config.get( 'galaxy_amqp', 'virtual_host' ) + + cmd_list = [ + 'add_user %s %s' % ( username, password ), + 'add_vhost %s' % config.get( 'galaxy_amqp', 'virtual_host' ), + 'set_permissions -p %s %s "%s.*" ".*" ".*"' % ( virtual_host, username, username ) + ] + + for cmd in cmd_list: + retval = os.system( rabbitmqctl_path + ' ' + cmd ) + if retval: + print "Failed command: %s" % cmd + sys.exit(1) + +if __name__ == '__main__': + main( sys.argv[1] )

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galaxy-dist commit 49c7938d5827: sample tracking web api cleaned up
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 1288122647 14400 # Node ID 49c7938d582799125a89f0d6ba38be0ddc6f4b4f # Parent d73fa5f14b013333b2e49bfbf775db8dd0197e2b sample tracking web api cleaned up - added a samples controller --- /dev/null +++ b/lib/galaxy/web/api/samples.py @@ -0,0 +1,44 @@ +""" +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 SamplesController( BaseController ): + + @web.expose_api + def index( self, trans, **kwd ): + """ + GET /api/requests/{encoded_request_id}/samples + Displays a collection (list) of sample of a sequencing request. + """ + try: + request_id = trans.security.decode_id( kwd[ 'request_id' ] ) + except TypeError: + trans.response.status = 400 + return "Malformed request id ( %s ) specified, unable to decode." % str( encoded_request_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 ) + rval = [] + for sample in request.samples: + item = sample.get_api_value() + item['url'] = url_for( 'samples', + request_id=trans.security.encode_id( request_id ), + id=trans.security.encode_id( sample.id ) ) + item['id'] = trans.security.encode_id( item['id'] ) + rval.append( item ) + return rval + + --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1767,6 +1767,7 @@ class RequestTypePermissions( object ): class Sample( object ): bulk_operations = Bunch( CHANGE_STATE = 'Change state', SELECT_LIBRARY = 'Select data library and folder' ) + api_collection_visible_keys = ( 'id', 'name' ) 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 @@ -1818,6 +1819,18 @@ class Sample( object ): pexpect.TIMEOUT:print_ticks}, timeout=10) return output.replace(filepath, '').strip() + 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 SampleState( object ): def __init__(self, name=None, desc=None, request_type=None): --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -104,8 +104,15 @@ def app_factory( global_conf, **kwargs ) # If enabled, add the web API if asbool( kwargs.get( 'enable_api', False ) ): 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( '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( 'sample', + 'samples', + path_prefix='/api/requests/:request_id', + parent_resources=dict( member_name='request', collection_name='requests' ) ) webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) webapp.finalize_config() # Wrap the webapp in some useful middleware --- a/lib/galaxy/web/api/requests.py +++ b/lib/galaxy/web/api/requests.py @@ -22,23 +22,57 @@ class RequestsController( BaseController 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() + # if admin user then return all requests + if trans.user_is_admin(): + query = trans.sa_session.query( trans.app.model.Request )\ + .filter( trans.app.model.Request.table.c.deleted == False )\ + .all() + else: + 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'] ) + if trans.user_is_admin(): + item['user'] = request.user.email rval.append( item ) return rval - + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + GET /api/requests/{encoded_request_id} + Displays details of a sequencing request. + """ + 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 ) + 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'] ) + item['user'] = request.user.email + item['num_of_samples'] = len(request.samples) + return item + @web.expose_api def update( self, trans, id, key, payload, **kwd ): """ PUT /api/requests/{encoded_request_id} - Displays information about a sequencing request. + Updates a request state, sample state or sample dataset transfer status + depending on the update_type """ params = util.Params( kwd ) update_type = None @@ -124,7 +158,3 @@ class RequestsController( BaseController new_status=new_status, error_msg=error_msg ) return status, output - - - -

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galaxy-dist commit e5f90080a2db: Merge with 29157e97e95453c5f9022d9c571527a6de4032e1
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 1288149696 14400 # Node ID e5f90080a2db9c16bad2300c5ef0b5c49a558638 # Parent 61c786bd2efb6f9cc4d5fa4d43dfb056ed99b909 # Parent 29157e97e95453c5f9022d9c571527a6de4032e1 Merge with 29157e97e95453c5f9022d9c571527a6de4032e1

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 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 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 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:

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 )

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