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commit/galaxy-central: dannon: Merged in jgoecks/galaxy-central-gcc-2014-fixes/stable (pull request #425)
by commits-noreply＠bitbucket.org 26 Jun '14

26 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8a863a311a6c/ Changeset: 8a863a311a6c Branch: stable User: dannon Date: 2014-06-26 15:02:02 Summary: Merged in jgoecks/galaxy-central-gcc-2014-fixes/stable (pull request #425) Trackster fixes Affected #: 2 files diff -r 8bf883f2638e1bae7a1761a0fab98a981d6fa315 -r 8a863a311a6c9f14b302799bffcf94df9186fef7 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").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();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").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_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").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();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){if(this.view.reference_track.tiles_div.is(":visible")){this.view.resize_viewport()}var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 8bf883f2638e1bae7a1761a0fab98a981d6fa315 -r 8a863a311a6c9f14b302799bffcf94df9186fef7 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1070,11 +1070,10 @@ var delta_chrom = Math.round(delta / view.viewport_container.width() * (view.high - view.low)); view.move_delta(delta_chrom); // Also capture mouse wheel for left/right scrolling - }).bind( 'mousewheel', function( e, d, dx, dy ) { - // Only act on x axis scrolling if we see if, y will be i - // handled by the browser when the event bubbles up - if ( dx ) { - dx *= 50; + }).bind( 'mousewheel', function( e, d, dx, dy ) { + // Only handle x axis scrolling; y axis scrolling is + // handled by the browser when the event bubbles up. + if (dx) { var delta_chrom = Math.round( - dx / view.viewport_container.width() * (view.high - view.low) ); view.move_delta( delta_chrom ); } @@ -1579,8 +1578,14 @@ this.request_redraw(); }, + /** Resize viewport. Use this method if header/footer content has changed in size. */ + resize_viewport: function() { + this.viewport_container.height( this.container.height() - this.top_container.height() - this.bottom_container.height() ); + }, + + /** Called when window is resized. */ resize_window: function() { - this.viewport_container.height( this.container.height() - this.top_container.height() - this.bottom_container.height() ); + this.resize_viewport(); this.request_redraw(); }, @@ -2940,6 +2945,12 @@ * drawn/fetched and shown. */ postdraw_actions: function(tiles, width, w_scale, clear_after) { + // If reference track is visible, adjust viewport to be smaller so that bottom content + // is visible. + if (this.view.reference_track.tiles_div.is(':visible')) { + this.view.resize_viewport(); + } + var line_track_tiles = _.filter(tiles, function(tile) { return (tile instanceof LineTrackTile); }); @@ -3618,15 +3629,15 @@ can_draw: Drawable.prototype.can_draw, /** - * Retrieves data and draws tile if reference data can be displayed. + * Draws and shows tile if reference data can be displayed; otherwise track is hidden. */ draw_helper: function(region, w_scale, options) { if (w_scale > this.view.canvas_manager.char_width_px) { - this.tiles_div.show(); + this.tiles_div.show(); return TiledTrack.prototype.draw_helper.call(this, region, w_scale, options); } else { - this.tiles_div.hide(); + this.tiles_div.hide(); return null; } }, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 26 Jun '14

26 Jun '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/093266098c84/ Changeset: 093266098c84 Branch: stable User: jgoecks Date: 2014-06-23 21:46:45 Summary: Trackster: resize viewport when showing reference track to avoid inadvertently hiding scroll bar. Affected #: 1 file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r 093266098c84ae56a0b4814e6c38d29e6727bda6 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1579,8 +1579,14 @@ this.request_redraw(); }, + /** Resize viewport. Use this method if header/footer content has changed in size. */ + resize_viewport: function() { + this.viewport_container.height( this.container.height() - this.top_container.height() - this.bottom_container.height() ); + }, + + /** Called when window is resized. */ resize_window: function() { - this.viewport_container.height( this.container.height() - this.top_container.height() - this.bottom_container.height() ); + this.resize_viewport(); this.request_redraw(); }, @@ -2940,6 +2946,12 @@ * drawn/fetched and shown. */ postdraw_actions: function(tiles, width, w_scale, clear_after) { + // If reference track is visible, adjust viewport to be smaller so that bottom content + // is visible. + if (this.view.reference_track.tiles_div.is(':visible')) { + this.view.resize_viewport(); + } + var line_track_tiles = _.filter(tiles, function(tile) { return (tile instanceof LineTrackTile); }); @@ -3618,15 +3630,15 @@ can_draw: Drawable.prototype.can_draw, /** - * Retrieves data and draws tile if reference data can be displayed. + * Draws and shows tile if reference data can be displayed; otherwise track is hidden. */ draw_helper: function(region, w_scale, options) { if (w_scale > this.view.canvas_manager.char_width_px) { - this.tiles_div.show(); + this.tiles_div.show(); return TiledTrack.prototype.draw_helper.call(this, region, w_scale, options); } else { - this.tiles_div.hide(); + this.tiles_div.hide(); return null; } }, https://bitbucket.org/galaxy/galaxy-central/commits/8d8e05b12abd/ Changeset: 8d8e05b12abd Branch: stable User: jgoecks Date: 2014-06-23 22:11:46 Summary: Trackster: remove mousewheel scrolling amplifier and clarify comment. Affected #: 1 file diff -r 093266098c84ae56a0b4814e6c38d29e6727bda6 -r 8d8e05b12abd0087d0eec517184232557a2e7945 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1070,11 +1070,10 @@ var delta_chrom = Math.round(delta / view.viewport_container.width() * (view.high - view.low)); view.move_delta(delta_chrom); // Also capture mouse wheel for left/right scrolling - }).bind( 'mousewheel', function( e, d, dx, dy ) { - // Only act on x axis scrolling if we see if, y will be i - // handled by the browser when the event bubbles up - if ( dx ) { - dx *= 50; + }).bind( 'mousewheel', function( e, d, dx, dy ) { + // Only handle x axis scrolling; y axis scrolling is + // handled by the browser when the event bubbles up. + if (dx) { var delta_chrom = Math.round( - dx / view.viewport_container.width() * (view.high - view.low) ); view.move_delta( delta_chrom ); } https://bitbucket.org/galaxy/galaxy-central/commits/059baf0a650c/ Changeset: 059baf0a650c Branch: stable User: jgoecks Date: 2014-06-26 14:49:37 Summary: Pack script. Affected #: 1 file diff -r 8d8e05b12abd0087d0eec517184232557a2e7945 -r 059baf0a650c0ea37f6e8c8a4e5613189985bf77 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").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();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").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_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").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();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){if(this.view.reference_track.tiles_div.is(":visible")){this.view.resize_viewport()}var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/8a863a311a6c/ Changeset: 8a863a311a6c Branch: stable User: dannon Date: 2014-06-26 15:02:02 Summary: Merged in jgoecks/galaxy-central-gcc-2014-fixes/stable (pull request #425) Trackster fixes Affected #: 2 files diff -r 8bf883f2638e1bae7a1761a0fab98a981d6fa315 -r 8a863a311a6c9f14b302799bffcf94df9186fef7 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").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_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").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();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").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_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").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();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){if(this.view.reference_track.tiles_div.is(":visible")){this.view.resize_viewport()}var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 8bf883f2638e1bae7a1761a0fab98a981d6fa315 -r 8a863a311a6c9f14b302799bffcf94df9186fef7 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1070,11 +1070,10 @@ var delta_chrom = Math.round(delta / view.viewport_container.width() * (view.high - view.low)); view.move_delta(delta_chrom); // Also capture mouse wheel for left/right scrolling - }).bind( 'mousewheel', function( e, d, dx, dy ) { - // Only act on x axis scrolling if we see if, y will be i - // handled by the browser when the event bubbles up - if ( dx ) { - dx *= 50; + }).bind( 'mousewheel', function( e, d, dx, dy ) { + // Only handle x axis scrolling; y axis scrolling is + // handled by the browser when the event bubbles up. + if (dx) { var delta_chrom = Math.round( - dx / view.viewport_container.width() * (view.high - view.low) ); view.move_delta( delta_chrom ); } @@ -1579,8 +1578,14 @@ this.request_redraw(); }, + /** Resize viewport. Use this method if header/footer content has changed in size. */ + resize_viewport: function() { + this.viewport_container.height( this.container.height() - this.top_container.height() - this.bottom_container.height() ); + }, + + /** Called when window is resized. */ resize_window: function() { - this.viewport_container.height( this.container.height() - this.top_container.height() - this.bottom_container.height() ); + this.resize_viewport(); this.request_redraw(); }, @@ -2940,6 +2945,12 @@ * drawn/fetched and shown. */ postdraw_actions: function(tiles, width, w_scale, clear_after) { + // If reference track is visible, adjust viewport to be smaller so that bottom content + // is visible. + if (this.view.reference_track.tiles_div.is(':visible')) { + this.view.resize_viewport(); + } + var line_track_tiles = _.filter(tiles, function(tile) { return (tile instanceof LineTrackTile); }); @@ -3618,15 +3629,15 @@ can_draw: Drawable.prototype.can_draw, /** - * Retrieves data and draws tile if reference data can be displayed. + * Draws and shows tile if reference data can be displayed; otherwise track is hidden. */ draw_helper: function(region, w_scale, options) { if (w_scale > this.view.canvas_manager.char_width_px) { - this.tiles_div.show(); + this.tiles_div.show(); return TiledTrack.prototype.draw_helper.call(this, region, w_scale, options); } else { - this.tiles_div.hide(); + this.tiles_div.hide(); return null; } }, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Fix Ctrl+C (make the UpdateRepositoryManager's updater thread a daemon).
by commits-noreply＠bitbucket.org 26 Jun '14

26 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1802e93a4f18/ Changeset: 1802e93a4f18 User: natefoo Date: 2014-06-26 02:07:58 Summary: Fix Ctrl+C (make the UpdateRepositoryManager's updater thread a daemon). Affected #: 1 file diff -r 6b672fb120994f308ce7914993418e67770aae14 -r 1802e93a4f1823f307de534d9b6ce73d911f6538 lib/tool_shed/galaxy_install/update_repository_manager.py --- a/lib/tool_shed/galaxy_install/update_repository_manager.py +++ b/lib/tool_shed/galaxy_install/update_repository_manager.py @@ -19,6 +19,7 @@ self.running = True self.sleeper = Sleeper() self.restarter = threading.Thread( target=self.__restarter ) + self.restarter.daemon = True self.restarter.start() self.seconds_to_sleep = int( app.config.hours_between_check * 3600 ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: davebgx: Enhance the tool shed repository API controller to allow filtering by owner's username or repository name.
by commits-noreply＠bitbucket.org 25 Jun '14

25 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6b672fb12099/ Changeset: 6b672fb12099 User: davebgx Date: 2014-06-25 21:07:43 Summary: Enhance the tool shed repository API controller to allow filtering by owner's username or repository name. Affected #: 1 file diff -r 8a161a3990b5e19dd2b324323ba934f8a5f37c8b -r 6b672fb120994f308ce7914993418e67770aae14 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -7,6 +7,7 @@ from galaxy import eggs from galaxy import util from galaxy import web +from galaxy.model.orm import and_ from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import HTTPBadRequest from galaxy.web.framework.helpers import time_ago @@ -297,16 +298,28 @@ return return_dict @web.expose_api_anonymous - def index( self, trans, deleted=False, **kwd ): + def index( self, trans, deleted=False, owner=None, name=None, **kwd ): """ GET /api/repositories + + :param deleted: True/False, displays repositories that are or are not set to deleted. + :param owner: the owner's public username. + :param name: the repository name. + Displays a collection (list) of repositories. """ # Example URL: http://localhost:9009/api/repositories repository_dicts = [] deleted = util.asbool( deleted ) + clause_list = [ and_( trans.app.model.Repository.table.c.deprecated == False, + trans.app.model.Repository.table.c.deleted == deleted ) ] + if owner is not None: + clause_list.append( and_( trans.app.model.User.table.c.username == owner, + trans.app.model.Repository.table.c.user_id == trans.app.model.User.table.c.id ) ) + if name is not None: + clause_list.append( trans.app.model.Repository.table.c.name == name ) for repository in trans.sa_session.query( trans.app.model.Repository ) \ - .filter( trans.app.model.Repository.table.c.deleted == deleted ) \ + .filter( *clause_list ) \ .order_by( trans.app.model.Repository.table.c.name ): repository_dict = repository.to_dict( view='collection', value_mapper=self.__get_value_mapper( trans ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Another docfix for recent local job runner changes.
by commits-noreply＠bitbucket.org 25 Jun '14

25 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8a161a3990b5/ Changeset: 8a161a3990b5 User: jmchilton Date: 2014-06-25 16:11:26 Summary: Another docfix for recent local job runner changes. Affected #: 1 file diff -r 1c40abf8bc5b7555dd276e540f487f8c288da4b2 -r 8a161a3990b5e19dd2b324323ba934f8a5f37c8b universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -804,7 +804,7 @@ # the cluster that should be sourced by the user to set up the environment # prior to running tools. This can be especially useful for running jobs as # the actual user, to remove the need to configure each user's environment -# individually. This only affects cluster jobs, not local jobs. +# individually. #environment_setup_file = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 25 Jun '14

25 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/75c63b579ccd/ Changeset: 75c63b579ccd User: jmchilton Date: 2014-06-25 15:01:52 Summary: Add documentation about local runner destination option embed_metadata_in_job. Affected #: 1 file diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r 75c63b579ccdd63e0558dd9aefce7786677dbacd job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -102,6 +102,12 @@  + <param id="embed_metadata_in_job">True</param> + <job_metrics /> + <param id="embed_metadata_in_job">True</param> + <job_metrics /><!-- Above element demonstrates embedded job metrics definition - see job_metrics_conf.xml.sample for full documentation on possible nested Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Fix: phantomjs apparently lacks the bind fn on the Function prototype - correct failures in history-panel (line 252) by using underscore bind instead; up the standard upload timeout interval for api tests
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aff21e09778e/ Changeset: aff21e09778e User: carlfeberhard Date: 2014-06-24 23:02:23 Summary: Fix: phantomjs apparently lacks the bind fn on the Function prototype - correct failures in history-panel (line 252) by using underscore bind instead; up the standard upload timeout interval for api tests Affected #: 2 files diff -r ae31e175f1cd836e89324a57d2c4276c5091f95f -r aff21e09778ece1bdbe987a4dad2adb6a26e5447 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -249,7 +249,7 @@ actions.push( { // TODO: Only show quick pair if two things selected. html: _l( 'Build List of Dataset Pairs (Experimental)' ), - func: panel._showPairedCollectionModal.bind( panel ) + func: _.bind( panel._showPairedCollectionModal, panel ) }); return new PopupMenu( $where.find( '.history-dataset-action-popup-btn' ), actions ); }, diff -r ae31e175f1cd836e89324a57d2c4276c5091f95f -r aff21e09778ece1bdbe987a4dad2adb6a26e5447 test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -555,7 +555,7 @@ }; /** amount of time allowed to upload a file (before erroring) */ -ToolsAPI.prototype.DEFAULT_UPLOAD_TIMEOUT = 12000; +ToolsAPI.prototype.DEFAULT_UPLOAD_TIMEOUT = 30 * 1000; /** add two casperjs steps - upload a file, wait for the job to complete, and run 'then' when they are */ ToolsAPI.prototype.thenUpload = function thenUpload( historyId, options, then ){ @@ -569,6 +569,9 @@ this.debug( 'uploadedId: ' + uploadedId ); }); + spaceghost.debug( '---------------------------------------------------------- timeout: ' + ( options.timeout || spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT ) ); + spaceghost.debug( 'timeout: ' + options.timeout ); + spaceghost.debug( 'timeout: ' + spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT ); spaceghost.then( function(){ this.waitFor( function testHdaState(){ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Style fix: use MS/IE specific syntax for flexbox to correct layout of paired-collection-creator in IE10 (Note: IE9 has no flexbox and this interface can't be used with it)
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ae31e175f1cd/ Changeset: ae31e175f1cd User: carlfeberhard Date: 2014-06-24 22:11:57 Summary: Style fix: use MS/IE specific syntax for flexbox to correct layout of paired-collection-creator in IE10 (Note: IE9 has no flexbox and this interface can't be used with it) Affected #: 2 files diff -r 17fbd073d94df628997df9df5af7d1de077bf82a -r ae31e175f1cd836e89324a57d2c4276c5091f95f static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1367,13 +1367,13 @@ .collection-creator .scroll-container{overflow:auto} .collection-creator .truncate{overflow:hidden;white-space:nowrap;text-overflow:ellipsis} .collection-creator .empty-message{color:grey;font-style:italic} -.collection-creator.flex-row-container,.collection-creator .flex-row-container,.collection-creator .flex-column-container{display:-webkit-box;display:-webkit-flex;display:flex;-webkit-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;align-content:stretch} -.collection-creator.flex-row-container,.collection-creator .flex-row-container{-webkit-flex-direction:column;flex-direction:column} -.collection-creator .flex-row{-webkit-flex:1 auto;flex:1 0 auto} -.collection-creator .flex-row.no-flex{-webkit-flex:0 auto;flex:0 0 auto} -.collection-creator .flex-column-container{-webkit-flex-direction:row;flex-direction:row} -.collection-creator .flex-column{-webkit-flex:1 auto;flex:1 1 auto} -.collection-creator .flex-column.no-flex{-webkit-flex:0 auto;flex:0 0 auto} +.collection-creator.flex-row-container,.collection-creator .flex-row-container,.collection-creator .flex-column-container{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;-webkit-align-items:stretch;-ms-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;-ms-align-content:stretch;align-content:stretch} +.collection-creator.flex-row-container,.collection-creator .flex-row-container{-webkit-flex-direction:column;-ms-flex-direction:column;flex-direction:column} +.collection-creator .flex-row{-webkit-flex:1 auto;-ms-flex:1 auto;flex:1 0 auto} +.collection-creator .flex-row.no-flex{-webkit-flex:0 auto;-ms-flex:0 auto;flex:0 0 auto} +.collection-creator .flex-column-container{-webkit-flex-direction:row;-ms-flex-direction:row;flex-direction:row} +.collection-creator .flex-column{-webkit-flex:1 auto;-ms-flex:1 auto;flex:1 1 auto} +.collection-creator .flex-column.no-flex{-webkit-flex:0 auto;-ms-flex:0 auto;flex:0 0 auto} .collection-creator .choose-filters .help{margin-bottom:2px;font-size:90%;color:grey} .collection-creator .choose-filters button{width:100%;margin-top:2px} .collection-creator .header .alert{display:none} diff -r 17fbd073d94df628997df9df5af7d1de077bf82a -r ae31e175f1cd836e89324a57d2c4276c5091f95f static/style/src/less/ui/paired-collection-creator.less --- a/static/style/src/less/ui/paired-collection-creator.less +++ b/static/style/src/less/ui/paired-collection-creator.less @@ -44,11 +44,15 @@ .flex-column-container { display: -webkit-box; display: -webkit-flex; + display: -ms-flexbox; display: flex; -webkit-align-items: stretch; + -ms-align-items: stretch; align-items: stretch; + -webkit-align-content: stretch; + -ms-align-content: stretch; align-content: stretch; } @@ -56,28 +60,34 @@ &.flex-row-container, .flex-row-container { -webkit-flex-direction: column; + -ms-flex-direction: column; flex-direction: column; } .flex-row { -webkit-flex: 1 auto; + -ms-flex: 1 auto; flex: 1 0 auto; } .flex-row.no-flex { -webkit-flex: 0 auto; + -ms-flex: 0 auto; flex: 0 0 auto; } // a series of horizontal elements that will expand to fill available space .flex-column-container { -webkit-flex-direction: row; + -ms-flex-direction: row; flex-direction: row; } .flex-column { -webkit-flex: 1 auto; + -ms-flex: 1 auto; flex: 1 1 auto; } .flex-column.no-flex { -webkit-flex: 0 auto; + -ms-flex: 0 auto; flex: 0 0 auto; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Style fix: use Safari/webkit specific syntax for flexbox to correct layout of paired-collection-creator in Safari
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/17fbd073d94d/ Changeset: 17fbd073d94d User: carlfeberhard Date: 2014-06-24 21:46:12 Summary: Style fix: use Safari/webkit specific syntax for flexbox to correct layout of paired-collection-creator in Safari Affected #: 5 files diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/scripts/mvc/collection/dataset-collection-edit.js --- a/static/scripts/mvc/collection/dataset-collection-edit.js +++ b/static/scripts/mvc/collection/dataset-collection-edit.js @@ -17,7 +17,7 @@ // ......................................................................... edit attr, delete /** Render icon-button group for the common, most easily accessed actions. - * Overrides _render_titleButtons to include editting related buttons. + * Overrides _render_titleButtons to include editing related buttons. * @see DatasetCollectionBaseView#_render_titleButtons * @returns {jQuery} rendered DOM */ diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -7,6 +7,8 @@ */ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ + className: 'collection-creator flex-row-container', + /** set up initial options, instance vars, behaviors, and autopair (if set to do so) */ initialize : function( attributes ){ //console.debug( '-- PairedCollectionCreator:', attributes ); @@ -541,7 +543,8 @@ /** render the entire interface */ render : function( speed, callback ){ //console.debug( '-- _render' ); - this.$el.empty().addClass( 'collection-creator' ).html( PairedCollectionCreator.templates.main() ); + //this.$el.empty().html( PairedCollectionCreator.templates.main() ); + this.$el.empty().html( PairedCollectionCreator.templates.main() ); this._renderHeader( speed ); this._renderMiddle( speed ); this._renderFooter( speed ); @@ -1191,9 +1194,9 @@ PairedCollectionCreator.templates = PairedCollectionCreator.templates || { /** the skeleton */ main : _.template([ - '<div class="header"></div>', - '<div class="middle"></div>', - '<div class="footer">' + '<div class="header flex-row no-flex"></div>', + '<div class="middle flex-row flex-row-container"></div>', + '<div class="footer flex-row no-flex">' ].join('')), /** the header (not including help text) */ @@ -1209,7 +1212,7 @@ '<span class="alert-message"></span>', '</div>', - '<div class="column-headers vertically-spaced row-flex-container">', + '<div class="column-headers vertically-spaced flex-column-container">', '<div class="forward-column flex-column column">', '<div class="column-header">', '<div class="column-title">', @@ -1221,7 +1224,7 @@ '</div>', '</div>', '</div>', - '<div class="paired-column flex-column column">', + '<div class="paired-column flex-column no-flex column">', '<div class="column-header">', '<a class="choose-filters-link" href="javascript:void(0)">', _l( 'Choose filters' ), @@ -1250,11 +1253,12 @@ /** the middle: unpaired, divider, and paired */ middle : _.template([ - '<div class="unpaired-columns row-flex-container scroll-container">', + // contains two flex rows (rows that fill available space) and a divider btwn + '<div class="unpaired-columns flex-column-container scroll-container flex-row">', '<div class="forward-column flex-column column">', '<ol class="column-datasets"></ol>', '</div>', - '<div class="paired-column flex-column column">', + '<div class="paired-column flex-column no-flex column">', '<ol class="column-datasets"></ol>', '</div>', '<div class="reverse-column flex-column column">', @@ -1272,11 +1276,11 @@ '</a>', '</div>', '</div>', - '<div class="paired-columns row-flex-container scroll-container">', + '<div class="paired-columns flex-column-container scroll-container flex-row">', '<div class="forward-column flex-column column">', '<ol class="column-datasets"></ol>', '</div>', - '<div class="paired-column flex-column column">', + '<div class="paired-column flex-column no-flex column">', '<ol class="column-datasets"></ol>', '</div>', '<div class="reverse-column flex-column column">', diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.View.extend(a.LoggableMixin).extend({initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return naturalSort(i.name,h.name)});return g},_ensureIds:function(){this.initialList.forEach(function(g){if(!g.hasOwnProperty("id")){g.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(i){var h=[],g=[];this.unpaired.forEach(function(j){if(this._filterFwdFn(j)){h.push(j)}if(this._filterRevFn(j)){g.push(j)}}.bind(this));return[h,g]},_filterFwdFn:function(g){return g.name.indexOf(this.filters[0])>=0},_filterRevFn:function(g){return g.name.indexOf(this.filters[1])>=0},_addToUnpaired:function(h){var g=function(i,k){if(i===k){return i}var j=Math.floor((k-i)/2)+i,l=naturalSort(h.name,this.unpaired[j].name);if(l<0){return g(i,j)}else{if(l>0){return g(j+1,k)}}while(this.unpaired[j]&&this.unpaired[j].name===h.name){j++}return j}.bind(this);this.unpaired.splice(g(0,this.unpaired.length),0,h)},autoPair:function(g){g=g||this.strategy;this.simpleAutoPair();return this[g].call(this)},simpleAutoPair:function(){var m=0,k,q=this._splitByFilters(),g=q[0],p=q[1],o,r,h=false;while(m<g.length){var l=g[m];o=l.name.replace(this.filters[0],"");h=false;for(k=0;k<p.length;k++){var n=p[k];r=n.name.replace(this.filters[1],"");if(l!==n&&o===r){h=true;this._pair(g.splice(m,1)[0],p.splice(k,1)[0],{silent:true});break}}if(!h){m+=1}}},autoPairLevenshtein:function(){var n=0,l,s=this._splitByFilters(),g=s[0],q=s[1],p,u,h,r,k;while(n<g.length){var m=g[n];p=m.name.replace(this.filters[0],"");k=Number.MAX_VALUE;for(l=0;l<q.length;l++){var o=q[l];u=o.name.replace(this.filters[1],"");if(m!==o){if(p===u){r=l;k=0;break}h=d(p,u);if(h<k){r=l;k=h}}}var t=1-(k/(Math.max(p.length,u.length)));if(t>=this.matchPercentage){this._pair(g.splice(n,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{n+=1}}},autoPairLCSs:function(){var l=0,h,s=this._splitByFilters(),g=s[0],q=s[1],p,v,u,r,n;if(!g.length||!q.length){return}while(l<g.length){var k=g[l];p=k.name.replace(this.filters[0],"");n=0;for(h=0;h<q.length;h++){var o=q[h];v=o.name.replace(this.filters[1],"");if(k!==o){if(p===v){r=h;n=p.length;break}var m=this._naiveStartingAndEndingLCS(p,v);u=m.length;if(u>n){r=h;n=u}}}var t=n/(Math.min(p.length,v.length));if(t>=this.matchPercentage){this._pair(g.splice(l,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{l+=1}}},_naiveStartingAndEndingLCS:function(l,h){var m="",n="",k=0,g=0;while(k<l.length&&k<h.length){if(l[k]!==h[k]){break}m+=l[k];k+=1}if(k===l.length){return l}if(k===h.length){return h}k=(l.length-1);g=(h.length-1);while(k>=0&&g>=0){if(l[k]!==h[g]){break}n=[l[k],n].join("");k-=1;g-=1}return m+n},_pair:function(i,g,h){h=h||{};var j=this._createPair(i,g,h.name);this.paired.push(j);this.unpaired=_.without(this.unpaired,i,g);if(!h.silent){this.trigger("pair:new",j)}return j},_createPair:function(i,g,h){if(!(i&&g)||(i===g)){throw new Error("Bad pairing: "+[JSON.stringify(i),JSON.stringify(g)])}h=h||this._guessNameForPair(i,g);return{forward:i,name:h,reverse:g}},_guessNameForPair:function(i,g){var h=this._naiveStartingAndEndingLCS(i.name.replace(this.filters[0],""),g.name.replace(this.filters[1],""));return h||(i.name+" & "+g.name)},_unpair:function(h,g){g=g||{};if(!h){throw new Error("Bad pair: "+JSON.stringify(h))}this.paired=_.without(this.paired,h);this._addToUnpaired(h.forward);this._addToUnpaired(h.reverse);if(!g.silent){this.trigger("pair:unpair",[h])}return h},unpairAll:function(){var g=[];while(this.paired.length){g.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",g)},_pairToJSON:function(g){return{collection_type:"paired",src:"new_collection",name:g.name,element_identifiers:[{name:"forward",id:g.forward.id,src:"hda"},{name:"reverse",id:g.reverse.id,src:"hda"}]}},createList:function(){var i=this,h;if(i.historyId){h="/api/histories/"+this.historyId+"/contents/dataset_collections"}var g={type:"dataset_collection",collection_type:"list:paired",name:_.escape(i.$(".collection-name").val()),element_identifiers:i.paired.map(function(j){return i._pairToJSON(j)})};return jQuery.ajax(h,{type:"POST",contentType:"application/json",data:JSON.stringify(g)}).fail(function(m,j,l){console.error(m,j,l);var k=e("An error occurred while creating this collection");if(m){if(m.readyState===0&&m.status===0){k+=": "+e("Galaxy could not be reached and may be updating.")+e(" Try again in a few minutes.")}else{if(m.responseJSON){k+="<br /><pre>"+JSON.stringify(m.responseJSON)+"</pre>"}else{k+=": "+l}}}i._showAlert(k,"alert-danger")}).done(function(j,k,l){i.trigger("collection:created",j,k,l);if(typeof i.oncreate==="function"){i.oncreate.call(this,j,k,l)}})},render:function(g,h){this.$el.empty().addClass("collection-creator").html(f.templates.main());this._renderHeader(g);this._renderMiddle(g);this._renderFooter(g);this._addPluginComponents();return this},_renderHeader:function(h,i){var g=this.$(".header").empty().html(f.templates.header()).find(".help-content").prepend($(f.templates.helpContent()));this._renderFilters();return g},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(h,i){var g=this.$(".middle").empty().html(f.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return g},_renderUnpaired:function(l,m){var j=this,k,h,g=[],i=this._splitByFilters();this.$(".forward-column .title").text([i[0].length,e("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[0].length));this.$(".reverse-column .title").text([i[1].length,e("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[1].length));this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty()}h=i[1].map(function(o,n){if((i[0][n]!==undefined)&&(i[0][n]!==o)){g.push(j._renderPairButton())}return j._renderUnpairedDataset(o)});k=i[0].map(function(n){return j._renderUnpairedDataset(n)});this.$(".unpaired-columns .column-datasets").empty();return this.$(".unpaired-columns .forward-column .column-datasets").append(k).add(this.$(".unpaired-columns .paired-column .column-datasets").append(g)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(h))},_renderUnpairedDisplayStr:function(g){return["(",g," ",e("filtered out"),")"].join("")},_renderUnpairedDataset:function(g){return $("<li/>").attr("id","dataset-"+g.id).addClass("dataset unpaired").attr("draggable",true).addClass(g.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(g.name)).data("dataset",g)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(e("Pair these datasets")))},_renderUnpairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+e("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").prepend(g);return g},_renderPaired:function(j,k){var i=[],g=[],h=[];this.$(".paired-column-title .title").text([this.paired.length,e("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty()}this.paired.forEach(function(m,l){i.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.forward.name)));g.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.name)));h.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.reverse.name)));h.push($("<button/>").addClass("unpair-btn").append($("<span/>").addClass("fa fa-unlink").attr("title",e("Unpair"))))});this.$(".paired-columns .column-datasets").empty();return this.$(".paired-columns .forward-column .column-datasets").prepend(i).add(this.$(".paired-columns .paired-column .column-datasets").prepend(g)).add(this.$(".paired-columns .reverse-column .column-datasets").prepend(h))},_renderPairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+e("no paired datasets yet")+")");this.$(".paired-columns .paired-column .column-datasets").prepend(g);return g},_renderFooter:function(h,i){var g=this.$(".footer").empty().html(f.templates.footer());if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return g},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 192, 255, 255, 1.0 )")},_chooseFiltersPopover:function(g){function h(k,j){return['<button class="filter-choice btn" ','data-forward="',k,'" data-reverse="',j,'">',e("Forward"),": ",k,", ",e("Reverse"),": ",j,"</button>"].join("")}var i=$(_.template(['<div class="choose-filters">','<div class="help">',e("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",h("_1","_2"),h("_R1","_R2"),"</div>"].join(""),{}));return this.$(g).popover({container:".collection-creator",placement:"bottom",html:true,content:i})},_validationWarning:function(h,g){var i="validation-warning";if(h==="name"){h=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(g){h=h||this.$("."+i);h.removeClass(i)}else{h.addClass(i)}},_setUpBehaviors:function(){this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(g){this._renderUnpaired();this._renderPaired()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired()});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click 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'} -.collection-creator .paired-column{text-align:center;width:22%;flex:0 1 auto} -.collection-creator .header{flex:0 0 auto;padding-bottom:8px}.collection-creator .header .main-help{max-height:36px;margin-bottom:16px;overflow:hidden;padding:8px;background:#f8f8f8}.collection-creator .header .main-help .help-content i{cursor:help;border-bottom:1px dotted grey;font-style:normal} +.collection-creator .paired-column{text-align:center;width:22%} +.collection-creator .header{padding-bottom:8px}.collection-creator .header .main-help{max-height:36px;margin-bottom:16px;overflow:hidden;padding:8px;background:#f8f8f8}.collection-creator .header .main-help .help-content i{cursor:help;border-bottom:1px dotted grey;font-style:normal} .collection-creator .header .main-help .help-content ul,.collection-creator .header .main-help .help-content li{list-style:circle;margin-left:16px} .collection-creator .header .main-help .help-content p:first-child{overflow:hidden;white-space:nowrap;text-overflow:ellipsis} .collection-creator .header .main-help .help-content .less-help{display:inline-block;width:100%;text-align:right} @@ -1383,11 +1390,7 @@ .collection-creator .header .column-headers .column-header .unpaired-filter{width:100%}.collection-creator .header .column-headers .column-header .unpaired-filter .search-query{width:100%;height:22px} .collection-creator .header .paired-column a:not(:last-child){margin-right:8px} .collection-creator .header .reverse-column .column-title{text-align:right} -.collection-creator .row-flex-container{display:flex;flex-direction:row;align-items:stretch;align-content:stretch} -.collection-creator .flex-column{flex:1 1 auto} -.collection-creator .middle{flex:1 0 auto;display:flex;flex-direction:column;align-items:stretch;align-content:stretch} -.collection-creator .unpaired-columns,.collection-creator .paired-columns{flex:1 0 auto;height:0;border:1px solid lightgrey;border-radius:3px;border-width:1px 0 1px 0;overflow-y:auto;padding:4px} -.collection-creator .unpaired-columns{flex:1 0 auto} +.collection-creator .unpaired-columns,.collection-creator .paired-columns{height:0;border:1px solid lightgrey;border-width:1px 0 1px 0;padding:4px} .collection-creator .paired-columns{margin-bottom:8px} .collection-creator .column-datasets{list-style:none;overflow:hidden}.collection-creator .column-datasets .dataset{height:32px;margin-bottom:2px;border:1px solid lightgrey;border-radius:3px;padding:0 8px 0 8px;line-height:28px;cursor:pointer;overflow:hidden}.collection-creator .column-datasets .dataset:last-child{margin-bottom:4px} .collection-creator .unpaired-columns .dataset.unpaired{border-color:grey}.collection-creator .unpaired-columns .dataset.unpaired:hover{border-color:black} @@ -1402,7 +1405,7 @@ .collection-creator .paired-columns .paired-column .dataset.paired{border-radius:0;border-width:2px 0 2px 0}.collection-creator .paired-columns .paired-column .dataset.paired .dataset-name:hover{text-decoration:underline} .collection-creator .paired-columns .reverse-column .dataset.paired{margin-right:32px;border-radius:0 3px 3px 0;border-left-color:grey;border-left-width:1px}.collection-creator .paired-columns .reverse-column .dataset.paired:before{margin-right:8px;font-family:FontAwesome;content:'\f060'} .collection-creator .paired-columns .reverse-column .unpair-btn{float:right;margin-top:-34px;width:31px;height:32px;border-color:transparent;background:transparent;font-size:120%}.collection-creator .paired-columns .reverse-column .unpair-btn:hover{border-color:#BFBFBF;background:#DEDEDE} -.collection-creator .footer{flex:0 0 auto;padding-bottom:8px}.collection-creator .footer .collection-name-prompt.validation-warning:before{content:'(required)';margin-right:4px;color:red} +.collection-creator .footer{padding-bottom:8px}.collection-creator .footer .collection-name-prompt.validation-warning:before{content:'(required)';margin-right:4px;color:red} .collection-creator .footer .collection-name{width:50%}.collection-creator .footer .collection-name.validation-warning{border-color:red} .collection-creator .footer .other-options>*{display:none;margin-left:4px} .collection-creator .footer .collection-name-prompt{margin:5px 4px 0 0} diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/style/src/less/ui/paired-collection-creator.less --- a/static/style/src/less/ui/paired-collection-creator.less +++ b/static/style/src/less/ui/paired-collection-creator.less @@ -2,11 +2,6 @@ .collection-creator { height: 100%; - display: flex; - flex-direction: column; - align-items: stretch; - align-content: stretch; - overflow: hidden; -webkit-user-select: none; @@ -43,6 +38,49 @@ font-style: italic; } + // ------------------------------------------------------------------------ flex + &.flex-row-container, + .flex-row-container, + .flex-column-container { + display: -webkit-box; + display: -webkit-flex; + display: flex; + + -webkit-align-items: stretch; + align-items: stretch; + -webkit-align-content: stretch; + align-content: stretch; + } + + // a series of vertical elements that will expand to fill available space + &.flex-row-container, + .flex-row-container { + -webkit-flex-direction: column; + flex-direction: column; + } + .flex-row { + -webkit-flex: 1 auto; + flex: 1 0 auto; + } + .flex-row.no-flex { + -webkit-flex: 0 auto; + flex: 0 0 auto; + } + + // a series of horizontal elements that will expand to fill available space + .flex-column-container { + -webkit-flex-direction: row; + flex-direction: row; + } + .flex-column { + -webkit-flex: 1 auto; + flex: 1 1 auto; + } + .flex-column.no-flex { + -webkit-flex: 0 auto; + flex: 0 0 auto; + } + // ------------------------------------------------------------------------ sub-components .choose-filters { .help { @@ -87,12 +125,10 @@ text-align: center; // mess with these two to make center more/less priority width: 22%; - flex: 0 1 auto; } // ------------------------------------------------------------------------ header .header { - flex: 0 0 auto; padding-bottom: 8px; .main-help { @@ -151,45 +187,21 @@ } - // ------------------------------------------------------------------------ flex - .row-flex-container { - display: flex; - flex-direction: row; - align-items: stretch; - align-content: stretch; - } - .flex-column { - flex: 1 1 auto; - } - // ------------------------------------------------------------------------ middle .middle { - // highest flex count - will priority fill with this - flex: 1 0 auto; - - display: flex; - flex-direction: column; - align-items: stretch; - align-content: stretch; } .unpaired-columns, .paired-columns { - flex: 1 0 auto; // huh! - giving these any static height will pull them in height: 0; // NOT setting the above will give a full-height page border: 1px solid lightgrey; - border-radius: 3px; border-width: 1px 0 1px 0; - overflow-y: auto; + //overflow-y: auto; padding: 4px; } // ------------------------------------------------------------------------ unpaired - .unpaired-columns { - flex: 1 0 auto; - } - .paired-columns { margin-bottom: 8px; } @@ -337,9 +349,6 @@ // ------------------------------------------------------------------------ footer .footer { - flex: 0 0 auto; - padding-bottom: 8px; - .collection-name-prompt.validation-warning:before { //TODO: localize (somehow) content: '(required)'; @@ -361,5 +370,6 @@ .collection-name-prompt { margin: 5px 4px 0 0; } + padding-bottom: 8px; } } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Merge
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/476aa78a1b1a/ Changeset: 476aa78a1b1a User: guerler Date: 2014-06-24 21:00:13 Summary: Merge Affected #: 76 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a15c52999493/ Changeset: a15c52999493 Branch: stable User: guerler Date: 2014-06-24 19:38:13 Summary: Charts plugin update Affected #: 164 files diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/app.css --- a/config/plugins/visualizations/charts/static/app.css +++ b/config/plugins/visualizations/charts/static/app.css @@ -1,3 +1,20 @@ +.charts-tooltip { + position: absolute; + text-align: center; + padding: 3px 5px 3px 5px; + font: 12px sans-serif; + background: white; + border: 1px solid gray; + border-radius: 4px; + pointer-events: none; +} + +.charts-tooltip-first { + font-weight: bold; + text-align: left; + padding-right: 5px; +} + .charts-grid .item { padding: 5px; margin: 5px; @@ -17,6 +34,7 @@ .charts-grid .image { padding: 10px; width: 100px; + height: 86px; } .charts-grid .title { @@ -47,6 +65,7 @@ margin-left: 5px; top: -1px; font-size: 1.0em; + display: inline; } .charts-viewport .icon { @@ -63,5 +82,6 @@ .charts-viewport .charts-viewport-canvas { display: block; width:100%; + min-height: 100px; height: inherit; } \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -86,6 +86,22 @@ } }, + // get root path + chartPath: function(chart_type) { + // create path from id + var path = chart_type.split(/_(.+)/); + + // check path + if (path.length >= 2) { + // return path + return path[0] + '/' + path[1]; + } else { + // log status + console.debug('FAILED App:chartPath() - Invalid format: ' + chart_type); + } + return undefined; + }, + // execute command execute: function(options) { }, diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var 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t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{url:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img src="'+e.url+'"/>'}}),r=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return'<label class="'+e.cls+'"><b>'+e.title+"</b></label>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),a=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. 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Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw 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u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var 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e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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diagrams"})}),define("plugin/charts/nvd3_bar_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_bar_horizontal_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from 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Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){e.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){s.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" 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t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new 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u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa 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o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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E=d3.select(this),T=this,N=(u||parseInt(E.style("width"))||960)-s.left-s.right,C=(a||parseInt(E.style("height"))||400)-s.top-s.bottom;x.update=function(){E.call(x)},x.container=this,g.disabled=d.map(function(e){return!!e.disabled});if(!y){var k;y={};for(k in g)g[k]instanceof Array?y[k]=g[k].slice(0):y[k]=g[k]}if(!d||!d.length||!d.filter(function(e){return e.values.length}).length){var L=E.selectAll(".nv-noData").data([b]);return L.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),L.attr("x",s.left+N/2).attr("y",s.top+C/2).text(function(e){return e}),x}E.selectAll(".nv-noData").remove(),v=t.xScale(),m=t.yScale();var A=E.selectAll("g.nv-wrap.nv-historicalBarChart").data([d]),O=A.enter().append("g").attr("class","nvd3 nv-wrap nv-historicalBarChart").append("g"),M=A.select("g");O.append("g").attr("class","nv-x nv-axis"),O.append("g").attr("class","nv-y 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t=e.models.historicalBar(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s={top:30,right:90,bottom:50,left:90},o=e.utils.defaultColor(),u=null,a=null,f=!1,l=!0,c=!0,h=!1,p=!0,d=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},v,m,g={},y=null,b="No Data Available.",w=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),E=0;n.orient("bottom").tickPadding(7),r.orient(h?"right":"left");var S=function(i,s){if(s){var o=d3.select(s).select("svg"),u=o.node()?o.attr("viewBox"):null;if(u){u=u.split(" ");var a=parseInt(o.style("width"))/u[2];i.pos[0]=i.pos[0]*a,i.pos[1]=i.pos[1]*a}}var f=i.pos[0]+(s.offsetLeft||0),l=i.pos[1]+(s.offsetTop||0),c=n.tickFormat()(t.x()(i.point,i.pointIndex)),h=r.tickFormat()(t.y()(i.point,i.pointIndex)),p=d(i.series.key,c,h,i,x);e.tooltip.show([f,l],p,null,null,s)};return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var 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grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"Heatmap",category:"Others",query_limit:1e3,library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/forms/default.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/forms/default.js @@ -0,0 +1,252 @@ +define([], function() { + +return { + title : '', + category : '', + library : '', + tag : '', + keywords : '', + query_limit : 0, + settings : { + separator_x : { + title : 'X axis', + type : 'separator' + }, + x_axis_label : { + title : 'Axis label', + info : 'Provide a label for the axis.', + type : 'text', + init : 'X-axis', + placeholder : 'Axis label' + }, + x_axis_type : { + title : 'Axis value type', + info : 'Select the value type of the axis.', + type : 'select', + init : 'auto', + data : [ + { + label : '-- Do not show values --', + value : 'hide', + operations : { + hide : ['x_axis_precision'] + } + }, + { + label : 'Auto', + value : 'auto', + operations : { + hide : ['x_axis_precision'] + } + }, + { + label : 'Float', + value : 'f', + operations : { + show : ['x_axis_precision'] + } + }, + { + label : 'Exponent', + value : 'e', + operations : { + show : ['x_axis_precision'] + } + }, + { + label : 'Integer', + value : 'd', + operations : { + hide : ['x_axis_precision'] + } + }, + { + label : 'Percentage', + value : 'p', + operations : { + show : ['x_axis_precision'] + } + }, + { + label : 'SI-prefix', + value : 's', + operations : { + hide : ['x_axis_precision'] + } + } + ] + }, + x_axis_precision : { + title : 'Axis tick format', + info : 'Select the tick format for the axis.', + type : 'select', + init : '1', + data : [ + { + label : '0.00001', + value : '5' + }, + { + label : '0.0001', + value : '4' + }, + { + label : '0.001', + value : '3' + }, + { + label : '0.01', + value : '2' + }, + { + label : '0.1', + value : '1' + }, + { + label : '1', + value : '0' + } + ] + + }, + separator_y : { + title : 'Y axis', + type : 'separator' + }, + y_axis_label : { + title : 'Axis label', + info : 'Provide a label for the axis.', + type : 'text', + init : 'Y-axis', + placeholder : 'Axis label' + }, + y_axis_type : { + title : 'Axis value type', + info : 'Select the value type of the axis.', + type : 'select', + init : 'auto', + data : [ + { + label : '-- Do not show values --', + value : 'hide', + operations : { + hide : ['y_axis_precision'] + } + }, + { + label : 'Auto', + value : 'auto', + operations : { + hide : ['y_axis_precision'] + } + }, + { + label : 'Float', + value : 'f', + operations : { + show : ['y_axis_precision'] + } + }, + { + label : 'Exponent', + value : 'e', + operations : { + show : ['y_axis_precision'] + } + }, + { + label : 'Integer', + value : 'd', + operations : { + hide : ['y_axis_precision'] + } + }, + { + label : 'Percentage', + value : 'p', + operations : { + show : ['y_axis_precision'] + } + }, + { + label : 'SI-prefix', + value : 's', + operations : { + hide : ['y_axis_precision'] + } + } + ] + }, + y_axis_precision : { + title : 'Axis tick format', + info : 'Select the tick format for the axis.', + type : 'select', + init : '1', + data : [ + { + label : '0.00001', + value : '5' + }, + { + label : '0.0001', + value : '4' + }, + { + label : '0.001', + value : '3' + }, + { + label : '0.01', + value : '2' + }, + { + label : '0.1', + value : '1' + }, + { + label : '1', + value : '0' + } + ] + + }, + separator_legend : { + title : 'Others', + type : 'separator' + }, + show_legend : { + title : 'Show legend', + info : 'Would you like to add a legend?', + type : 'radiobutton', + init : 'true', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] + }, + use_panels : { + title : 'Use multi-panels', + info : 'Would you like to separate your data into individual panels?', + type : 'radiobutton', + init : 'false', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] + } + } +}; + +}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/config.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/config.js +++ /dev/null @@ -1,195 +0,0 @@ -define([], function() { - -return { - title : 'Heatmap', - category : 'Data processing (requires \'charts\' tool from Toolshed)', - library : '', - tag : 'div', - use_panels : true, - execute : 'heatmap', - - // columns - columns : { - row_label : { - title : 'Row labels', - is_label : true - }, - col_label : { - title : 'Column labels', - is_label : true - }, - value : { - title : 'Observations' - }, - }, - - // settings - settings: { - /*limit : { - title : 'Limit', - info : 'Which to ranked clusters would you like to visualize', - type : 'select', - init : '20', - data : [ - { - label : '20', - value : '20' - }, - { - label : '30', - value : '30' - }, - { - label : '40', - value : '40' - }, - { - label : '50', - value : '50' - }, - { - label : '60', - value : '60' - }, - { - label : '70', - value : '70' - }, - { - label : '80', - value : '80' - }, - { - label : '90', - value : '90' - }, - { - label : '100', - value : '100' - } - ] - },*/ - color_set : { - title : 'Color scheme', - info : 'Select a color scheme for your heatmap', - type : 'select', - init : 'ocean', - data : [ - { - label : 'Cold-to-Hot', - value : 'hot' - }, - { - label : 'Cool', - value : 'cool' - }, - { - label : 'Copper', - value : 'copper' - }, - { - label : 'Gebco', - value : 'gebco' - }, - { - label : 'Globe', - value : 'globe' - }, - { - label : 'Gray scale', - value : 'gray' - }, - { - label : 'Haxby', - value : 'haxby' - }, - { - label : 'Jet', - value : 'jet' - }, - { - label : 'No-Green', - value : 'no_green' - }, - { - label : 'Ocean', - value : 'ocean' - }, - { - label : 'Polar', - value : 'polar' - }, - { - label : 'Rainbow', - value : 'rainbow' - }, - { - label : 'Red-to-Green', - value : 'redgreen' - }, - { - label : 'Red-to-green (saturated)', - value : 'red2green' - }, - { - label : 'Relief', - value : 'relief' - }, - { - label : 'Seismograph', - value : 'seis' - }, - { - label : 'Sealand', - value : 'sealand' - }, - { - label : 'Split', - value : 'split' - }, - { - label : 'Topo', - value : 'topo' - }, - { - label : 'Wysiwyg', - value : 'wysiwyg' - } - ] - }, - - sorting : { - title : 'Sorting', - info : 'How should the columns be clustered?', - type : 'select', - init : 'hclust', - data : [ - { - label : 'Read from dataset', - value : 'hclust' - }, - { - label : 'Sort column and row labels', - value : 'byboth' - }, - { - label : 'Sort column labels', - value : 'bycolumns' - }, - { - label : 'Sort by rows', - value : 'byrow' - } - ] - } - }, - - // menu definition - menu : function() { - return { - color_set : this.settings.color_set - } - } -}; - -}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js +++ /dev/null @@ -1,52 +0,0 @@ -// dependencies -define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin'], function(Utils, HeatmapPlugin) { - -// color palettes -var colorSets = { - seis: ['#AA0000', '#D00000', '#F70000', '#FF1D00', '#FF4400', '#FF6A00', '#FF9000', '#FFB700', '#FFDD00', '#FFFF00', '#FFFF00', '#FFFF00', '#BDFF0C', '#73FF1A', '#3FFA36', '#16F45A', '#00D08B', '#0087CD', '#0048FA', '#0024E3'], - - sealand: ['#8C66FF', '#6A66FF', '#6684FF', '#66A7FF', '#66CAFF', '#66ECFF', '#66FFF0', '#66FFCE', '#66FFAB', '#66FF88', '#66FF66', '#88FF66', '#ABFF66', '#CEFF66', '#FFEEA6', '#FFD3A6', '#FFB8A6', '#FFAAB0', '#FFB5CB', '#FFC0E1'], - - redgreen: ['#005824', '#1A693B', '#347B53', '#4F8D6B', '#699F83', '#83B09B', '#9EC2B3', '#B8D4CB', '#D2E6E3', '#EDF8FB', '#FFFFFF', '#F1EEF6', '#E6D3E1','#DBB9CD', '#D19EB9', '#C684A4', '#BB6990', '#B14F7C', '#A63467', '#9B1A53', '#91003F'], - - ocean: ['#000000', '#000209', '#000413', '#00061E', '#000728', '#000932', '#002650', '#00426E', '#005E8C', '#007AAA', '#0096C8', '#22A9C2', '#45BCBB', '#67CFB5', '#8AE2AE', '#ACF6A8', '#BCF8B9', '#CBF9CA', '#DBFBDC', '#EBFDED'], - - cool: ['#00FFFF', '#0DF2FF', '#19E6FF', '#26D9FF', '#33CCFF', '#3FBFFF', '#4CB3FF', '#59A6FF', '#6699FF', '#738CFF', '#7F7FFF', '#8C73FF', '#9966FF', '#A659FF', '#B24DFF', '#BF3FFF', '#CC33FF', '#D926FF', '#E619FF', '#F20DFF'], - - copper: ['#000000', '#100906', '#1F130D', '#301E13', '#40281A', '#50321F', '#603C26', '#70462D', '#805033', '#905A3A', '#A06440', '#B06E46', '#C0784D', '#D08253', '#E08C5A', '#F09660', '#FFA066', '#FFAA6D', '#FFB473', '#FFBE7A'], - - gebco: ['#00F0FF', '#00F0FF', '#00F0FF', '#23FFFF', '#23FFFF', '#23FFFF', '#5AFFFF', '#5AFFFF', '#5AFFFF', '#8CFFE6', '#8CFFE6', '#8CFFE6', '#A5FFD7', '#A5FFD7', '#A5FFD7', '#C3FFD7', '#C3FFD7', '#C3FFD7', '#D2FFD7', '#E6FFF0'], - - globe: ['#9900FF', '#9900FF', '#7722FF', '#5544FF', '#3366FF', '#1188FF', '#1BA4FF', '#51BAFF', '#86D0FF', '#BCE6FF', '#336600', '#F3CA89', '#D9A627', '#A49019', '#9F7B0D', '#996600', '#B27676', '#C2B0B0', '#E5E5E5', '#FFFFFF'], - - gray: ['#000000', '#0D0D0D', '#191919', '#262626', '#333333', '#3F3F3F', '#4C4C4C', '#595959', '#666666', '#737373', '#7F7F7F', '#8C8C8C', '#999999', '#A6A6A6', '#B2B2B2', '#BFBFBF', '#CCCCCC', '#D9D9D9', '#E6E6E6', '#F2F2F2'], - - haxby: ['#090079', '#280096', '#0009C8', '#0019D4', '#1A66F0', '#19AFFF', '#32BEFF', '#61E1F0', '#6AECE1', '#8AECAE', '#CDFFA2', '#DFF68D', '#F8D768', '#FFBD57', '#F4754B', '#FF5A5A', '#FF7C7C', '#F6B3AE', '#FFC4C4', '#FFECEC'], - - hot: ['#000000', '#220000', '#440000', '#660000', '#880000', '#AA0000', '#CC0000', '#EE0000', '#FF1100', '#FF3300', '#FF5500', '#FF7700', '#FF9900', '#FFBB00', '#FFDD00', '#FFFF00', '#FFFF33', '#FFFF66', '#FFFF99', '#FFFFCC'], - - jet: ['#00007F', '#0000B2', '#0000E5', '#0019FF', '#004DFF', '#007FFF', '#00B2FF', '#00E5FF', '#FFFFF2', '#FFFFD9', '#FFFFBF', '#FFFFA5', '#FFFF8C', '#FFE500', '#FFB300', '#FF7F00', '#FF4C00', '#FF1900', '#E50000', '#B20000'], - - no_green: ['#1F60FF', '#1F60FF', '#1F9FFF', '#1FBFFF', '#00CFFF', '#2AFFFF', '#2AFFFF', '#55FFFF', '#7FFFFF', '#AAFFFF', '#FFFF54', '#FFFF54', '#FFF000', '#FFBF00', '#FFA800', '#FF8A00', '#FF8A00', '#FF7000', '#FF4D00', '#FF0000'], - - polar: ['#0000FF', '#1919FF', '#3333FF', '#4C4CFF', '#6666FF', '#7F7FFF', '#9999FF', '#B2B2FF', '#CCCCFF', '#E6E6FF', '#FFFFFF', '#FFE5E5', '#FFCCCC', '#FFB2B2', '#FF9999', '#FF7F7F', '#FF6666', '#FF4C4C', '#FF3333', '#FF1A1A'], - - rainbow: ['#FF00FF', '#BF00FF', '#7F00FF', '#3F00FF', '#0000FF', '#003FFF', '#007FFF', '#00BFFF', '#00FFFF', '#00FFBF', '#00FF7F', '#00FF3F', '#00FF00', '#3FFF00', '#7FFF00', '#BFFF00', '#FFFF00', '#FFBF00', '#FF7F00', '#FF3F00'], - - red2green: ['#FF0000', '#FF1919', '#FF3333', '#FF4C4C', '#FF6666', '#FF7F7F', '#FF9999', '#FFB2B2', '#FFCCCC', '#FFE6E6', '#FFFFFF', '#E5FFE5', '#CCFFCC', '#B2FFB2', '#99FF99', '#7FFF7F', '#66FF66', '#4CFF4C', '#33FF33', '#1AFF1A'], - - relief: ['#000000', '#000413', '#000728', '#002650', '#005E8C', '#0096C8', '#45BCBB', '#8AE2AE', '#BCF8B9', '#DBFBDC', '#467832', '#887438', '#B19D48', '#DBC758', '#FAE769', '#FAEB7E', '#FCED93', '#FCF1A7', '#FCF6C1', '#FDFAE0'], - - split: ['#7F7FFF', '#6666E6', '#4D4DCC', '#3333B3', '#1A1A99', '#00007F', '#000066', '#00004D', '#000033', '#00001A', '#000000', '#1A0000', '#330000', '#4D0000', '#660000', '#7F0000', '#991A1A', '#B33333', '#CC4D4D', '#E66666'], - - topo: ['#C977D9', '#A18AE6', '#8AA2E6', '#8BD1E7', '#8AF3CF', '#85F38E', '#BDF385', '#EDE485', '#F0B086', '#DE9F8B', '#74A3B3', '#99CC70', '#DCD68E', '#EDDFAD', '#F7E8CA', '#FFF9F3', '#FFF9F6', '#FFFBF9', '#FFFCFA', '#FFFEFD'], - - wysiwyg: ['#3F003F', '#3F003F', '#3F00BF', '#003FFF', '#00A0FF', '#3FBFFF', '#3FBFFF', '#40E0FF', '#3FFFBF', '#3FFF3F', '#7FFF3F', '#BFFF3F', '#BFFF3F', '#FFE040', '#FFE040', '#FF6040', '#FF1F40', '#FF60C0', '#FFA0FF', '#FFA0FF'] -} - -// return -return { - colorSets: colorSets -} - -}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js +++ /dev/null @@ -1,739 +0,0 @@ -// dependencies -define(['utils/utils'], -function(Utils) { - -// widget -return Backbone.View.extend( -{ - // number of columns and rows - colNumber: 0, - rowNumber: 0, - - // indices - rowIndex: [], - colIndex: [], - - // labels - rowLabel: [], - colLabel: [], - - // cell size - cellSize: 0, - - // font size - fontSize: 0, - - // color buckets - nColors: 0, - - // margins as cells - margin : { - top : 5, - right : 5, - bottom : 5, - left : 5 - }, - - // default settings - optionsDefault: { - title : '', - pace : 1000, - }, - - // initialize - initialize: function(options) { - // link this - var self = this; - - // load options - this.options = Utils.merge(options, this.optionsDefault) - - // check requirements - if (!this.options.data || !this.options.div || !this.options.colors) { - console.debug('FAILED - HeatMapPlugin::initialize() - Parameters (container and/or data and/or colors) missing.'); - return; - } - - // link data - this.data = this.options.data; - - // set element - this.setElement(this.options.div); - - // - // data indexing - // - - // labels (in alphabetical order) - this.rowLabel = []; - this.colLabel = []; - - // index (order from original dataset) - this.rowIndex = []; - this.colIndex = []; - - // unique keys (key indices are unique per label and indicate the labels rank in the alphabetical sorting) - this.colRank = {}; - this.rowRank = {}; - - // - // identify and parse labels - // - for (var i in this.data) { - var cell = this.data[i]; - - // add label to index list - var col_label = cell.col_label; - if (this.colRank[col_label] === undefined) { - this.colRank[col_label] = true; - this.colLabel.push(col_label); - this.colIndex.push(col_label); - } - var row_label = cell.row_label; - if (this.rowRank[row_label] === undefined) { - this.rowRank[row_label] = true; - this.rowLabel.push(row_label); - this.rowIndex.push(row_label); - } - } - - // - // sort labels and update rank dictionary - // - - // set sizes - this.rowNumber = this.rowLabel.length - this.colNumber = this.colLabel.length - - // sort labels alphabetical - this.rowLabel.sort(); - this.colLabel.sort(); - - // generate sorted key list for rows - for (var i in this.rowLabel) { - var row_label = this.rowLabel[i]; - var row = parseInt(i); - this.rowRank[row_label] = row; - } - - // generate sorted key list for columns - for (var i in this.colLabel) { - var col_label = this.colLabel[i]; - var col = parseInt(i); - this.colRank[col_label] = col; - } - - // - // parse indexing from rank dictionary to cells - // - - // min/max - this.max = undefined; - this.min = undefined - - // add indices to data - for (var i in this.data) { - // get cell data - var cell = this.data[i]; - - // add rank - cell.col = this.colRank[cell.col_label]; - cell.row = this.rowRank[cell.row_label]; - - // identify max/min values - if (this.min == undefined || this.min > cell.value) { - this.min = cell.value; - } - if (this.max == undefined || this.max < cell.value) { - this.max = cell.value; - } - } - - // - // translate original create cluster from order in original data - // - - // generate sorted key list for columns - for (var i in this.colIndex) { - this.colIndex[i] = this.colRank[this.colIndex[i]]; - } - // generate sorted key list for columns - for (var i in this.rowIndex) { - this.rowIndex[i] = this.rowRank[this.rowIndex[i]]; - } - - // middle - this.mid = (this.max + this.min) / 2; - - // - // set colors - // - - // identify buckets - this.nColors = this.options.colors.length; - - // color scale - this.colorScale = d3.scale.quantile() - .domain([this.min, this.mid, this.max]) - .range(this.options.colors); - - // - // add ui elements - // - // create tooltip - this.$tooltip = $(this._templateTooltip()); - this.$el.append(this.$tooltip); - - // - // finally draw the heatmap - // - this._build(); - - // catch window resize event - $(window).resize(function () { - self._build(); - }); - }, - - _build: function() { - // link this - var self = this; - - // container (full draw area) - this.widthContainer = this.$el.width(); - this.heightContainer = this.$el.height(); - - // get grid dimensions - this.width = this.widthContainer; - this.height = this.heightContainer; - - // calculate cell size - this.cellSize = Math.min(((this.height) / (this.rowNumber + this.margin.top + this.margin.bottom)), - (this.width / (this.colNumber + this.margin.left + this.margin.right))); - - // set font size - this.fontSize = Math.min(this.cellSize, 16); - - // set width/height for plugin - this.width = this.cellSize * this.colNumber; - this.height = this.cellSize * this.rowNumber; - - // get dimensions - var margin = this.options.margin; - var width = this.width; - var height = this.height; - - // reset svg - if (this.svg !== undefined) { - this.$el.find('svg').remove(); - } - - // add main group and translate - this.svg = d3.select(this.$el[0]).append('svg') - .append('g') - .attr('transform', 'translate(' + (this.widthContainer - width) / 2 + ',' + - (this.heightContainer - height) / 2 + ')'); - - // reset sorting - this.rowSortOrder = false; - this.colSortOrder = false; - - // build - this.d3RowLabels = this._buildRowLabels(); - this.d3ColLabels = this._buildColLabels(); - this.d3HeatMap = this._buildHeatMap(); - this.d3Legend = this._buildLegend(); - this.d3Title = this._buildTitle(); - }, - - // build title - _buildTitle: function() { - // link this - var self = this; - - // gather data - var height = this.height; - var width = this.width; - var cellSize = this.cellSize; - var fontSize = this.fontSize; - var title = this.options.title; - - // add title - return this.svg.append('g') - .append('text') - .attr('x', width / 2) - .attr('y', height + 3 * cellSize + fontSize + 3) - .attr('text-anchor', 'middle') - .text(title); - }, - - // build legend - _buildLegend: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var fontSize = this.fontSize; - var height = this.height; - var legendCellWidth = this.width / this.nColors; - - // create range labels - var dataRange = []; - for(var i = 0; i < this.nColors; i++) { - dataRange.push(''); - } - - // prepare indices - var dataRangeMin = 0; - var dataRangeMid = parseInt((dataRange.length - 1) / 2); - var dataRangeMax = dataRange.length - 1; - - // add labels - dataRange[dataRangeMin] = this.min; - dataRange[dataRangeMid] = this.mid; - dataRange[dataRangeMax] = this.max; - - // create legend - var legend = this.svg.selectAll('.legend') - .data(dataRange) - .enter().append('g') - .attr('class', 'legend'); - - // add boxes - legend.append('rect') - .attr('x', function(d, i) { - return legendCellWidth * i; - }) - .attr('y', height + cellSize) - .attr('width', legendCellWidth) - .attr('height', cellSize) - .style('fill', function(d, i) { - return self.options.colors[i]; - }); - - // add text - legend.append('text') - .attr('class', 'mono') - .text(function(d) { - return d; - }) - .attr('width', legendCellWidth) - .attr('x', function(d, i) { - return legendCellWidth * i; - }) - .attr('y', height + cellSize - 3) - .style('font-size', fontSize + 'px'); - - // return - return legend; - }, - - // build column labels - _buildColLabels: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var fontSize = this.fontSize; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - - // column labels - var colLabels = this.svg.append('g') - .selectAll('.colLabelg') - .data(colLabel) - .enter() - .append('text') - .text(function (d) { - return d; - }) - .attr('x', 0) - .attr('y', function (d, i) { - return colIndex.indexOf(i) * cellSize; - }) - .style('font-size', fontSize + 'px') - .style('text-anchor', 'left') - .attr('transform', 'translate(' + cellSize / 2 + ', -17) rotate (-90)') - .attr('class', function (d, i) { - return 'colLabel mono c' + i; - }) - .on('mouseover', function(d) { - d3.select(this).classed('text-hover',true); - }) - .on('mouseout' , function(d) { - d3.select(this).classed('text-hover',false); - }) - .on('click', function(d, i) { - self.colSortOrder=!self.colSortOrder; - self._sortByLabel('c', 'row', self.rowNumber, i, self.colSortOrder); - d3.select('#order').property('selectedIndex', 4).node().focus(); - }); - - // return - return colLabels; - }, - - // build row labels - _buildRowLabels: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var fontSize = this.fontSize; - var rowIndex = this.rowIndex; - var rowLabel = this.rowLabel; - - // draw labels - var rowLabels = this.svg.append('g') - .selectAll('.rowLabelg') - .data(rowLabel) - .enter() - .append('text') - .text(function (d) { - return d; - }) - .attr('x', 0) - .attr('y', function (d, i) { - return rowIndex.indexOf(i) * cellSize; - }) - .style('font-size', fontSize + 'px') - .style('text-anchor', 'end') - .attr('transform', 'translate(-10,' + cellSize / 1.5 + ')') - .attr('class', function (d, i) { - return 'rowLabel mono r' + i; - } ) - .on('mouseover', function(d) { - d3.select(this).classed('text-hover',true); - }) - .on('mouseout' , function(d) { - d3.select(this).classed('text-hover',false); - }) - .on('click', function(d, i) { - self.rowSortOrder=!self.rowSortOrder; - self._sortByLabel('r', 'col', self.colNumber, i, self.rowSortOrder); - d3.select('#order').property('selectedIndex', 4).node().focus(); - }); - - // return - return rowLabels; - }, - - // build heat map - _buildHeatMap: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var rowIndex = this.rowIndex; - var rowLabel = this.rowLabel; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - - // heat map - var heatmap = this.svg.append('g').attr('class','g3') - .selectAll('.cellg') - .data(self.data, function(d) { - return d.row + ':' + d.col; - }) - .enter() - .append('rect') - .attr('x', function(d) { - return colIndex.indexOf(d.col) * cellSize; - }) - .attr('y', function(d) { - return rowIndex.indexOf(d.row) * cellSize; - }) - .attr('class', function(d){ - return 'cell cell-border cr' + d.row + ' cc' + d.col; - }) - .attr('width', cellSize) - .attr('height', cellSize) - .style('fill', function(d) { - return self.colorScale(d.value); - }) - .on('mouseover', function(d){ - // highlight text - d3.select(this).classed('cell-hover',true); - d3.selectAll('.rowLabel').classed('text-highlight',function(r,ri){ return ri==(d.row);}); - d3.selectAll('.colLabel').classed('text-highlight',function(c,ci){ return ci==(d.col);}); - - // update the tooltip position and value - d3.select('#heatmap-tooltip') - .style('left', (d3.event.pageX+10) + 'px') - .style('top', (d3.event.pageY-10) + 'px') - .select('#value') - .text('Label: ' + rowLabel[d.row] + ' | ' + colLabel[d.col] + ', Value: ' + d.value); - // show the tooltip - d3.select('#heatmap-tooltip').classed('hidden', false); - }) - .on('mouseout', function(){ - d3.select(this).classed('cell-hover',false); - d3.selectAll('.rowLabel').classed('text-highlight',false); - d3.selectAll('.colLabel').classed('text-highlight',false); - d3.select('#heatmap-tooltip').classed('hidden', true); - }); - - // return - return heatmap; - }, - - // change ordering of cells - _sortByLabel: function(rORc, rowORcol, n, index, sortOrder) { - // get cell size - var cellSize = this.cellSize; - - // define transition / prepare element - var t = this.svg.transition().duration(this.options.pace); - - // create cells - var cells=[]; - for (var i = 0; i < n; i++) { - cells[i] = { - value: this.min - 1 - } - cells[i][rowORcol] = i; - } - - // collect cells - t.selectAll('.c' + rORc + index).filter(function(ce) { - cells[ce[rowORcol]].value = ce.value; - }); - - // sort cells - cells.sort(function(a, b) { - if (sortOrder) { - return b.value - a.value; - } else { - return a.value - b.value; - } - }); - - // get sorted key list - var sorted = []; - for (var i in cells) { - sorted.push(cells[i][rowORcol]); - } - - // rows or columns - if(rORc == 'r') { - // sort cells - t.selectAll('.cell') - .attr('x', function(d) { - return sorted.indexOf(d.col) * cellSize; - }); - - // sort labels - t.selectAll('.colLabel') - .attr('y', function (d, i) { - return sorted.indexOf(i) * cellSize; - }); - } else { - // sort cells - t.selectAll('.cell') - .attr('y', function(d) { - return sorted.indexOf(d.row) * cellSize; - }); - - // sort labels - t.selectAll('.rowLabel') - .attr('y', function (d, i) { - return sorted.indexOf(i) * cellSize; - }); - } - }, - - // sort function - _sortByOrder: function (value) { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var rowIndex = this.rowIndex; - var rowLabel = this.rowLabel; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - - // set duration / select element - var t = this.svg.transition().duration(this.options.pace); - if(value=='hclust'){ - t.selectAll('.cell') - .attr('x', function(d) { - return colIndex.indexOf(d.col) * cellSize; - }) - .attr('y', function(d) { - return rowIndex.indexOf(d.row) * cellSize; - }); - - t.selectAll('.rowLabel') - .attr('y', function(d, i) { - return rowIndex.indexOf(i) * cellSize; - }); - - t.selectAll('.colLabel') - .attr('y', function(d, i) { - return colIndex.indexOf(i) * cellSize; - }); - - } else if (value=='byboth') { - t.selectAll('.cell') - .attr('x', function(d) { - return d.col * cellSize; - }) - .attr('y', function(d) { - return d.row * cellSize; - }); - - t.selectAll('.rowLabel') - .attr('y', function (d, i) { - return i * cellSize; - }); - - t.selectAll('.colLabel') - .attr('y', function (d, i) { - return i * cellSize; - }); - } else if (value=='byrow') { - t.selectAll('.cell') - .attr('y', function(d) { - return d.row * cellSize; - }); - - t.selectAll('.rowLabel') - .attr('y', function (d, i) { - return i * cellSize; - }); - } else if (value=='bycol'){ - t.selectAll('.cell') - .attr('x', function(d) { - return d.col * cellSize; - }); - t.selectAll('.colLabel') - .attr('y', function (d, i) { - return i * cellSize; - }); - } - }, - - // selection of cells - _addSelectionTool: function() { - // - // selection - // - var sa=d3.select('.g3') - .on('mousedown', function() { - if( !d3.event.altKey) { - d3.selectAll('.cell-selected').classed('cell-selected', false); - d3.selectAll('.rowLabel').classed('text-selected', false); - d3.selectAll('.colLabel').classed('text-selected', false); - } - var p = d3.mouse(this); - sa.append('rect') - .attr({ - rx : 0, - ry : 0, - class : 'selection', - x : p[0], - y : p[1], - width : 1, - height : 1 - }) - }) - .on('mousemove', function() { - var s = sa.select('rect.selection'); - - if(!s.empty()) { - var p = d3.mouse(this), - d = { - x : parseInt(s.attr('x'), 10), - y : parseInt(s.attr('y'), 10), - width : parseInt(s.attr('width'), 10), - height : parseInt(s.attr('height'), 10) - }, - move = { - x : p[0] - d.x, - y : p[1] - d.y - }; - - if(move.x < 1 || (move.x*2<d.width)) { - d.x = p[0]; - d.width -= move.x; - } else { - d.width = move.x; - } - - if(move.y < 1 || (move.y*2<d.height)) { - d.y = p[1]; - d.height -= move.y; - } else { - d.height = move.y; - } - s.attr(d); - - // deselect all temporary selected state objects - d3.selectAll('.cell-selection.cell-selected').classed('cell-selected', false); - d3.selectAll('.text-selection.text-selected').classed('text-selected',false); - d3.selectAll('.cell').filter(function(cell_d, i) { - if(!d3.select(this).classed('cell-selected') && - // inner circle inside selection frame - (this.x.baseVal.value)+cellSize >= d.x && (this.x.baseVal.value)<=d.x+d.width && - (this.y.baseVal.value)+cellSize >= d.y && (this.y.baseVal.value)<=d.y+d.height) - { - d3.select(this) - .classed('cell-selection', true) - .classed('cell-selected', true); - - d3.select('.r' + cell_d.row) - .classed('text-selection',true) - .classed('text-selected',true); - - d3.select('.c' + cell_d.col) - .classed('text-selection',true) - .classed('text-selected',true); - } - }); - } - }) - .on('mouseup', function() { - // remove selection frame - sa.selectAll('rect.selection').remove(); - - // remove temporary selection marker class - d3.selectAll('.cell-selection').classed('cell-selection', false); - d3.selectAll('.text-selection').classed('text-selection', false); - }) - .on('mouseout', function() { - if(d3.event.relatedTarget.tagName=='html') { - // remove selection frame - sa.selectAll('rect.selection').remove(); - - // remove temporary selection marker class - d3.selectAll('.cell-selection').classed('cell-selection', false); - d3.selectAll('.rowLabel').classed('text-selected',false); - d3.selectAll('.colLabel').classed('text-selected',false); - } - }); - }, - - // template - _templateSelect: function() { - return '<select id="order">' + - '<option value="hclust">Cluster</option>' + - '<option value="byboth">Sort by row and column</option>' + - '<option value="byrow">Sort by row label</option>' + - '<option value="bycol">Sort by column label</option>' + - '</select>'; - }, - - // template - _templateTooltip: function() { - return '<div id="heatmap-tooltip" class="hidden">' + - '<p><span id="value"></p>' - '</div>'; - } -}); -}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/logo.png Binary file config/plugins/visualizations/charts/static/charts/heatmap/logo.png has changed diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js +++ /dev/null @@ -1,86 +0,0 @@ -// dependencies -define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin', 'plugin/charts/heatmap/heatmap-parameters'], -function(Utils, HeatmapPlugin, HeatmapParameters) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - // link this - var self = this; - - // loop through data groups - var index = 0; - for (var group_index in request_dictionary.groups) { - - // configure request - var tmp_dict = { - id : request_dictionary.id, - groups : [{ - key : request_dictionary.groups[group_index].key, - columns : { - row_label: { - index : index++, - is_label : true - }, - col_label: { - index : index++, - is_label : true - }, - value: { - index : index++ - } - } - }] - }; - - // target div - var group_div = self.options.canvas[group_index]; - - // draw group - this._draw_group(group_index, group_div, chart, tmp_dict, function(group_index) { - if (group_index == request_dictionary.groups.length - 1) { - // set chart state - chart.state('ok', 'Heat map drawn.'); - - // unregister process - chart.deferred.done(process_id); - } - }); - } - }, - - // draw group - _draw_group: function(group_index, div, chart, request_dictionary, callback) { - // link this - var self = this; - - // request data - this.app.datasets.request(request_dictionary, function() { - - // get group - var group = request_dictionary.groups[0]; - - // draw plot - var heatmap = new HeatmapPlugin({ - 'title' : group.key, - 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], - 'data' : group.values, - 'div' : div - }); - - // callback on completion - callback (group_index); - }); - } -}); - -}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js +++ /dev/null @@ -1,40 +0,0 @@ -define([], function() { - -return { - title : 'Box plot', - category : 'Data processing (requires \'charts\' tool from Toolshed)', - library : 'highcharts.js', - tag : 'div', - execute : 'boxplot', - columns : { - y : { - title : 'Observations' - } - }, - settings : { - separator_label : { - title : 'X axis', - type : 'separator' - }, - x_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'X-axis', - placeholder : 'Axis label' - }, - separator_tick : { - title : 'Y axis', - type : 'separator' - }, - y_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'Y-axis', - placeholder : 'Axis label' - } - } -}; - -}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png has changed diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js +++ /dev/null @@ -1,122 +0,0 @@ -// dependencies -define(['utils/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // highcharts configuration - hc_config : { - chart: { - type: 'boxplot' - }, - - title: { - text: '' - }, - - legend: { - enabled: false - }, - - credits: { - enabled: false - }, - - plotOptions: { - series: { - animation: false - } - }, - - xAxis: { - categories: [], - title: { - text: '' - } - }, - - yAxis: { - title: { - text: '' - } - }, - - series: [{ - name: 'Details:', - data: [], - tooltip: { - headerFormat: '<em>{point.key}</em><br/>' - } - }] - }, - - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - // configure request - var index = 0; - for (var i in request_dictionary.groups) { - var group = request_dictionary.groups[i]; - group.columns = null; - group.columns = { - x: { - index: index++ - } - } - } - - // set axis labels - this.hc_config.xAxis.title.text = chart.settings.get('x_axis_label'); - this.hc_config.yAxis.title.text = chart.settings.get('y_axis_label'); - - // request data - var self = this; - this.app.datasets.request(request_dictionary, function() { - - // reset data/categories - var data = []; - var categories = []; - - // loop through data groups - for (var key in request_dictionary.groups) { - // get group - var group = request_dictionary.groups[key]; - - // add category - categories.push(group.key); - - // format chart data - var point = []; - for (var key in group.values) { - point.push(group.values[key].x); - } - - // add to data - data.push (point); - } - - // categories - self.hc_config.xAxis.categories = categories; - - // update data - self.hc_config.series[0].data = data; - - // draw plot - self.options.canvas[0].highcharts(self.hc_config); - - // set chart state - chart.state('ok', 'Box plot drawn.'); - - // unregister process - chart.deferred.done(process_id); - }); - } -}); - -}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js @@ -0,0 +1,20 @@ +define(['plugin/charts/jqplot/common/config'], function(plot_config) { + +return $.extend(true, {}, plot_config, { + title : 'Regular', + category : 'Bar diagrams', + columns : { + x : { + title : 'Values for x-axis', + is_label : true, + is_auto : true, + is_unique : true + }, + y : { + title : 'Values for y-axis', + is_numeric : true + } + } +}); + +}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png Binary file config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png has changed diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js @@ -0,0 +1,26 @@ +// dependencies +define(['plugin/charts/jqplot/common/wrapper'], function(Plot) { + +// widget +return Backbone.Model.extend({ + initialize: function(app, options) { + options.makeConfig = function(groups, plot_config){ + $.extend(true, plot_config, { + seriesDefaults: { + renderer : $.jqplot.BarRenderer + }, + axes: { + xaxis: { + min : -1 + }, + yaxis: { + pad : 1.2 + } + } + }); + }; + new Plot(app, options); + } +}); + +}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js @@ -0,0 +1,23 @@ +define(['plugin/charts/jqplot/common/config'], function(plot_config) { + +return $.extend(true, {}, plot_config, { + title : 'Box plot', + category : 'Data processing (requires \'charts\' tool from Toolshed)', + library : 'jqPlot', + tag : 'div', + execute : 'boxplot', + keywords : 'small medium large', + columns : { + y : { + title : 'Observations', + is_numeric : true + } + }, + settings : { + show_legend : { + init : 'false' + } + } +}); + +}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png Binary file config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png has changed diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js @@ -0,0 +1,127 @@ +// dependencies +define(['plugin/charts/jqplot/common/wrapper', 'plugin/charts/tools'], function(Plot, Tools) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + // get request dictionary + var request_dictionary = options.request_dictionary; + var chart = options.chart; + + // modify request + var index = 0; + for (var i in request_dictionary.groups) { + var group = request_dictionary.groups[i]; + group.columns = null; + group.columns = { + x: { + index: index++ + } + } + } + + // create plot + var plot = new Plot(app, { + process_id : options.process_id, + chart : options.chart, + request_dictionary : options.request_dictionary, + canvas_list : options.canvas_list, + makeConfig : function(groups, plot_config){ + var boundary = Tools.getDomains(groups, 'x'); + $.extend(true, plot_config, { + seriesDefaults: { + renderer: $.jqplot.OHLCRenderer, + rendererOptions : { + candleStick : true, + fillUpBody : true, + fillDownBody : true + } + }, + axes : { + xaxis: { + min: -1, + max: groups.length + 0.01 + }, + yaxis: { + min: boundary.x.min, + max: boundary.x.max + } + } + }); + }, + makeCategories: function(groups) { + // define custom category labels + var x_labels = []; + for (var group_index in groups) { + x_labels.push(groups[group_index].key); + } + + // use default mapping + Tools.mapCategories (groups, x_labels); + + // return labels array for x axis + return { + array: { + x : x_labels + } + } + }, + makeSeriesLabels : function (groups, plot_config) { + return [{ + label: 'Boxplot values' + }]; + }, + makeSeries: function (groups) { + /*/ example data + var catOHLC = [ + [0, 138.7, 139.68, 135.18, 135.4], + [1, 143.46, 144.66, 139.79, 140.02], + [2, 140.67, 143.56, 132.88, 142.44], + [3, 136.01, 139.5, 134.53, 139.48] + ]; + return [catOHLC];*/ + + // plot data + var plot_data = []; + + // check group length + if (groups.length == 0 || groups[0].values.length < 5) { + chart.state('failed', 'Boxplot data could not be found.'); + return [plot_data]; + } + + // loop through data groups + var indeces = [2, 4, 0, 1]; + for (var group_index in groups) { + // get group + var group = groups[group_index]; + + // format chart data + var point = []; + point.push(parseInt(group_index)); + for (var key in indeces) { + point.push(group.values[indeces[key]].x); + } + + // add to data + plot_data.push (point); + } + + // HACK: the boxplot renderer has an issue with single elements + var point = []; + point[0] = plot_data.length; + for (var key in indeces) { + point.push(0); + } + plot_data.push (point); + + // return + return [plot_data]; + } + }); + } +}); + +}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/common/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js @@ -0,0 +1,51 @@ +define(['plugin/charts/forms/default'], function(config_default) { + +return $.extend(true, {}, config_default, { + title : '', + category : '', + library : 'jqPlot', + tag : 'div', + zoomable : true, + keywords : 'medium', + query_limit : 10000, + settings : { + separator_grid : { + title : 'Grids', + type : 'separator' + }, + x_axis_grid : { + title : 'Axis grid', + info : 'Would you like to show grid lines for the X axis?', + type : 'radiobutton', + init : 'false', + data : [ + { + label : 'On', + value : 'true' + }, + { + label : 'Off', + value : 'false' + } + ] + }, + y_axis_grid : { + title : 'Axis grid', + info : 'Would you like to show grid lines for the Y axis?', + type : 'radiobutton', + init : 'true', + data : [ + { + label : 'On', + value : 'true' + }, + { + label : 'Off', + value : 'false' + } + ] + } + } +}); + +}); \ No newline at end of file This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/8bf883f2638e/ Changeset: 8bf883f2638e Branch: stable User: guerler Date: 2014-06-24 19:50:03 Summary: Charts style update Affected #: 2 files diff -r a15c52999493cd723c114899d4224912b2c28ffc -r 8bf883f2638e1bae7a1761a0fab98a981d6fa315 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -148,7 +148,7 @@ .form-control::-moz-placeholder{color:#999} .form-control:-ms-input-placeholder{color:#999} .form-control::-webkit-input-placeholder{color:#999} -.form-control{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} +.form-control,.ui-input{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} .form-control[disabled],.form-control[readonly],fieldset[disabled] .form-control{cursor:not-allowed;background-color:#eee} textarea.form-control{height:auto} .form-group{margin-bottom:15px} @@ -1278,17 +1278,25 @@ .upload-ftp .upload-ftp-help{margin-bottom:10px} .upload-ftp .upload-ftp-warning{text-align:center;margin-top:20px} .upload-settings .upload-settings-cover{position:absolute;width:100%;height:100%;top:0px;left:0px;background:#fff;opacity:0.4;cursor:no-drop} +.ui-radiobutton label{height:23px;line-height:1em} +.ui-table-form-separator{font-weight:bold;font-size:0.9em} +.ui-label{font-weight:bold} +.ui-message{padding:2px 2px 2px 10px} +.ui-icon{font-size:1.2em} +.ui-button-icon{margin-right:5px}.ui-button-icon ul i{font-size:1.2em;margin-right:5px;position:relative;top:1px} +.ui-button-icon .button{margin-right:5px;margin-left:5px} +.ui-button-icon .title{position:relative;font-size:0.8em;font-weight:normal;top:-1px} +.ui-tabs .ui-tabs-add{font-size:0.8em;margin-right:5px} +.ui-tabs .ui-tabs-delete{font-size:0.8em;margin-left:5px;cursor:pointer} .no-highlight{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} -.portlet-view{min-width:300px}.portlet-view .portlet-title-icon{float:left;font-size:1.2em;padding-top:4px} -.portlet-view .portlet-title{overflow:hidden;padding:2px 5px 2px 10px} -.portlet-view .portlet-title-text{float:left;padding-top:2px} -.portlet-view .portlet-operations{float:right;cursor:pointer} -.portlet-view .portlet-buttons{height:50px;padding:10px} -.portlet-view .portlet-content{height:inherit;padding:10px} -.popover-view{max-width:700px;display:none}.popover-view .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer} -.popover-view .popover-title{padding:4px 10px} -.styled-select{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.styled-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;padding-left:9px;padding-top:4px;background:#f2f2f2} -.styled-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none} +.ui-portlet{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header{padding:5px 10px;background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header h1,.ui-portlet .portlet-header h2,.ui-portlet .portlet-header h3,.ui-portlet .portlet-header h4,.ui-portlet .portlet-header h5,.ui-portlet .portlet-header h6{float:left;font-weight:normal;display:inline-block;vertical-align:middle;font-size:1em;margin:3px}.ui-portlet .portlet-header h1 .icon,.ui-portlet .portlet-header h2 .icon,.ui-portlet .portlet-header h3 .icon,.ui-portlet .portlet-header h4 .icon,.ui-portlet .portlet-header h5 .icon,.ui-portlet .portlet-header h6 .icon{font-size:1.2em} +.ui-portlet .portlet-buttons{height:50px;padding:10px} +.ui-portlet .portlet-content{height:inherit;padding:10px;clear:both}.ui-portlet .portlet-content .content{padding:10px;height:100%;width:100%}.ui-portlet .portlet-content .content .buttons{height:50px;padding:10px} +.ui-portlet .no-scroll{height:calc(100% - 80px)} +.ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer} +.ui-popover .popover-title{padding:4px 10px} +.ui-select{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.ui-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;padding-left:9px;padding-top:4px;background:#f2f2f2} +.ui-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none} .libraryRow{background-color:#ebd9b2} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} @@ -1453,7 +1461,7 @@ div.form-row-input{width:90%;float:left} div.form-row-input label{font-weight:normal;display:inline} div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0} -.form-row .help,.toolParamHelp{color:#666}.form-row .help a,.toolParamHelp a{color:#666} +.form-row .help,.toolParamHelp,.ui-table-form-info{color:#666}.form-row .help a,.toolParamHelp a{color:#666} .form-row.form-actions{background:whiteSmoke;border-top:solid #ddd 1px;padding-top:10px;padding-bottom:10px;margin-top:5px} select{padding:2px;font-size:12px;line-height:1.428571429} select,input,textarea{font:inherit} @@ -1519,13 +1527,13 @@ .grid-header{padding-bottom:1em} .grid-header h2{margin:0;margin-bottom:0.5em} .grid-header .title{font-weight:bold} -.grid{padding-top:1em;border-collapse:collapse;width:100%} -.grid tbody td{line-height:1.428571429;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px} +.grid,.ui-table{padding-top:1em;border-collapse:collapse;width:100%} +.grid tbody td,.ui-table tbody td{line-height:1.428571429;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px} .grid tbody td:empty{padding:0} .grid thead tr{height:2em} .grid thead th{line-height:1.428571429;background:#ebd9b2;color:#000;border-top:solid #d6b161 1px;border-bottom:solid #d6b161 1px;padding:5px;text-align:left;white-space:nowrap} .grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px} -.grid .current{background-color:#EEEEFF} +.grid .current,.ui-table .current{background-color:#EEEEFF} .count-box{min-width:1.1em;padding:5px;border-width:1px;border-style:solid;text-align:center;display:inline-block} .text-filter-val{border:solid 1px #AAAAAA;padding:1px 2px 1px 3px;margin-right:5px;-moz-border-radius:.5em;-webkit-border-radius:.5em;font-style:italic} .page-link a,.inactive-link{padding:0px 7px 0px 7px;color:#555} diff -r a15c52999493cd723c114899d4224912b2c28ffc -r 8bf883f2638e1bae7a1761a0fab98a981d6fa315 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -1,3 +1,80 @@ +.ui-radiobutton { + label { + height: 23px; + line-height: 1em; + } +} + +.ui-table { + &:extend(.grid); + + tbody td { + &:extend(.grid tbody td); + } + .current { + &:extend(.grid .current); + } +} + +.ui-table-form-info { + &:extend(.toolParamHelp); +} + +.ui-table-form-separator { + font-weight: bold; + font-size: 0.9em; +} + +.ui-label { + font-weight: bold; +} + +.ui-message { + padding: 2px 2px 2px 10px; +} + +.ui-icon { + font-size: 1.2em; +} + +.ui-button-icon { + margin-right: 5px; + ul { + i { + font-size: 1.2em; margin-right: 5px; position: relative; top: 1px; + } + } +} + +.ui-button-icon .button { + margin-right: 5px; + margin-left: 5px; +} + +.ui-button-icon .title { + position: relative; + font-size: 0.8em; + font-weight: normal; + top: -1px; +} + +.ui-input { + &:extend(.form-control); +} + +.ui-tabs { + .ui-tabs-add { + font-size : 0.8em; + margin-right : 5px; + } + + .ui-tabs-delete { + font-size : 0.8em; + margin-left : 5px; + cursor : pointer; + } +} + .no-highlight { -webkit-user-select: none; /* webkit (safari, chrome) browsers */ -moz-user-select: none; /* mozilla browsers */ @@ -5,30 +82,38 @@ -ms-user-select: none; /* IE10+ */ } -.portlet-view { - min-width: 300px; +.ui-portlet { + border: solid @form-border 1px; + .border-radius(@panel-border-radius); - .portlet-title-icon { - float: left; - font-size: 1.2em; - padding-top: 4px; - } - - .portlet-title { - overflow: hidden; - padding: 2px 5px 2px 10px; + position: relative; + clear: both; + width: auto; + height: 100%; + + .portlet-header { + padding: 5px 10px; + background: @form-heading-bg; + border-bottom: solid @form-border 1px; + padding: 2px 8px; + overflow: visible; + float: right; + width:100%; + + h1, h2, h3, h4, h5, h6 { + float: left; + font-weight: normal; + display: inline-block; + vertical-align: middle; + font-size: 1em; + margin: 3px; + + .icon { + font-size: 1.2em; + } + } } - .portlet-title-text { - float: left; - padding-top: 2px; - } - - .portlet-operations { - float: right; - cursor: pointer; - } - .portlet-buttons { height: 50px; padding: 10px; @@ -37,10 +122,26 @@ .portlet-content { height: inherit; padding: 10px; + clear: both; + + .content { + padding : 10px; + height : 100%; + width : 100%; + + .buttons { + height: 50px; + padding: 10px; + } + } + } + + .no-scroll { + height: ~'calc(100% - 80px)'; } } -.popover-view { +.ui-popover { max-width: 700px; display: none; @@ -57,7 +158,7 @@ } } -.styled-select { +.ui-select { position: relative; height: 27px; overflow: hidden; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Handle exporting and importing repository capsules with new ExportRepositoryManager and ImportRepositoryMnager classes respectively.
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fdaad2cad392/ Changeset: fdaad2cad392 User: greg Date: 2014-06-24 19:11:24 Summary: Handle exporting and importing repository capsules with new ExportRepositoryManager and ImportRepositoryMnager classes respectively. Affected #: 10 files diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -10,14 +10,14 @@ from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import HTTPBadRequest from galaxy.web.framework.helpers import time_ago +from tool_shed.capsule import capsule_manager import tool_shed.repository_types.util as rt_util -import tool_shed.util.shed_util_common as suc from tool_shed.util import basic_util from tool_shed.util import encoding_util from tool_shed.util import hg_util -from tool_shed.util import import_util from tool_shed.util import metadata_util from tool_shed.util import repository_maintenance_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util log = logging.getLogger( __name__ ) @@ -248,10 +248,14 @@ except tarfile.ReadError, e: log.debug( 'Error opening capsule file %s: %s' % ( str( capsule_file_name ), str( e ) ) ) return {} + irm = capsule_manager.ImportRepositoryManager( trans.app, + trans.request.host, + trans.user, + trans.user_is_admin() ) capsule_dict[ 'tar_archive' ] = tar_archive capsule_dict[ 'capsule_file_name' ] = capsule_file_name - capsule_dict = import_util.extract_capsule_files( **capsule_dict ) - capsule_dict = import_util.validate_capsule( **capsule_dict ) + capsule_dict = irm.extract_capsule_files( **capsule_dict ) + capsule_dict = irm.validate_capsule( **capsule_dict ) status = capsule_dict.get( 'status', 'error' ) if status == 'error': log.debug( 'The capsule contents are invalid and cannot be imported:<br/>%s' % \ @@ -263,15 +267,12 @@ return {} file_path = encoding_util.tool_shed_decode( encoded_file_path ) export_info_file_path = os.path.join( file_path, 'export_info.xml' ) - export_info_dict = import_util.get_export_info_dict( export_info_file_path ) + export_info_dict = irm.get_export_info_dict( export_info_file_path ) manifest_file_path = os.path.join( file_path, 'manifest.xml' ) # The manifest.xml file has already been validated, so no error_message should be returned here. - repository_info_dicts, error_message = import_util.get_repository_info_from_manifest( manifest_file_path ) + repository_info_dicts, error_message = irm.get_repository_info_from_manifest( manifest_file_path ) # Determine the status for each exported repository archive contained within the capsule. - repository_status_info_dicts = import_util.get_repository_status_from_tool_shed( trans.app, - trans.user, - trans.user_is_admin(), - repository_info_dicts ) + repository_status_info_dicts = irm.get_repository_status_from_tool_shed( repository_info_dicts ) # Generate a list of repository name / import results message tuples for display after the capsule is imported. import_results_tups = [] # Only create repositories that do not yet exist and that the current user is authorized to create. The @@ -280,12 +281,9 @@ # Add the capsule_file_name and encoded_file_path to the repository_status_info_dict. repository_status_info_dict[ 'capsule_file_name' ] = capsule_file_name repository_status_info_dict[ 'encoded_file_path' ] = encoded_file_path - import_results_tups = import_util.create_repository_and_import_archive( trans.app, - trans.request.host, - trans.user, - repository_status_info_dict, - import_results_tups ) - import_util.check_status_and_reset_downloadable( trans.app, import_results_tups ) + import_results_tups = irm.create_repository_and_import_archive( repository_status_info_dict, + import_results_tups ) + irm.check_status_and_reset_downloadable( import_results_tups ) basic_util.remove_dir( file_path ) # NOTE: the order of installation is defined in import_results_tups, but order will be lost # when transferred to return_dict. diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -5,7 +5,7 @@ from galaxy import util from galaxy.model.orm import and_, not_, select from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest -from tool_shed.util import export_util +from tool_shed.capsule import capsule_manager from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc @@ -53,15 +53,14 @@ log.debug( error_message ) return None, error_message repository_id = trans.security.encode_id( repository.id ) - return export_util.export_repository( trans.app, - trans.user, - tool_shed_url, - repository_id, - str( repository.name ), - changeset_revision, - file_type, - export_repository_dependencies, - api=True ) + erm = capsule_manager.ExportRepositoryManager( app=trans.app, + user=trans.user, + tool_shed_url=tool_shed_url, + repository=repository, + changeset_revision=changeset_revision, + export_repository_dependencies=export_repository_dependencies, + using_api=True ) + return erm.export_repository() def __get_value_mapper( self, trans ): value_mapper = { 'id' : trans.security.encode_id, diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -14,20 +14,19 @@ from galaxy.web.framework.helpers import grids from galaxy.util import json from galaxy.model.orm import and_ -import tool_shed.util.shed_util_common as suc +from tool_shed.capsule import capsule_manager from tool_shed.util import basic_util from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import encoding_util -from tool_shed.util import export_util from tool_shed.util import hg_util -from tool_shed.util import import_util from tool_shed.util import metadata_util from tool_shed.util import readme_util from tool_shed.util import repository_dependency_util from tool_shed.util import repository_maintenance_util from tool_shed.util import review_util from tool_shed.util import search_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import workflow_util @@ -1149,7 +1148,7 @@ # server account's .hgrc file to include the following setting: # [web] # allow_archive = bz2, gz, zip - file_type_str = export_util.get_file_type_str( changeset_revision, file_type ) + file_type_str = basic_util.get_file_type_str( changeset_revision, file_type ) repository.times_downloaded += 1 trans.sa_session.add( repository ) trans.sa_session.flush() @@ -1172,15 +1171,14 @@ file_type = 'gz' export_repository_dependencies = CheckboxField.is_checked( export_repository_dependencies ) tool_shed_url = web.url_for( '/', qualified=True ) - repositories_archive, error_message = export_util.export_repository( trans.app, - trans.user, - tool_shed_url, - repository_id, - str( repository.name ), - changeset_revision, - file_type, - export_repository_dependencies, - api=False ) + erm = capsule_manager.ExportRepositoryManager( app=trans.app, + user=trans.user, + tool_shed_url=tool_shed_url, + repository=repository, + changeset_revision=changeset_revision, + export_repository_dependencies=export_repository_dependencies, + using_api=False ) + repositories_archive, error_message = erm.export_repository() repositories_archive_filename = os.path.basename( repositories_archive.name ) if error_message: message = error_message @@ -1969,15 +1967,16 @@ encoded_file_path = kwd.get( 'encoded_file_path', None ) file_path = encoding_util.tool_shed_decode( encoded_file_path ) export_info_file_path = os.path.join( file_path, 'export_info.xml' ) - export_info_dict = import_util.get_export_info_dict( export_info_file_path ) + irm = capsule_manager.ImportRepositoryManager( trans.app, + trans.request.host, + trans.user, + trans.user_is_admin() ) + export_info_dict = irm.get_export_info_dict( export_info_file_path ) manifest_file_path = os.path.join( file_path, 'manifest.xml' ) # The manifest.xml file has already been validated, so no error_message should be returned here. - repository_info_dicts, error_message = import_util.get_repository_info_from_manifest( manifest_file_path ) + repository_info_dicts, error_message = irm.get_repository_info_from_manifest( manifest_file_path ) # Determine the status for each exported repository archive contained within the capsule. - repository_status_info_dicts = import_util.get_repository_status_from_tool_shed( trans.app, - trans.user, - trans.user_is_admin(), - repository_info_dicts ) + repository_status_info_dicts = irm.get_repository_status_from_tool_shed( repository_info_dicts ) if 'import_capsule_button' in kwd: # Generate a list of repository name / import results message tuples for display after the capsule is imported. import_results_tups = [] @@ -1987,12 +1986,9 @@ # Add the capsule_file_name and encoded_file_path to the repository_status_info_dict. repository_status_info_dict[ 'capsule_file_name' ] = capsule_file_name repository_status_info_dict[ 'encoded_file_path' ] = encoded_file_path - import_results_tups = import_util.create_repository_and_import_archive( trans.app, - trans.request.host, - trans.user, - repository_status_info_dict, - import_results_tups ) - import_util.check_status_and_reset_downloadable( trans.app, import_results_tups ) + import_results_tups = irm.create_repository_and_import_archive( repository_status_info_dict, + import_results_tups ) + irm.check_status_and_reset_downloadable( import_results_tups ) basic_util.remove_dir( file_path ) return trans.fill_template( '/webapps/tool_shed/repository/import_capsule_results.mako', export_info_dict=export_info_dict, @@ -3081,13 +3077,17 @@ status = kwd.get( 'status', 'done' ) url = kwd.get( 'url', '' ) if 'upload_capsule_button' in kwd: - capsule_dict = import_util.upload_capsule( **kwd ) + irm = capsule_manager.ImportRepositoryManager( trans.app, + trans.request.host, + trans.user, + trans.user_is_admin() ) + capsule_dict = irm.upload_capsule( **kwd ) status = capsule_dict.get( 'status', 'error' ) if status == 'error': message = capsule_dict.get( 'error_message', '' ) else: - capsule_dict = import_util.extract_capsule_files( **capsule_dict ) - capsule_dict = import_util.validate_capsule( **capsule_dict ) + capsule_dict = irm.extract_capsule_files( **capsule_dict ) + capsule_dict = irm.validate_capsule( **capsule_dict ) status = capsule_dict.get( 'status', 'error' ) if status == 'ok': return trans.response.send_redirect( web.url_for( controller='repository', diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/capsule/capsule_manager.py --- /dev/null +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -0,0 +1,867 @@ +import logging +import os +import shutil +import tarfile +import tempfile +import threading +import urllib +from time import gmtime +from time import strftime +import tool_shed.repository_types.util as rt_util +from galaxy import web +from galaxy.util import asbool +from galaxy.util import CHUNK_SIZE +from galaxy.util.odict import odict +from tool_shed.dependencies import dependency_manager +from tool_shed.util import basic_util +from tool_shed.util import commit_util +from tool_shed.util import common_util +from tool_shed.util import encoding_util +from tool_shed.util import hg_util +from tool_shed.util import metadata_util +from tool_shed.util import repository_dependency_util +from tool_shed.util import repository_maintenance_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util +from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager + +log = logging.getLogger( __name__ ) + + +class ExportedRepositoryRegistry( object ): + + def __init__( self ): + self.exported_repository_elems = [] + +class ExportRepositoryManager( object ): + + def __init__( self, app, user, tool_shed_url, repository, changeset_revision, export_repository_dependencies, using_api ): + self.app = app + self.capsule_filename = 'capsule' + self.capsule_with_dependencies_filename = 'capsule_with_dependencies' + self.changeset_revision = changeset_revision + self.export_repository_dependencies = asbool( export_repository_dependencies ) + self.file_type = 'gz' + self.repository = repository + self.repository_id = self.app.security.encode_id( repository.id ) + self.tool_shed_url = tool_shed_url + self.user = user + self.using_api = using_api + + def export_repository( self ): + repositories_archive_filename = self.generate_repository_archive_filename( use_tmp_archive_dir=True ) + if self.export_repository_dependencies: + repo_info_dicts = self.get_repo_info_dicts() + repository_ids = self.get_repository_ids( repo_info_dicts ) + ordered_repository_ids, ordered_repositories, ordered_changeset_revisions = \ + self.order_components_for_import( repository_ids, repo_info_dicts ) + else: + ordered_repository_ids = [] + ordered_repositories = [] + ordered_changeset_revisions = [] + if self.repository: + repository_metadata = \ + suc.get_current_repository_metadata_for_changeset_revision( self.app, + self.repository, + self.changeset_revision ) + if repository_metadata: + ordered_repository_ids = [ self.repository_id ] + ordered_repositories = [ self.repository ] + ordered_changeset_revisions = [ repository_metadata.changeset_revision ] + repositories_archive = None + error_messages = '' + lock = threading.Lock() + lock.acquire( True ) + try: + repositories_archive = tarfile.open( repositories_archive_filename, "w:%s" % self.file_type ) + exported_repository_registry = ExportedRepositoryRegistry() + for index, repository_id in enumerate( ordered_repository_ids ): + work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-export-er" ) + ordered_repository = ordered_repositories[ index ] + ordered_changeset_revision = ordered_changeset_revisions[ index ] + repository_archive, error_message = self.generate_repository_archive( ordered_repository, + ordered_changeset_revision, + work_dir ) + if error_message: + error_messages = '%s %s' % ( error_messages, error_message ) + else: + archive_name = str( os.path.basename( repository_archive.name ) ) + repositories_archive.add( repository_archive.name, arcname=archive_name ) + attributes, sub_elements = self.get_repository_attributes_and_sub_elements( ordered_repository, + archive_name ) + elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) + exported_repository_registry.exported_repository_elems.append( elem ) + basic_util.remove_dir( work_dir ) + # Keep information about the export in a file named export_info.xml in the archive. + sub_elements = self.generate_export_elem() + export_elem = xml_util.create_element( 'export_info', attributes=None, sub_elements=sub_elements ) + tmp_export_info = xml_util.create_and_write_tmp_file( export_elem, use_indent=True ) + repositories_archive.add( tmp_export_info, arcname='export_info.xml' ) + # Write the manifest, which must preserve the order in which the repositories should be imported. + exported_repository_root = xml_util.create_element( 'repositories' ) + for exported_repository_elem in exported_repository_registry.exported_repository_elems: + exported_repository_root.append( exported_repository_elem ) + tmp_manifest = xml_util.create_and_write_tmp_file( exported_repository_root, use_indent=True ) + repositories_archive.add( tmp_manifest, arcname='manifest.xml' ) + except Exception, e: + log.exception( str( e ) ) + finally: + lock.release() + if repositories_archive is not None: + repositories_archive.close() + if self.using_api: + encoded_repositories_archive_name = encoding_util.tool_shed_encode( repositories_archive_filename ) + params = '?encoded_repositories_archive_name=%s' % encoded_repositories_archive_name + download_url = common_util.url_join( web.url_for( '/', qualified=True ), + 'repository/export_via_api%s' % params ) + return dict( download_url=download_url, error_messages=error_messages ) + return repositories_archive, error_messages + + def generate_export_elem( self ): + sub_elements = odict() + sub_elements[ 'export_time' ] = strftime( '%a, %d %b %Y %H:%M:%S +0000', gmtime() ) + sub_elements[ 'tool_shed' ] = str( self.tool_shed_url.rstrip( '/' ) ) + sub_elements[ 'repository_name' ] = str( self.repository.name ) + sub_elements[ 'repository_owner' ] = str( self.repository.user.username ) + sub_elements[ 'changeset_revision' ] = str( self.changeset_revision ) + sub_elements[ 'export_repository_dependencies' ] = str( self.export_repository_dependencies ) + sub_elements[ 'exported_via_api' ] = str( self.using_api ) + return sub_elements + + def generate_repository_archive( self, repository, changeset_revision, work_dir ): + rdah = dependency_manager.RepositoryDependencyAttributeHandler( self.app, unpopulate=True ) + tdah = dependency_manager.ToolDependencyAttributeHandler( self.app, unpopulate=True ) + file_type_str = basic_util.get_file_type_str( changeset_revision, self.file_type ) + file_name = '%s-%s' % ( repository.name, file_type_str ) + return_code, error_message = hg_util.archive_repository_revision( self.app, + repository, + work_dir, + changeset_revision ) + if return_code: + return None, error_message + repository_archive_name = os.path.join( work_dir, file_name ) + # Create a compressed tar archive that will contain only valid files and possibly altered dependency definition files. + repository_archive = tarfile.open( repository_archive_name, "w:%s" % self.file_type ) + for root, dirs, files in os.walk( work_dir ): + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: + for dir in dirs: + if dir in commit_util.UNDESIRABLE_DIRS: + dirs.remove( dir ) + for name in files: + name = str( name ) + if str( name ) in commit_util.UNDESIRABLE_FILES: + continue + full_path = os.path.join( root, name ) + relative_path = full_path.replace( work_dir, '' ).lstrip( '/' ) + # See if we have a repository dependencies defined. + if name == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: + # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. + altered, root_elem, error_message = rdah.handle_tag_attributes( full_path ) + if error_message: + return None, error_message + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True ) + shutil.move( tmp_filename, full_path ) + elif name == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: + # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. + altered, root_elem, error_message = tdah.handle_tag_attributes( full_path ) + if error_message: + return None, error_message + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True ) + shutil.move( tmp_filename, full_path ) + repository_archive.add( full_path, arcname=relative_path ) + repository_archive.close() + return repository_archive, error_message + + def generate_repository_archive_filename( self, use_tmp_archive_dir=False ): + tool_shed = self.remove_protocol_from_tool_shed_url() + file_type_str = basic_util.get_file_type_str( self.changeset_revision, self.file_type ) + if self.export_repository_dependencies: + repositories_archive_filename = '%s_%s_%s_%s_%s' % ( self.capsule_with_dependencies_filename, + tool_shed, + str( self.repository.name ), + str( self.repository.user.username ), + file_type_str ) + else: + repositories_archive_filename = '%s_%s_%s_%s_%s' % ( self.capsule_filename, + tool_shed, + str( self.repository.name ), + str( self.repository.user.username ), + file_type_str ) + if use_tmp_archive_dir: + tmp_archive_dir = tempfile.mkdtemp( prefix="tmp-toolshed-arcdir" ) + repositories_archive_filename = os.path.join( tmp_archive_dir, repositories_archive_filename ) + return repositories_archive_filename + + def get_components_from_repo_info_dict( self, repo_info_dict ): + """ + Return the repository and the associated latest installable changeset_revision (including + # updates) for the repository defined by the received repo_info_dict. + """ + for repository_name, repo_info_tup in repo_info_dict.items(): + # There should only be one entry in the received repo_info_dict. + description, \ + repository_clone_url, \ + changeset_revision, \ + ctx_rev, \ + repository_owner, \ + repository_dependencies, \ + tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tup ) + repository = suc.get_repository_by_name_and_owner( self.app, repository_name, repository_owner ) + repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( self.app, + repository, + changeset_revision ) + if repository_metadata: + return repository, repository_metadata.changeset_revision + return None, None + + def get_repo_info_dict_for_import( self, encoded_repository_id, encoded_repository_ids, repo_info_dicts ): + """ + The received encoded_repository_ids and repo_info_dicts are lists that contain associated + elements at each location in the list. This method will return the element from repo_info_dicts + associated with the received encoded_repository_id by determining its location in the received + encoded_repository_ids list. + """ + for index, repository_id in enumerate( encoded_repository_ids ): + if repository_id == encoded_repository_id: + repo_info_dict = repo_info_dicts[ index ] + return repo_info_dict + return None + + def get_repo_info_dicts( self ): + """ + Return a list of dictionaries defining repositories that are required by the repository + associated with self.repository_id. + """ + rdm = RepositoryDependencyManager( self.app ) + repository = suc.get_repository_in_tool_shed( self.app, self.repository_id ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + self.repository_id, + self.changeset_revision ) + # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. + toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) + repository_dependencies = \ + repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=self.app, + repository=self.repository, + repository_metadata=repository_metadata, + toolshed_base_url=toolshed_base_url, + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None ) + repo = hg_util.get_repo_for_repository( self.app, + repository=self.repository, + repo_path=None, + create=False ) + ctx = hg_util.get_changectx_for_changeset( repo, self.changeset_revision ) + repo_info_dict = {} + # Cast unicode to string. + repo_info_dict[ str( repository.name ) ] = ( str( self.repository.description ), + common_util.generate_clone_url_for_repository_in_tool_shed( self.user, + self.repository ), + str( self.changeset_revision ), + str( ctx.rev() ), + str( self.repository.user.username ), + repository_dependencies, + None ) + all_required_repo_info_dict = rdm.get_required_repo_info_dicts( self.tool_shed_url, [ repo_info_dict ] ) + all_repo_info_dicts = all_required_repo_info_dict.get( 'all_repo_info_dicts', [] ) + return all_repo_info_dicts + + def get_repository_attributes_and_sub_elements( self, repository, archive_name ): + """ + Get the information about a repository to create and populate an XML tag set. The + generated attributes will be contained within the <repository> tag, while the sub_elements + will be tag sets contained within the <repository> tag set. + """ + attributes = odict() + sub_elements = odict() + attributes[ 'name' ] = str( repository.name ) + attributes[ 'type' ] = str( repository.type ) + # We have to associate the public username since the user_id will be different between tool sheds. + attributes[ 'username' ] = str( repository.user.username ) + # Don't coerce description or long description from unicode to string because the fields are free text. + sub_elements[ 'description' ] = repository.description + sub_elements[ 'long_description' ] = repository.long_description + sub_elements[ 'archive' ] = archive_name + # Keep track of Category associations. + categories = [] + for rca in repository.categories: + category = rca.category + categories.append( ( 'category', str( category.name ) ) ) + sub_elements[ 'categories' ] = categories + return attributes, sub_elements + + def get_repository_ids( self, repo_info_dicts ): + """Return a list of repository ids associated with each dictionary in the received repo_info_dicts.""" + repository_ids = [] + for repo_info_dict in repo_info_dicts: + for repository_name, repo_info_tup in repo_info_dict.items(): + description, \ + repository_clone_url, \ + changeset_revision, \ + ctx_rev, \ + repository_owner, \ + repository_dependencies, \ + tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tup ) + repository = suc.get_repository_by_name_and_owner( self.app, repository_name, repository_owner ) + repository_ids.append( self.app.security.encode_id( repository.id ) ) + return repository_ids + + def order_components_for_import( self, repository_ids, repo_info_dicts ): + """ + Some repositories may have repository dependencies that must be imported and have metadata set on + them before the dependent repository is imported. This method will inspect the list of repositories + about to be exported and make sure to order them appropriately for proper import. For each repository + about to be exported, if required repositories are not contained in the list of repositories about to + be exported, then they are not considered. Repository dependency definitions that contain circular + dependencies should not result in an infinite loop, but obviously ordering the list will not be handled + for one or more of the repositories that require prior import. + """ + # The received list of repository_ids are the ids of all of the primary exported repository's + # repository dependencies. The primary repository will always be last in the returned lists. + ordered_repository_ids = [] + ordered_repositories = [] + ordered_changeset_revisions = [] + # Create a dictionary whose keys are the received repository_ids and whose values are a list of + # repository_ids, each of which is contained in the received list of repository_ids and whose associated + # repository must be imported prior to the repository associated with the repository_id key. + prior_import_required_dict = suc.get_prior_import_or_install_required_dict( self.app, + repository_ids, + repo_info_dicts ) + processed_repository_ids = [] + # Process the list of repository dependencies defined for the primary exported repository. + while len( processed_repository_ids ) != len( prior_import_required_dict.keys() ): + repository_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_import_required_dict, + processed_repository_ids ) + if repository_id == self.repository_id: + # Append self.repository_id without processing it since it must be returned last in the order. + # It will be processed below after all dependencies are processed. + processed_repository_ids.append( self.repository_id ) + continue + processed_repository_ids.append( repository_id ) + if repository_id not in ordered_repository_ids: + prior_import_required_ids = prior_import_required_dict[ repository_id ] + for prior_import_required_id in prior_import_required_ids: + if prior_import_required_id not in ordered_repository_ids: + # Import the associated repository dependency first. + prior_repo_info_dict = \ + self.get_repo_info_dict_for_import( prior_import_required_id, + repository_ids, + repo_info_dicts ) + prior_repository, prior_import_changeset_revision = \ + self.get_components_from_repo_info_dict( prior_repo_info_dict ) + if prior_repository and prior_import_changeset_revision: + ordered_repository_ids.append( prior_import_required_id ) + ordered_repositories.append( prior_repository ) + ordered_changeset_revisions.append( prior_import_changeset_revision ) + repo_info_dict = self.get_repo_info_dict_for_import( repository_id, repository_ids, repo_info_dicts ) + repository, changeset_revision = self.get_components_from_repo_info_dict( repo_info_dict ) + if repository and changeset_revision: + ordered_repository_ids.append( repository_id ) + ordered_repositories.append( repository ) + ordered_changeset_revisions.append( changeset_revision ) + # Process the repository associated with self.repository_id last. + repo_info_dict = self.get_repo_info_dict_for_import( self.repository_id, repository_ids, repo_info_dicts ) + repository, changeset_revision = self.get_components_from_repo_info_dict( repo_info_dict ) + if repository and changeset_revision: + ordered_repository_ids.append( repository_id ) + ordered_repositories.append( repository ) + ordered_changeset_revisions.append( changeset_revision ) + return ordered_repository_ids, ordered_repositories, ordered_changeset_revisions + + def remove_protocol_from_tool_shed_url( self ): + protocol, base = self.tool_shed_url.split( '://' ) + base = base.replace( ':', '_colon_' ) + base = base.rstrip( '/' ) + return base + + +class ImportRepositoryManager( object ): + + def __init__( self, app, host, user, user_is_admin ): + self.app = app + self.host = host + self.user = user + self.user_is_admin = user_is_admin + + def check_status_and_reset_downloadable( self, import_results_tups ): + """Check the status of each imported repository and set downloadable to False if errors.""" + sa_session = self.app.model.context.current + flush = False + for import_results_tup in import_results_tups: + ok, name_owner, message = import_results_tup + name, owner = name_owner + if not ok: + repository = suc.get_repository_by_name_and_owner( self.app, name, owner ) + if repository is not None: + # Do not allow the repository to be automatically installed if population resulted in errors. + tip_changeset_revision = repository.tip( self.app ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + self.app.security.encode_id( repository.id ), + tip_changeset_revision ) + if repository_metadata: + if repository_metadata.downloadable: + repository_metadata.downloadable = False + sa_session.add( repository_metadata ) + if not flush: + flush = True + # Do not allow dependent repository revisions to be automatically installed if population + # resulted in errors. + dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( self.app, repository_metadata ) + for dependent_downloadable_revision in dependent_downloadable_revisions: + if dependent_downloadable_revision.downloadable: + dependent_downloadable_revision.downloadable = False + sa_session.add( dependent_downloadable_revision ) + if not flush: + flush = True + if flush: + sa_session.flush() + + def create_repository_and_import_archive( self, repository_archive_dict, import_results_tups ): + """ + Create a new repository in the tool shed and populate it with the contents of a gzip compressed + tar archive that was exported as part or all of the contents of a capsule. + """ + results_message = '' + name = repository_archive_dict.get( 'name', None ) + username = repository_archive_dict.get( 'owner', None ) + if name is None or username is None: + ok = False + results_message += 'Import failed: required repository name <b>%s</b> or owner <b>%s</b> is missing.' % \ + ( str( name ), str( username )) + import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) + else: + status = repository_archive_dict.get( 'status', None ) + if status is None: + # The repository does not yet exist in this Tool Shed and the current user is authorized to import + # the current archive file. + type = repository_archive_dict.get( 'type', 'unrestricted' ) + description = repository_archive_dict.get( 'description', '' ) + long_description = repository_archive_dict.get( 'long_description', '' ) + # The owner entry in the repository_archive_dict is the public username of the user associated with + # the exported repository archive. + user = suc.get_user_by_username( self.app, username ) + if user is None: + ok = False + results_message += 'Import failed: repository owner <b>%s</b> does not have an account in this Tool Shed.' % \ + str( username ) + import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) + else: + user_id = user.id + # The categories entry in the repository_archive_dict is a list of category names. If a name does not + # exist in the current Tool Shed, the category will not be created, so it will not be associated with + # the repository. + category_ids = [] + category_names = repository_archive_dict.get( 'category_names', [] ) + for category_name in category_names: + category = suc.get_category_by_name( self.app, category_name ) + if category is None: + results_message += 'This Tool Shed does not have the category <b>%s</b> so it ' % str( category_name ) + results_message += 'will not be associated with this repository.' + else: + category_ids.append( self.app.security.encode_id( category.id ) ) + # Create the repository record in the database. + repository, create_message = repository_maintenance_util.create_repository( self.app, + name, + type, + description, + long_description, + user_id=user_id, + category_ids=category_ids ) + if create_message: + results_message += create_message + # Populate the new repository with the contents of exported repository archive. + results_dict = self.import_repository_archive( repository, repository_archive_dict ) + ok = results_dict.get( 'ok', False ) + error_message = results_dict.get( 'error_message', '' ) + if error_message: + results_message += error_message + import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) + else: + # The repository either already exists in this Tool Shed or the current user is not authorized to create it. + ok = True + results_message += 'Import not necessary: repository status for this Tool Shed is: %s.' % str( status ) + import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) + return import_results_tups + + def extract_capsule_files( self, **kwd ): + """ + Extract the uploaded capsule archive into a temporary location for inspection, validation + and potential import. + """ + return_dict = {} + tar_archive = kwd.get( 'tar_archive', None ) + capsule_file_name = kwd.get( 'capsule_file_name', None ) + if tar_archive is not None and capsule_file_name is not None: + return_dict.update( kwd ) + extract_directory_path = tempfile.mkdtemp( prefix="tmp-capsule-ecf" ) + if capsule_file_name.endswith( '.tar.gz' ): + extract_directory_name = capsule_file_name.replace( '.tar.gz', '' ) + elif capsule_file_name.endswith( '.tar' ): + extract_directory_name = capsule_file_name.replace( '.tar', '' ) + else: + extract_directory_name = capsule_file_name + file_path = os.path.join( extract_directory_path, extract_directory_name ) + return_dict[ 'encoded_file_path' ] = encoding_util.tool_shed_encode( file_path ) + tar_archive.extractall( path=file_path ) + try: + tar_archive.close() + except Exception, e: + log.exception( "Cannot close tar_archive: %s" % str( e ) ) + del return_dict[ 'tar_archive' ] + return return_dict + + def get_archives_from_manifest( self, manifest_file_path ): + """ + Return the list of archive names defined in the capsule manifest. This method will validate + the manifest by ensuring all <repository> tag sets contain a valid <archive> sub-element. + """ + archives = [] + error_message = '' + manifest_tree, error_message = xml_util.parse_xml( manifest_file_path ) + if error_message: + return archives, error_message + manifest_root = manifest_tree.getroot() + for elem in manifest_root: + # <repository name="package_lapack_3_4" type="tool_dependency_definition" username="test"> + if elem.tag != 'repository': + error_message = 'All level one sub-elements in the manifest.xml file must be <repository> tag sets. ' + error_message += 'The tag <b><%s></b> is invalid.' % str( elem.tag ) + return [], error_message + archive_file_name = None + for repository_elem in elem: + if repository_elem.tag == 'archive': + # <archive>package_lapack_3_4-9e7a45ad3522.tar.gz</archive> + archive_file_name = repository_elem.text + break + if archive_file_name is None: + error_message = 'The %s tag set is missing a required <archive> sub-element.' % str( elem.tag ) + return [], error_message + archives.append( archive_file_name ) + return archives, error_message + + def get_export_info_dict( self, export_info_file_path ): + """ + Parse the export_info.xml file contained within the capsule and return a dictionary + containing its entries. + """ + export_info_tree, error_message = xml_util.parse_xml( export_info_file_path ) + export_info_root = export_info_tree.getroot() + export_info_dict = {} + for elem in export_info_root: + if elem.tag == 'export_time': + export_info_dict[ 'export_time' ] = elem.text + elif elem.tag == 'tool_shed': + export_info_dict[ 'tool_shed' ] = elem.text + elif elem.tag == 'repository_name': + export_info_dict[ 'repository_name' ] = elem.text + elif elem.tag == 'repository_owner': + export_info_dict[ 'repository_owner' ] = elem.text + elif elem.tag == 'changeset_revision': + export_info_dict[ 'changeset_revision' ] = elem.text + elif elem.tag == 'export_repository_dependencies': + if asbool( elem.text ): + export_info_dict[ 'export_repository_dependencies' ] = 'Yes' + else: + export_info_dict[ 'export_repository_dependencies' ] = 'No' + return export_info_dict + + def get_repository_info_from_manifest( self, manifest_file_path ): + """ + Parse the capsule manifest and return a list of dictionaries containing information about + each exported repository archive contained within the capsule. + """ + repository_info_dicts = [] + manifest_tree, error_message = xml_util.parse_xml( manifest_file_path ) + if error_message: + return repository_info_dicts, error_message + manifest_root = manifest_tree.getroot() + for elem in manifest_root: + # <repository name="package_lapack_3_4" type="tool_dependency_definition" username="test"> + if elem.tag != 'repository': + error_message = 'All level one sub-elements in the manifest.xml file must be <repository> tag sets. ' + error_message += 'The tag <b><%s></b> is invalid.' % str( elem.tag ) + return [], error_message + name = elem.get( 'name', None ) + owner = elem.get( 'username', None ) + type = elem.get( 'type', None ) + if name is None or owner is None or type is None: + error_message = 'Missing required name, type, owner attributes from the tag %s' % str( elem.tag ) + return [], error_message + repository_info_dict = dict( name=name, owner=owner, type=type ) + for repository_elem in elem: + if repository_elem.tag == 'archive': + # <archive>package_lapack_3_4-9e7a45ad3522.tar.gz</archive> + archive_file_name = repository_elem.text + repository_info_dict[ 'archive_file_name' ] = archive_file_name + items = archive_file_name.split( '-' ) + changeset_revision = items[ 1 ].rstrip( '.tar.gz' ) + repository_info_dict [ 'changeset_revision' ] = changeset_revision + elif repository_elem.tag == 'categories': + category_names = [] + for category_elem in repository_elem: + if category_elem.tag == 'category': + category_names.append( category_elem.text ) + repository_info_dict[ 'category_names' ] = category_names + elif repository_elem.tag == 'description': + repository_info_dict[ 'description' ] = repository_elem.text + elif repository_elem.tag == 'long_description': + repository_info_dict[ 'long_description' ] = repository_elem.text + repository_info_dicts.append( repository_info_dict ) + return repository_info_dicts, error_message + + def get_repository_status_from_tool_shed( self, repository_info_dicts ): + """ + For each exported repository archive contained in the capsule, inspect the Tool Shed to + see if that repository already exists or if the current user is authorized to create the + repository and set a status appropriately. If repository dependencies are included in the + capsule, repositories may have various owners. We will keep repositories associated with + owners, so we need to restrict created repositories to those the current user can create. + If the current user is an admin or a member of the IUC, all repositories will be created + no matter the owner. Otherwise only repositories whose associated owner is the current + user will be created. + """ + repository_status_info_dicts = [] + for repository_info_dict in repository_info_dicts: + repository = suc.get_repository_by_name_and_owner( self.app, + repository_info_dict[ 'name' ], + repository_info_dict[ 'owner' ] ) + if repository: + if repository.deleted: + repository_info_dict[ 'status' ] = 'Exists, deleted' + elif repository.deprecated: + repository_info_dict[ 'status' ] = 'Exists, deprecated' + else: + repository_info_dict[ 'status' ] = 'Exists' + else: + # No repository with the specified name and owner currently exists, so make sure + # the current user can create one. + if self.user_is_admin: + repository_info_dict[ 'status' ] = None + elif self.app.security_agent.user_can_import_repository_archive( self.user, + repository_info_dict[ 'owner' ] ): + repository_info_dict[ 'status' ] = None + else: + repository_info_dict[ 'status' ] = 'Not authorized to import' + repository_status_info_dicts.append( repository_info_dict ) + return repository_status_info_dicts + + def import_repository_archive( self, repository, repository_archive_dict ): + """Import a repository archive contained within a repository capsule.""" + rdah = dependency_manager.RepositoryDependencyAttributeHandler( self.app, unpopulate=False ) + tdah = dependency_manager.ToolDependencyAttributeHandler( self.app, unpopulate=False ) + archive_file_name = repository_archive_dict.get( 'archive_file_name', None ) + capsule_file_name = repository_archive_dict[ 'capsule_file_name' ] + encoded_file_path = repository_archive_dict[ 'encoded_file_path' ] + file_path = encoding_util.tool_shed_decode( encoded_file_path ) + results_dict = dict( ok=True, error_message='' ) + archive_file_path = os.path.join( file_path, archive_file_name ) + archive = tarfile.open( archive_file_path, 'r:*' ) + repo_dir = repository.repo_path( self.app ) + repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) + undesirable_dirs_removed = 0 + undesirable_files_removed = 0 + ok, error_message = commit_util.check_archive( repository, archive ) + if ok: + full_path = os.path.abspath( repo_dir ) + filenames_in_archive = [] + for tarinfo_obj in archive.getmembers(): + # Check files and directories in the archive. + ok = os.path.basename( tarinfo_obj.name ) not in commit_util.UNDESIRABLE_FILES + if ok: + for file_path_item in tarinfo_obj.name.split( '/' ): + if file_path_item in commit_util.UNDESIRABLE_DIRS: + undesirable_dirs_removed += 1 + error_message = 'Import failed: invalid file path <b>%s</b> in archive <b>%s</b>' % \ + ( str( file_path_item ), str( archive_file_name ) ) + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + return results_dict + filenames_in_archive.append( tarinfo_obj.name ) + else: + undesirable_files_removed += 1 + # Extract the uploaded archive to the repository root. + archive.extractall( path=full_path ) + archive.close() + for filename in filenames_in_archive: + uploaded_file_name = os.path.join( full_path, filename ) + if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if toolshed or changeset_revision attributes + # are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) + if error_message: + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) + elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) + if error_message: + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) + commit_message = 'Imported from capsule %s' % str( capsule_file_name ) + # Send email notification to those that have registered to receive alerts for new repositories in this Tool Shed. + new_repo_alert = True + # Since the repository is new, the following must be False. + remove_repo_files_not_in_tar = False + ok, error_message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ + commit_util.handle_directory_changes( self.app, + self.host, + self.user.username, + repository, + full_path, + filenames_in_archive, + remove_repo_files_not_in_tar, + new_repo_alert, + commit_message, + undesirable_dirs_removed, + undesirable_files_removed ) + if error_message: + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + try: + status, error_message = metadata_util.set_repository_metadata_due_to_new_tip( self.app, + self.host, + self.user, + repository, + content_alert_str=content_alert_str ) + if error_message: + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + except Exception, e: + log.debug( "Error setting metadata on repository %s created from imported archive %s: %s" % \ + ( str( repository.name ), str( archive_file_name ), str( e ) ) ) + else: + archive.close() + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + return results_dict + + def upload_capsule( self, **kwd ): + """Upload and prepare an exported repository capsule for validation.""" + file_data = kwd.get( 'file_data', '' ) + url = kwd.get( 'url', '' ) + uploaded_file = None + return_dict = dict( error_message='', + encoded_file_path=None, + status='ok', + tar_archive=None, + uploaded_file=None, + capsule_file_name=None ) + if file_data == '' and url == '': + message = 'No files were entered on the import form.' + status = 'error' + elif url: + valid_url = True + try: + stream = urllib.urlopen( url ) + except Exception, e: + valid_url = False + message = 'Error importing file via http: %s' % str( e ) + status = 'error' + if valid_url: + fd, uploaded_file_name = tempfile.mkstemp() + uploaded_file = open( uploaded_file_name, 'wb' ) + while 1: + chunk = stream.read( CHUNK_SIZE ) + if not chunk: + break + uploaded_file.write( chunk ) + uploaded_file.flush() + uploaded_file_filename = url.split( '/' )[ -1 ] + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 + elif file_data not in ( '', None ): + uploaded_file = file_data.file + uploaded_file_name = uploaded_file.name + uploaded_file_filename = os.path.split( file_data.filename )[ -1 ] + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 + if uploaded_file is not None: + if isempty: + uploaded_file.close() + return_dict[ 'error_message' ] = 'Your uploaded capsule file is empty.' + return_dict[ 'status' ] = 'error' + return return_dict + try: + # Open for reading with transparent compression. + tar_archive = tarfile.open( uploaded_file_name, 'r:*' ) + except tarfile.ReadError, e: + error_message = 'Error opening file %s: %s' % ( str( uploaded_file_name ), str( e ) ) + log.exception( error_message ) + return_dict[ 'error_message' ] = error_message + return_dict[ 'status' ] = 'error' + uploaded_file.close() + return return_dict + return_dict[ 'tar_archive' ] = tar_archive + return_dict[ 'capsule_file_name' ] = uploaded_file_filename + uploaded_file.close() + else: + return_dict[ 'error_message' ] = 'No files were entered on the import form.' + return_dict[ 'status' ] = 'error' + return return_dict + return return_dict + + def validate_capsule( self, **kwd ): + """ + Inspect the uploaded capsule's manifest and its contained files to ensure it is a valid + repository capsule. + """ + capsule_dict = {} + capsule_dict.update( kwd ) + encoded_file_path = capsule_dict.get( 'encoded_file_path', '' ) + file_path = encoding_util.tool_shed_decode( encoded_file_path ) + # The capsule must contain a valid XML file named export_info.xml. + export_info_file_path = os.path.join( file_path, 'export_info.xml' ) + export_info_tree, error_message = xml_util.parse_xml( export_info_file_path ) + if error_message: + capsule_dict[ 'error_message' ] = error_message + capsule_dict[ 'status' ] = 'error' + return capsule_dict + # The capsule must contain a valid XML file named manifest.xml. + manifest_file_path = os.path.join( file_path, 'manifest.xml' ) + # Validate the capsule manifest by inspecting name, owner, changeset_revision and type + # information contained within each <repository> tag set. + repository_info_dicts, error_message = self.get_repository_info_from_manifest( manifest_file_path ) + if error_message: + capsule_dict[ 'error_message' ] = error_message + capsule_dict[ 'status' ] = 'error' + return capsule_dict + # Validate the capsule manifest by ensuring all <repository> tag sets contain a valid + # <archive> sub-element. + archives, error_message = self.get_archives_from_manifest( manifest_file_path ) + if error_message: + capsule_dict[ 'error_message' ] = error_message + capsule_dict[ 'status' ] = 'error' + return capsule_dict + # Validate the capsule manifest by ensuring each defined archive file name exists within + # the capsule. + error_message = self.verify_archives_in_capsule( file_path, archives ) + if error_message: + capsule_dict[ 'error_message' ] = error_message + capsule_dict[ 'status' ] = 'error' + return capsule_dict + capsule_dict[ 'status' ] = 'ok' + return capsule_dict + + def verify_archives_in_capsule( self, file_path, archives ): + """ + Inspect the files contained within the capsule and make sure each is defined correctly + in the capsule manifest. + """ + error_message = '' + for archive_file_name in archives: + full_path = os.path.join( file_path, archive_file_name ) + if not os.path.exists( full_path ): + error_message = 'The uploaded capsule is invalid because the contained manifest.xml ' + error_message += 'file defines an archive file named <b>%s</b> which ' % str( archive_file_name ) + error_message += 'is not contained within the capsule.' + break + return error_message diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/scripts/api/export.py --- a/lib/tool_shed/scripts/api/export.py +++ b/lib/tool_shed/scripts/api/export.py @@ -1,6 +1,7 @@ #!/usr/bin/env python """ -Export a specified repository revision and optionally all of its defined repository dependencies from the tool shed into a compressed archive. +Export a specified repository revision and optionally all of its defined repository +dependencies from the tool shed into a compressed archive. Here is a working example of how to use this script to export a repository from the tool shed. ./export.py --url http://testtoolshed.g2.bx.psu.edu --name chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d --export_repository_dependencies True --download_dir /tmp @@ -8,15 +9,45 @@ import os import sys +import tempfile import argparse import urllib2 sys.path.insert( 0, os.path.dirname( __file__ ) ) from common import display from common import submit -from tool_shed.util import export_util +from tool_shed.util import basic_util +CAPSULE_FILENAME = 'capsule' +CAPSULE_WITH_DEPENDENCIES_FILENAME = 'capsule_with_dependencies' CHUNK_SIZE = 2**20 # 1Mb +def generate_repository_archive_filename( tool_shed_url, name, owner, changeset_revision, file_type, + export_repository_dependencies, use_tmp_archive_dir=False ): + tool_shed = remove_protocol_from_tool_shed_url( tool_shed_url ) + file_type_str = basic_util.get_file_type_str( changeset_revision, file_type ) + if self.export_repository_dependencies: + repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_WITH_DEPENDENCIES_FILENAME, + tool_shed, + name, + owner, + file_type_str ) + else: + repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_FILENAME, + tool_shed, + name, + owner, + file_type_str ) + if use_tmp_archive_dir: + tmp_archive_dir = tempfile.mkdtemp( prefix="tmp-toolshed-arcdir" ) + repositories_archive_filename = os.path.join( tmp_archive_dir, repositories_archive_filename ) + return repositories_archive_filename + +def remove_protocol_from_tool_shed_url( tool_shed_url ): + protocol, base = tool_shed_url.split( '://' ) + base = base.replace( ':', '_colon_' ) + base = base.rstrip( '/' ) + return base + def string_as_bool( string ): if str( string ).lower() in ( 'true', 'yes', 'on' ): return True @@ -50,14 +81,15 @@ if error_messages: print "Error attempting to export revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner, ":\n", error_messages else: + export_repository_dependencies = string_as_bool( options.export_repository_dependencies ) repositories_archive_filename = \ - export_util.generate_repository_archive_filename( base_tool_shed_url, - options.name, - options.owner, - options.changeset_revision, - file_type, - export_repository_dependencies=string_as_bool( options.export_repository_dependencies ), - use_tmp_archive_dir=False ) + generate_repository_archive_filename( base_tool_shed_url, + options.name, + options.owner, + options.changeset_revision, + file_type, + export_repository_dependencies=export_repository_dependencies, + use_tmp_archive_dir=False ) download_url = export_dict[ 'download_url' ] download_dir = os.path.abspath( options.download_dir ) file_path = os.path.join( download_dir, repositories_archive_filename ) diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -45,6 +45,17 @@ env_var_dict[ '__is64bit__' ] = sys.maxsize > 2**32 return env_var_dict +def get_file_type_str( changeset_revision, file_type ): + if file_type == 'zip': + file_type_str = '%s.zip' % changeset_revision + elif file_type == 'bz2': + file_type_str = '%s.tar.bz2' % changeset_revision + elif file_type == 'gz': + file_type_str = '%s.tar.gz' % changeset_revision + else: + file_type_str = '' + return file_type_str + def move_file( current_dir, source, destination, rename_to=None ): source_path = os.path.abspath( os.path.join( current_dir, source ) ) source_file = os.path.basename( source_path ) diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ /dev/null @@ -1,355 +0,0 @@ -import logging -import os -import shutil -import tarfile -import tempfile -import threading -from time import gmtime -from time import strftime -import tool_shed.repository_types.util as rt_util -from galaxy import web -from galaxy.util.odict import odict -from tool_shed.dependencies import dependency_manager -from tool_shed.util import basic_util -from tool_shed.util import commit_util -from tool_shed.util import common_util -from tool_shed.util import encoding_util -from tool_shed.util import hg_util -from tool_shed.util import repository_dependency_util -from tool_shed.util import shed_util_common as suc -from tool_shed.util import xml_util -from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager - -log = logging.getLogger( __name__ ) - -CAPSULE_FILENAME = 'capsule' -CAPSULE_WITH_DEPENDENCIES_FILENAME = 'capsule_with_dependencies' - -class ExportedRepositoryRegistry( object ): - - def __init__( self ): - self.exported_repository_elems = [] - -def export_repository( app, user, tool_shed_url, repository_id, repository_name, changeset_revision, file_type, - export_repository_dependencies, api=False ): - repository = suc.get_repository_in_tool_shed( app, repository_id ) - repositories_archive_filename = generate_repository_archive_filename( tool_shed_url, - str( repository.name ), - str( repository.user.username ), - changeset_revision, - file_type, - export_repository_dependencies=export_repository_dependencies, - use_tmp_archive_dir=True ) - if export_repository_dependencies: - repo_info_dicts = get_repo_info_dicts( app, user, tool_shed_url, repository_id, changeset_revision ) - repository_ids = get_repository_ids( app, repo_info_dicts ) - ordered_repository_ids, ordered_repositories, ordered_changeset_revisions = \ - order_components_for_import( app, repository_id, repository_ids, repo_info_dicts ) - else: - ordered_repository_ids = [] - ordered_repositories = [] - ordered_changeset_revisions = [] - if repository: - repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app, - repository, - changeset_revision ) - if repository_metadata: - ordered_repository_ids = [ repository_id ] - ordered_repositories = [ repository ] - ordered_changeset_revisions = [ repository_metadata.changeset_revision ] - repositories_archive = None - error_messages = '' - lock = threading.Lock() - lock.acquire( True ) - try: - repositories_archive = tarfile.open( repositories_archive_filename, "w:%s" % file_type ) - exported_repository_registry = ExportedRepositoryRegistry() - for index, repository_id in enumerate( ordered_repository_ids ): - work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-export-er" ) - ordered_repository = ordered_repositories[ index ] - ordered_changeset_revision = ordered_changeset_revisions[ index ] - repository_archive, error_message = generate_repository_archive( app, - work_dir, - tool_shed_url, - ordered_repository, - ordered_changeset_revision, - file_type ) - if error_message: - error_messages = '%s %s' % ( error_messages, error_message ) - else: - archive_name = str( os.path.basename( repository_archive.name ) ) - repositories_archive.add( repository_archive.name, arcname=archive_name ) - attributes, sub_elements = get_repository_attributes_and_sub_elements( ordered_repository, archive_name ) - elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) - exported_repository_registry.exported_repository_elems.append( elem ) - basic_util.remove_dir( work_dir ) - # Keep information about the export in a file name export_info.xml in the archive. - sub_elements = generate_export_elem( tool_shed_url, repository, changeset_revision, export_repository_dependencies, api ) - export_elem = xml_util.create_element( 'export_info', attributes=None, sub_elements=sub_elements ) - tmp_export_info = xml_util.create_and_write_tmp_file( export_elem, use_indent=True ) - repositories_archive.add( tmp_export_info, arcname='export_info.xml' ) - # Write the manifest, which must preserve the order in which the repositories should be imported. - exported_repository_root = xml_util.create_element( 'repositories' ) - for exported_repository_elem in exported_repository_registry.exported_repository_elems: - exported_repository_root.append( exported_repository_elem ) - tmp_manifest = xml_util.create_and_write_tmp_file( exported_repository_root, use_indent=True ) - repositories_archive.add( tmp_manifest, arcname='manifest.xml' ) - except Exception, e: - log.exception( str( e ) ) - finally: - lock.release() - repositories_archive.close() - if api: - encoded_repositories_archive_name = encoding_util.tool_shed_encode( repositories_archive_filename ) - params = '?encoded_repositories_archive_name=%s' % encoded_repositories_archive_name - download_url = common_util.url_join( web.url_for( '/', qualified=True ), - 'repository/export_via_api%s' % params ) - return dict( download_url=download_url, error_messages=error_messages ) - return repositories_archive, error_messages - -def generate_repository_archive( app, work_dir, tool_shed_url, repository, changeset_revision, file_type ): - rdah = dependency_manager.RepositoryDependencyAttributeHandler( app, unpopulate=True ) - tdah = dependency_manager.ToolDependencyAttributeHandler( app, unpopulate=True ) - file_type_str = get_file_type_str( changeset_revision, file_type ) - file_name = '%s-%s' % ( repository.name, file_type_str ) - return_code, error_message = hg_util.archive_repository_revision( app, - repository, - work_dir, - changeset_revision ) - if return_code: - return None, error_message - repository_archive_name = os.path.join( work_dir, file_name ) - # Create a compressed tar archive that will contain only valid files and possibly altered dependency definition files. - repository_archive = tarfile.open( repository_archive_name, "w:%s" % file_type ) - for root, dirs, files in os.walk( work_dir ): - if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: - for dir in dirs: - if dir in commit_util.UNDESIRABLE_DIRS: - dirs.remove( dir ) - for name in files: - name = str( name ) - if str( name ) in commit_util.UNDESIRABLE_FILES: - continue - full_path = os.path.join( root, name ) - relative_path = full_path.replace( work_dir, '' ).lstrip( '/' ) - # See if we have a repository dependencies defined. - if name == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. - altered, root_elem, error_message = rdah.handle_tag_attributes( full_path ) - if error_message: - return None, error_message - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True ) - shutil.move( tmp_filename, full_path ) - elif name == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: - # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. - altered, root_elem, error_message = tdah.handle_tag_attributes( full_path ) - if error_message: - return None, error_message - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True ) - shutil.move( tmp_filename, full_path ) - repository_archive.add( full_path, arcname=relative_path ) - repository_archive.close() - return repository_archive, error_message - -def generate_repository_archive_filename( tool_shed_url, name, owner, changeset_revision, file_type, - export_repository_dependencies=False, use_tmp_archive_dir=False ): - tool_shed = remove_protocol_from_tool_shed_url( tool_shed_url ) - file_type_str = get_file_type_str( changeset_revision, file_type ) - if export_repository_dependencies: - repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_WITH_DEPENDENCIES_FILENAME, tool_shed, name, owner, file_type_str ) - else: - repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_FILENAME, tool_shed, name, owner, file_type_str ) - if use_tmp_archive_dir: - tmp_archive_dir = tempfile.mkdtemp( prefix="tmp-toolshed-arcdir" ) - repositories_archive_filename = os.path.join( tmp_archive_dir, repositories_archive_filename ) - return repositories_archive_filename - -def generate_export_elem( tool_shed_url, repository, changeset_revision, export_repository_dependencies, api ): - sub_elements = odict() - sub_elements[ 'export_time' ] = strftime( '%a, %d %b %Y %H:%M:%S +0000', gmtime() ) - sub_elements[ 'tool_shed' ] = str( tool_shed_url.rstrip( '/' ) ) - sub_elements[ 'repository_name' ] = str( repository.name ) - sub_elements[ 'repository_owner' ] = str( repository.user.username ) - sub_elements[ 'changeset_revision' ] = str( changeset_revision ) - sub_elements[ 'export_repository_dependencies' ] = str( export_repository_dependencies ) - sub_elements[ 'exported_via_api' ] = str( api ) - return sub_elements - -def get_components_from_repo_info_dict( app, repo_info_dict ): - """ - Return the repository and the associated latest installable changeset_revision (including updates) for the - repository defined by the received repo_info_dict. - """ - for repository_name, repo_info_tup in repo_info_dict.items(): - # There should only be one entry in the received repo_info_dict. - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tup ) - repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) - repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app, - repository, - changeset_revision ) - if repository_metadata: - return repository, repository_metadata.changeset_revision - return None, None - -def get_file_type_str( changeset_revision, file_type ): - if file_type == 'zip': - file_type_str = '%s.zip' % changeset_revision - elif file_type == 'bz2': - file_type_str = '%s.tar.bz2' % changeset_revision - elif file_type == 'gz': - file_type_str = '%s.tar.gz' % changeset_revision - else: - file_type_str = '' - return file_type_str - -def get_repo_info_dict_for_import( encoded_repository_id, encoded_repository_ids, repo_info_dicts ): - """ - The received encoded_repository_ids and repo_info_dicts are lists that contain associated elements at each - location in the list. This method will return the element from repo_info_dicts associated with the received - encoded_repository_id by determining its location in the received encoded_repository_ids list. - """ - for index, repository_id in enumerate( encoded_repository_ids ): - if repository_id == encoded_repository_id: - repo_info_dict = repo_info_dicts[ index ] - return repo_info_dict - return None - -def get_repo_info_dicts( app, user, tool_shed_url, repository_id, changeset_revision ): - """ - Return a list of dictionaries defining repositories that are required by the repository associated with the - received repository_id. - """ - rdm = RepositoryDependencyManager( app ) - repository = suc.get_repository_in_tool_shed( app, repository_id ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, repository_id, changeset_revision ) - # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. - toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) - repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=app, - repository=repository, - repository_metadata=repository_metadata, - toolshed_base_url=toolshed_base_url, - key_rd_dicts_to_be_processed=None, - all_repository_dependencies=None, - handled_key_rd_dicts=None ) - repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) - ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) - repo_info_dict = {} - # Cast unicode to string. - repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), - common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ), - str( changeset_revision ), - str( ctx.rev() ), - str( repository.user.username ), - repository_dependencies, - None ) - all_required_repo_info_dict = rdm.get_required_repo_info_dicts( tool_shed_url, [ repo_info_dict ] ) - all_repo_info_dicts = all_required_repo_info_dict.get( 'all_repo_info_dicts', [] ) - return all_repo_info_dicts - -def get_repository_attributes_and_sub_elements( repository, archive_name ): - """ - Get the information about a repository to create and populate an XML tag set. The generated attributes will - be contained within the <repository> tag, while the sub_elements will be tag sets contained within the <repository> - tag set. - """ - attributes = odict() - sub_elements = odict() - attributes[ 'name' ] = str( repository.name ) - attributes[ 'type' ] = str( repository.type ) - # We have to associate the public username since the user_id will be different between tool sheds. - attributes[ 'username' ] = str( repository.user.username ) - # Don't coerce description or long description from unicode to string because the fields are free text. - sub_elements[ 'description' ] = repository.description - sub_elements[ 'long_description' ] = repository.long_description - sub_elements[ 'archive' ] = archive_name - # Keep track of Category associations. - categories = [] - for rca in repository.categories: - category = rca.category - categories.append( ( 'category', str( category.name ) ) ) - sub_elements[ 'categories' ] = categories - return attributes, sub_elements - -def get_repository_ids( app, repo_info_dicts ): - """Return a list of repository ids associated with each dictionary in the received repo_info_dicts.""" - repository_ids = [] - for repo_info_dict in repo_info_dicts: - for repository_name, repo_info_tup in repo_info_dict.items(): - description, \ - repository_clone_url, \ - changeset_revision, \ - ctx_rev, \ - repository_owner, \ - repository_dependencies, \ - tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tup ) - repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) - repository_ids.append( app.security.encode_id( repository.id ) ) - return repository_ids - -def order_components_for_import( app, primary_repository_id, repository_ids, repo_info_dicts ): - """ - Some repositories may have repository dependencies that must be imported and have metadata set on - them before the dependent repository is imported. This method will inspect the list of repositories - about to be exported and make sure to order them appropriately for proper import. For each repository - about to be exported, if required repositories are not contained in the list of repositories about to - be exported, then they are not considered. Repository dependency definitions that contain circular - dependencies should not result in an infinite loop, but obviously ordering the list will not be handled - for one or more of the repositories that require prior import. - """ - # The received primary_repository_id is the id of the repository being exported, with the received list - # of repository_ids being only the ids of all of its repository dependencies. The primary repository will - # always be last in the returned lists. - ordered_repository_ids = [] - ordered_repositories = [] - ordered_changeset_revisions = [] - # Create a dictionary whose keys are the received repository_ids and whose values are a list of - # repository_ids, each of which is contained in the received list of repository_ids and whose associated - # repository must be imported prior to the repository associated with the repository_id key. - prior_import_required_dict = suc.get_prior_import_or_install_required_dict( app, repository_ids, repo_info_dicts ) - processed_repository_ids = [] - # Process the list of repository dependencies defined for the repository associated with the received - # primary_repository_id. - while len( processed_repository_ids ) != len( prior_import_required_dict.keys() ): - repository_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_import_required_dict, processed_repository_ids ) - if repository_id == primary_repository_id: - # Append the primary_repository_id without processing it since it must be returned last in the order. - # It will be processed below after all dependencies are processed. - processed_repository_ids.append( primary_repository_id ) - continue - processed_repository_ids.append( repository_id ) - if repository_id not in ordered_repository_ids: - prior_import_required_ids = prior_import_required_dict[ repository_id ] - for prior_import_required_id in prior_import_required_ids: - if prior_import_required_id not in ordered_repository_ids: - # Import the associated repository dependency first. - prior_repo_info_dict = get_repo_info_dict_for_import( prior_import_required_id, repository_ids, repo_info_dicts ) - prior_repository, prior_import_changeset_revision = get_components_from_repo_info_dict( app, prior_repo_info_dict ) - if prior_repository and prior_import_changeset_revision: - ordered_repository_ids.append( prior_import_required_id ) - ordered_repositories.append( prior_repository ) - ordered_changeset_revisions.append( prior_import_changeset_revision ) - repo_info_dict = get_repo_info_dict_for_import( repository_id, repository_ids, repo_info_dicts ) - repository, changeset_revision = get_components_from_repo_info_dict( app, repo_info_dict ) - if repository and changeset_revision: - ordered_repository_ids.append( repository_id ) - ordered_repositories.append( repository ) - ordered_changeset_revisions.append( changeset_revision ) - # Process the repository associated with the received primary_repository_id last. - repo_info_dict = get_repo_info_dict_for_import( primary_repository_id, repository_ids, repo_info_dicts ) - repository, changeset_revision = get_components_from_repo_info_dict( app, repo_info_dict ) - if repository and changeset_revision: - ordered_repository_ids.append( repository_id ) - ordered_repositories.append( repository ) - ordered_changeset_revisions.append( changeset_revision ) - return ordered_repository_ids, ordered_repositories, ordered_changeset_revisions - -def remove_protocol_from_tool_shed_url( base_url ): - protocol, base = base_url.split( '://' ) - base = base.replace( ':', '_colon_' ) - base = base.rstrip( '/' ) - return base This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Make galaxy.util.in_directory slightly more generic to match Pulsar's variant.
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fbf4b5ab17a9/ Changeset: fbf4b5ab17a9 User: jmchilton Date: 2014-06-24 04:55:11 Summary: Make galaxy.util.in_directory slightly more generic to match Pulsar's variant. Fixes failing unit test in just added code. Affected #: 1 file diff -r 566388d623749dad4259ea04cf44a5d858a56671 -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -417,17 +417,16 @@ return slug_base -def in_directory( file, directory ): +def in_directory( file, directory, local_path_module=os.path ): """ Return true, if the common prefix of both is equal to directory e.g. /a/b/c/d.rst and directory is /a/b, the common prefix is /a/b """ # Make both absolute. - directory = os.path.abspath( directory ) - file = os.path.abspath( file ) - - return os.path.commonprefix( [ file, directory ] ) == directory + directory = local_path_module.abspath(directory) + file = local_path_module.abspath(file) + return local_path_module.commonprefix([file, directory]) == directory def merge_sorted_iterables( operator, *iterables ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Merged in jmchilton/galaxy-central-fork-1 (pull request #422)
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/566388d62374/ Changeset: 566388d62374 User: jmchilton Date: 2014-06-24 04:27:51 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #422) Implement Pulsar job runners. Affected #: 32 files diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -19,27 +19,30 @@ <param id="drmaa_library_path">/sge/lib/libdrmaa.so</param></plugin> - <plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr:LwrJobRunner"> -  -  + <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> + <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> + <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> +  + <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"> +  -  - </plugin> - <plugin id="amqp_lwr" type="runner" load="galaxy.jobs.runners.lwr:LwrJobRunner"> - <param id="url">amqp://guest:guest@localhost:5672//</param> -  + <plugin id="pulsar_mq" type="runner" load="galaxy.jobs.runners.pulsar:PulsarMQJobRunner"> +  + <param id="amqp_url">amqp://guest:guest@localhost:5672//</param> + <param id="galaxy_url">http://localhost:8080</param> -  + </plugin> - <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> - <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> - <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> + <plugin id="pulsar_legacy" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner"> +  + </plugin></plugins><handlers default="handlers"> @@ -213,87 +224,71 @@ <param id="function">foo</param></destination> - <destination id="secure_lwr" runner="lwr"> - <param id="url">https://windowshost.examle.com:8913/</param> -  + <destination id="secure_pulsar_rest_dest" runner="pulsar_rest"> + <param id="url">https://examle.com:8913/</param> + <param id="private_token">123456789changeme</param> -  -  +  -  -  -  +  -  -  -  +  +  + </destination> - <destination id="amqp_lwr_dest" runner="amqp_lwr" > -  -  - <param id="jobs_directory">/path/to/remote/lwr/lwr_staging/</param> -  - <param id="default_file_action">remote_transfer</param></destination><destination id="ssh_torque" runner="cli"><param id="shell_plugin">SecureShell</param> diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/jobs/runners/pulsar.py --- /dev/null +++ b/lib/galaxy/jobs/runners/pulsar.py @@ -0,0 +1,707 @@ +from __future__ import absolute_import # Need to import pulsar_client absolutely. + +import logging + +from galaxy import model +from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner +from galaxy.jobs import ComputeEnvironment +from galaxy.jobs import JobDestination +from galaxy.jobs.command_factory import build_command +from galaxy.tools.deps import dependencies +from galaxy.util import string_as_bool_or_none +from galaxy.util.bunch import Bunch +from galaxy.util import specs + +import errno +from time import sleep +import os + +from pulsar.client import build_client_manager +from pulsar.client import url_to_destination_params +from pulsar.client import finish_job as pulsar_finish_job +from pulsar.client import submit_job as pulsar_submit_job +from pulsar.client import ClientJobDescription +from pulsar.client import PulsarOutputs +from pulsar.client import ClientOutputs +from pulsar.client import PathMapper + +log = logging.getLogger( __name__ ) + +__all__ = [ 'PulsarLegacyJobRunner', 'PulsarRESTJobRunner', 'PulsarMQJobRunner' ] + +NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "Pulsar misconfiguration - Pulsar client configured to set metadata remotely, but remote Pulsar isn't properly configured with a galaxy_home directory." +NO_REMOTE_DATATYPES_CONFIG = "Pulsar client is configured to use remote datatypes configuration when setting metadata externally, but Pulsar is not configured with this information. Defaulting to datatypes_conf.xml." +GENERIC_REMOTE_ERROR = "Failed to communicate with remote job server." + +# Is there a good way to infer some default for this? Can only use +# url_for from web threads. https://gist.github.com/jmchilton/9098762 +DEFAULT_GALAXY_URL = "http://localhost:8080" + +PULSAR_PARAM_SPECS = dict( + transport=dict( + map=specs.to_str_or_none, + valid=specs.is_in("urllib", "curl", None), + default=None + ), + cache=dict( + map=specs.to_bool_or_none, + default=None, + ), + amqp_url=dict( + map=specs.to_str_or_none, + default=None, + ), + galaxy_url=dict( + map=specs.to_str_or_none, + default=DEFAULT_GALAXY_URL, + ), + manager=dict( + map=specs.to_str_or_none, + default=None, + ), + amqp_consumer_timeout=dict( + map=lambda val: None if val == "None" else float(val), + default=None, + ), + amqp_connect_ssl_ca_certs=dict( + map=specs.to_str_or_none, + default=None, + ), + amqp_connect_ssl_keyfile=dict( + map=specs.to_str_or_none, + default=None, + ), + amqp_connect_ssl_certfile=dict( + map=specs.to_str_or_none, + default=None, + ), + amqp_connect_ssl_cert_reqs=dict( + map=specs.to_str_or_none, + default=None, + ), + # http://kombu.readthedocs.org/en/latest/reference/kombu.html#kombu.Producer.… + amqp_publish_retry=dict( + map=specs.to_bool, + default=False, + ), + amqp_publish_priority=dict( + map=int, + valid=lambda x: 0 <= x and x <= 9, + default=0, + ), + # http://kombu.readthedocs.org/en/latest/reference/kombu.html#kombu.Exchange.… + amqp_publish_delivery_mode=dict( + map=str, + valid=specs.is_in("transient", "persistent"), + default="persistent", + ), + amqp_publish_retry_max_retries=dict( + map=int, + default=None, + ), + amqp_publish_retry_interval_start=dict( + map=int, + default=None, + ), + amqp_publish_retry_interval_step=dict( + map=int, + default=None, + ), + amqp_publish_retry_interval_max=dict( + map=int, + default=None, + ), +) + + +PARAMETER_SPECIFICATION_REQUIRED = object() +PARAMETER_SPECIFICATION_IGNORED = object() + + +class PulsarJobRunner( AsynchronousJobRunner ): + """ + Pulsar Job Runner + """ + runner_name = "PulsarJobRunner" + + def __init__( self, app, nworkers, **kwds ): + """Start the job runner """ + super( PulsarJobRunner, self ).__init__( app, nworkers, runner_param_specs=PULSAR_PARAM_SPECS, **kwds ) + self._init_worker_threads() + galaxy_url = self.runner_params.galaxy_url + if galaxy_url: + galaxy_url = galaxy_url.rstrip("/") + self.galaxy_url = galaxy_url + self.__init_client_manager() + self._monitor() + + def _monitor( self ): + # Extension point allow MQ variant to setup callback instead + self._init_monitor_thread() + + def __init_client_manager( self ): + client_manager_kwargs = {} + for kwd in 'manager', 'cache', 'transport': + client_manager_kwargs[ kwd ] = self.runner_params[ kwd ] + for kwd in self.runner_params.keys(): + if kwd.startswith( 'amqp_' ): + client_manager_kwargs[ kwd ] = self.runner_params[ kwd ] + self.client_manager = build_client_manager(**client_manager_kwargs) + + def url_to_destination( self, url ): + """Convert a legacy URL to a job destination""" + return JobDestination( runner="pulsar", params=url_to_destination_params( url ) ) + + def check_watched_item(self, job_state): + try: + client = self.get_client_from_state(job_state) + status = client.get_status() + except Exception: + # An orphaned job was put into the queue at app startup, so remote server went down + # either way we are done I guess. + self.mark_as_finished(job_state) + return None + job_state = self._update_job_state_for_status(job_state, status) + return job_state + + def _update_job_state_for_status(self, job_state, pulsar_status): + if pulsar_status == "complete": + self.mark_as_finished(job_state) + return None + if pulsar_status == "failed": + self.fail_job(job_state) + return None + if pulsar_status == "running" and not job_state.running: + job_state.running = True + job_state.job_wrapper.change_state( model.Job.states.RUNNING ) + return job_state + + def queue_job(self, job_wrapper): + job_destination = job_wrapper.job_destination + self._populate_parameter_defaults( job_destination ) + + command_line, client, remote_job_config, compute_environment = self.__prepare_job( job_wrapper, job_destination ) + + if not command_line: + return + + try: + dependencies_description = PulsarJobRunner.__dependencies_description( client, job_wrapper ) + rewrite_paths = not PulsarJobRunner.__rewrite_parameters( client ) + unstructured_path_rewrites = {} + if compute_environment: + unstructured_path_rewrites = compute_environment.unstructured_path_rewrites + + client_job_description = ClientJobDescription( + command_line=command_line, + input_files=self.get_input_files(job_wrapper), + client_outputs=self.__client_outputs(client, job_wrapper), + working_directory=job_wrapper.working_directory, + tool=job_wrapper.tool, + config_files=job_wrapper.extra_filenames, + dependencies_description=dependencies_description, + env=client.env, + rewrite_paths=rewrite_paths, + arbitrary_files=unstructured_path_rewrites, + ) + job_id = pulsar_submit_job(client, client_job_description, remote_job_config) + log.info("Pulsar job submitted with job_id %s" % job_id) + job_wrapper.set_job_destination( job_destination, job_id ) + job_wrapper.change_state( model.Job.states.QUEUED ) + except Exception: + job_wrapper.fail( "failure running job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + return + + pulsar_job_state = AsynchronousJobState() + pulsar_job_state.job_wrapper = job_wrapper + pulsar_job_state.job_id = job_id + pulsar_job_state.old_state = True + pulsar_job_state.running = False + pulsar_job_state.job_destination = job_destination + self.monitor_job(pulsar_job_state) + + def __prepare_job(self, job_wrapper, job_destination): + """ Build command-line and Pulsar client for this job. """ + command_line = None + client = None + remote_job_config = None + compute_environment = None + try: + client = self.get_client_from_wrapper(job_wrapper) + tool = job_wrapper.tool + remote_job_config = client.setup(tool.id, tool.version) + rewrite_parameters = PulsarJobRunner.__rewrite_parameters( client ) + prepare_kwds = {} + if rewrite_parameters: + compute_environment = PulsarComputeEnvironment( client, job_wrapper, remote_job_config ) + prepare_kwds[ 'compute_environment' ] = compute_environment + job_wrapper.prepare( **prepare_kwds ) + self.__prepare_input_files_locally(job_wrapper) + remote_metadata = PulsarJobRunner.__remote_metadata( client ) + dependency_resolution = PulsarJobRunner.__dependency_resolution( client ) + metadata_kwds = self.__build_metadata_configuration(client, job_wrapper, remote_metadata, remote_job_config) + remote_command_params = dict( + working_directory=remote_job_config['working_directory'], + metadata_kwds=metadata_kwds, + dependency_resolution=dependency_resolution, + ) + remote_working_directory = remote_job_config['working_directory'] + # TODO: Following defs work for Pulsar, always worked for Pulsar but should be + # calculated at some other level. + remote_job_directory = os.path.abspath(os.path.join(remote_working_directory, os.path.pardir)) + remote_tool_directory = os.path.abspath(os.path.join(remote_job_directory, "tool_files")) + container = self._find_container( + job_wrapper, + compute_working_directory=remote_working_directory, + compute_tool_directory=remote_tool_directory, + compute_job_directory=remote_job_directory, + ) + command_line = build_command( + self, + job_wrapper=job_wrapper, + container=container, + include_metadata=remote_metadata, + include_work_dir_outputs=False, + remote_command_params=remote_command_params, + ) + except Exception: + job_wrapper.fail( "failure preparing job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + + # If we were able to get a command line, run the job + if not command_line: + job_wrapper.finish( '', '' ) + + return command_line, client, remote_job_config, compute_environment + + def __prepare_input_files_locally(self, job_wrapper): + """Run task splitting commands locally.""" + prepare_input_files_cmds = getattr(job_wrapper, 'prepare_input_files_cmds', None) + if prepare_input_files_cmds is not None: + for cmd in prepare_input_files_cmds: # run the commands to stage the input files + if 0 != os.system(cmd): + raise Exception('Error running file staging command: %s' % cmd) + job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line + + def _populate_parameter_defaults( self, job_destination ): + updated = False + params = job_destination.params + for key, value in self.destination_defaults.iteritems(): + if key in params: + if value is PARAMETER_SPECIFICATION_IGNORED: + log.warn( "Pulsar runner in selected configuration ignores parameter %s" % key ) + continue + #if self.runner_params.get( key, None ): + # # Let plugin define defaults for some parameters - + # # for instance that way jobs_directory can be + # # configured next to AMQP url (where it belongs). + # params[ key ] = self.runner_params[ key ] + # continue + + if not value: + continue + + if value is PARAMETER_SPECIFICATION_REQUIRED: + raise Exception( "Pulsar destination does not define required parameter %s" % key ) + elif value is not PARAMETER_SPECIFICATION_IGNORED: + params[ key ] = value + updated = True + return updated + + def get_output_files(self, job_wrapper): + output_paths = job_wrapper.get_output_fnames() + return [ str( o ) for o in output_paths ] # Force job_path from DatasetPath objects. + + def get_input_files(self, job_wrapper): + input_paths = job_wrapper.get_input_paths() + return [ str( i ) for i in input_paths ] # Force job_path from DatasetPath objects. + + def get_client_from_wrapper(self, job_wrapper): + job_id = job_wrapper.job_id + if hasattr(job_wrapper, 'task_id'): + job_id = "%s_%s" % (job_id, job_wrapper.task_id) + params = job_wrapper.job_destination.params.copy() + for key, value in params.iteritems(): + if value: + params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) + + env = getattr( job_wrapper.job_destination, "env", [] ) + return self.get_client( params, job_id, env ) + + def get_client_from_state(self, job_state): + job_destination_params = job_state.job_destination.params + job_id = job_state.job_id + return self.get_client( job_destination_params, job_id ) + + def get_client( self, job_destination_params, job_id, env=[] ): + # Cannot use url_for outside of web thread. + #files_endpoint = url_for( controller="job_files", job_id=encoded_job_id ) + + encoded_job_id = self.app.security.encode_id(job_id) + job_key = self.app.security.encode_id( job_id, kind="jobs_files" ) + files_endpoint = "%s/api/jobs/%s/files?job_key=%s" % ( + self.galaxy_url, + encoded_job_id, + job_key + ) + get_client_kwds = dict( + job_id=str( job_id ), + files_endpoint=files_endpoint, + env=env + ) + return self.client_manager.get_client( job_destination_params, **get_client_kwds ) + + def finish_job( self, job_state ): + stderr = stdout = '' + job_wrapper = job_state.job_wrapper + try: + client = self.get_client_from_state(job_state) + run_results = client.full_status() + remote_working_directory = run_results.get("working_directory", None) + stdout = run_results.get('stdout', '') + stderr = run_results.get('stderr', '') + exit_code = run_results.get('returncode', None) + pulsar_outputs = PulsarOutputs.from_status_response(run_results) + # Use Pulsar client code to transfer/copy files back + # and cleanup job if needed. + completed_normally = \ + job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] + cleanup_job = self.app.config.cleanup_job + client_outputs = self.__client_outputs(client, job_wrapper) + finish_args = dict( client=client, + job_completed_normally=completed_normally, + cleanup_job=cleanup_job, + client_outputs=client_outputs, + pulsar_outputs=pulsar_outputs ) + failed = pulsar_finish_job( **finish_args ) + if failed: + job_wrapper.fail("Failed to find or download one or more job outputs from remote server.", exception=True) + except Exception: + message = GENERIC_REMOTE_ERROR + job_wrapper.fail( message, exception=True ) + log.exception("failure finishing job %d" % job_wrapper.job_id) + return + if not PulsarJobRunner.__remote_metadata( client ): + self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) + # Finish the job + try: + job_wrapper.finish( + stdout, + stderr, + exit_code, + remote_working_directory=remote_working_directory + ) + except Exception: + log.exception("Job wrapper finish method failed") + job_wrapper.fail("Unable to finish job", exception=True) + + def fail_job( self, job_state ): + """ + Seperated out so we can use the worker threads for it. + """ + self.stop_job( self.sa_session.query( self.app.model.Job ).get( job_state.job_wrapper.job_id ) ) + job_state.job_wrapper.fail( getattr( job_state, "fail_message", GENERIC_REMOTE_ERROR ) ) + + def check_pid( self, pid ): + try: + os.kill( pid, 0 ) + return True + except OSError, e: + if e.errno == errno.ESRCH: + log.debug( "check_pid(): PID %d is dead" % pid ) + else: + log.warning( "check_pid(): Got errno %s when attempting to check PID %d: %s" % ( errno.errorcode[e.errno], pid, e.strerror ) ) + return False + + def stop_job( self, job ): + #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished + job_ext_output_metadata = job.get_external_output_metadata() + if job_ext_output_metadata: + pid = job_ext_output_metadata[0].job_runner_external_pid # every JobExternalOutputMetadata has a pid set, we just need to take from one of them + if pid in [ None, '' ]: + log.warning( "stop_job(): %s: no PID in database for job, unable to stop" % job.id ) + return + pid = int( pid ) + if not self.check_pid( pid ): + log.warning( "stop_job(): %s: PID %d was already dead or can't be signaled" % ( job.id, pid ) ) + return + for sig in [ 15, 9 ]: + try: + os.killpg( pid, sig ) + except OSError, e: + log.warning( "stop_job(): %s: Got errno %s when attempting to signal %d to PID %d: %s" % ( job.id, errno.errorcode[e.errno], sig, pid, e.strerror ) ) + return # give up + sleep( 2 ) + if not self.check_pid( pid ): + log.debug( "stop_job(): %s: PID %d successfully killed with signal %d" % ( job.id, pid, sig ) ) + return + else: + log.warning( "stop_job(): %s: PID %d refuses to die after signaling TERM/KILL" % ( job.id, pid ) ) + else: + # Remote kill + pulsar_url = job.job_runner_name + job_id = job.job_runner_external_id + log.debug("Attempt remote Pulsar kill of job with url %s and id %s" % (pulsar_url, job_id)) + client = self.get_client(job.destination_params, job_id) + client.kill() + + def recover( self, job, job_wrapper ): + """Recovers jobs stuck in the queued/running state when Galaxy started""" + job_state = self._job_state( job, job_wrapper ) + job_wrapper.command_line = job.get_command_line() + state = job.get_state() + if state in [model.Job.states.RUNNING, model.Job.states.QUEUED]: + log.debug( "(Pulsar/%s) is still in running state, adding to the Pulsar queue" % ( job.get_id()) ) + job_state.old_state = True + job_state.running = state == model.Job.states.RUNNING + self.monitor_queue.put( job_state ) + + def shutdown( self ): + super( PulsarJobRunner, self ).shutdown() + self.client_manager.shutdown() + + def _job_state( self, job, job_wrapper ): + job_state = AsynchronousJobState() + # TODO: Determine why this is set when using normal message queue updates + # but not CLI submitted MQ updates... + raw_job_id = job.get_job_runner_external_id() or job_wrapper.job_id + job_state.job_id = str( raw_job_id ) + job_state.runner_url = job_wrapper.get_job_runner_url() + job_state.job_destination = job_wrapper.job_destination + job_state.job_wrapper = job_wrapper + return job_state + + def __client_outputs( self, client, job_wrapper ): + work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) + output_files = self.get_output_files( job_wrapper ) + client_outputs = ClientOutputs( + working_directory=job_wrapper.working_directory, + work_dir_outputs=work_dir_outputs, + output_files=output_files, + version_file=job_wrapper.get_version_string_path(), + ) + return client_outputs + + @staticmethod + def __dependencies_description( pulsar_client, job_wrapper ): + dependency_resolution = PulsarJobRunner.__dependency_resolution( pulsar_client ) + remote_dependency_resolution = dependency_resolution == "remote" + if not remote_dependency_resolution: + return None + requirements = job_wrapper.tool.requirements or [] + installed_tool_dependencies = job_wrapper.tool.installed_tool_dependencies or [] + return dependencies.DependenciesDescription( + requirements=requirements, + installed_tool_dependencies=installed_tool_dependencies, + ) + + @staticmethod + def __dependency_resolution( pulsar_client ): + dependency_resolution = pulsar_client.destination_params.get( "dependency_resolution", "local" ) + if dependency_resolution not in ["none", "local", "remote"]: + raise Exception("Unknown dependency_resolution value encountered %s" % dependency_resolution) + return dependency_resolution + + @staticmethod + def __remote_metadata( pulsar_client ): + remote_metadata = string_as_bool_or_none( pulsar_client.destination_params.get( "remote_metadata", False ) ) + return remote_metadata + + @staticmethod + def __use_remote_datatypes_conf( pulsar_client ): + """ When setting remote metadata, use integrated datatypes from this + Galaxy instance or use the datatypes config configured via the remote + Pulsar. + + Both options are broken in different ways for same reason - datatypes + may not match. One can push the local datatypes config to the remote + server - but there is no guarentee these datatypes will be defined + there. Alternatively, one can use the remote datatype config - but + there is no guarentee that it will contain all the datatypes available + to this Galaxy. + """ + use_remote_datatypes = string_as_bool_or_none( pulsar_client.destination_params.get( "use_remote_datatypes", False ) ) + return use_remote_datatypes + + @staticmethod + def __rewrite_parameters( pulsar_client ): + return string_as_bool_or_none( pulsar_client.destination_params.get( "rewrite_parameters", False ) ) or False + + def __build_metadata_configuration(self, client, job_wrapper, remote_metadata, remote_job_config): + metadata_kwds = {} + if remote_metadata: + remote_system_properties = remote_job_config.get("system_properties", {}) + remote_galaxy_home = remote_system_properties.get("galaxy_home", None) + if not remote_galaxy_home: + raise Exception(NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE) + metadata_kwds['exec_dir'] = remote_galaxy_home + outputs_directory = remote_job_config['outputs_directory'] + configs_directory = remote_job_config['configs_directory'] + working_directory = remote_job_config['working_directory'] + # For metadata calculation, we need to build a list of of output + # file objects with real path indicating location on Galaxy server + # and false path indicating location on compute server. Since the + # Pulsar disables from_work_dir copying as part of the job command + # line we need to take the list of output locations on the Pulsar + # server (produced by self.get_output_files(job_wrapper)) and for + # each work_dir output substitute the effective path on the Pulsar + # server relative to the remote working directory as the + # false_path to send the metadata command generation module. + work_dir_outputs = self.get_work_dir_outputs(job_wrapper, job_working_directory=working_directory) + outputs = [Bunch(false_path=os.path.join(outputs_directory, os.path.basename(path)), real_path=path) for path in self.get_output_files(job_wrapper)] + for output in outputs: + for pulsar_workdir_path, real_path in work_dir_outputs: + if real_path == output.real_path: + output.false_path = pulsar_workdir_path + metadata_kwds['output_fnames'] = outputs + metadata_kwds['compute_tmp_dir'] = working_directory + metadata_kwds['config_root'] = remote_galaxy_home + default_config_file = os.path.join(remote_galaxy_home, 'universe_wsgi.ini') + metadata_kwds['config_file'] = remote_system_properties.get('galaxy_config_file', default_config_file) + metadata_kwds['dataset_files_path'] = remote_system_properties.get('galaxy_dataset_files_path', None) + if PulsarJobRunner.__use_remote_datatypes_conf( client ): + remote_datatypes_config = remote_system_properties.get('galaxy_datatypes_config_file', None) + if not remote_datatypes_config: + log.warn(NO_REMOTE_DATATYPES_CONFIG) + remote_datatypes_config = os.path.join(remote_galaxy_home, 'datatypes_conf.xml') + metadata_kwds['datatypes_config'] = remote_datatypes_config + else: + integrates_datatypes_config = self.app.datatypes_registry.integrated_datatypes_configs + # Ensure this file gets pushed out to the remote config dir. + job_wrapper.extra_filenames.append(integrates_datatypes_config) + + metadata_kwds['datatypes_config'] = os.path.join(configs_directory, os.path.basename(integrates_datatypes_config)) + return metadata_kwds + + +class PulsarLegacyJobRunner( PulsarJobRunner ): + destination_defaults = dict( + rewrite_parameters="false", + dependency_resolution="local", + ) + + +class PulsarMQJobRunner( PulsarJobRunner ): + destination_defaults = dict( + default_file_action="remote_transfer", + rewrite_parameters="true", + dependency_resolution="remote", + jobs_directory=PARAMETER_SPECIFICATION_REQUIRED, + url=PARAMETER_SPECIFICATION_IGNORED, + private_token=PARAMETER_SPECIFICATION_IGNORED + ) + + def _monitor( self ): + # This is a message queue driven runner, don't monitor + # just setup required callback. + self.client_manager.ensure_has_status_update_callback(self.__async_update) + + def __async_update( self, full_status ): + job_id = None + try: + job_id = full_status[ "job_id" ] + job, job_wrapper = self.app.job_manager.job_handler.job_queue.job_pair_for_id( job_id ) + job_state = self._job_state( job, job_wrapper ) + self._update_job_state_for_status(job_state, full_status[ "status" ] ) + except Exception: + log.exception( "Failed to update Pulsar job status for job_id %s" % job_id ) + raise + # Nothing else to do? - Attempt to fail the job? + + +class PulsarRESTJobRunner( PulsarJobRunner ): + destination_defaults = dict( + default_file_action="transfer", + rewrite_parameters="true", + dependency_resolution="remote", + url=PARAMETER_SPECIFICATION_REQUIRED, + ) + + +class PulsarComputeEnvironment( ComputeEnvironment ): + + def __init__( self, pulsar_client, job_wrapper, remote_job_config ): + self.pulsar_client = pulsar_client + self.job_wrapper = job_wrapper + self.local_path_config = job_wrapper.default_compute_environment() + self.unstructured_path_rewrites = {} + # job_wrapper.prepare is going to expunge the job backing the following + # computations, so precalculate these paths. + self._wrapper_input_paths = self.local_path_config.input_paths() + self._wrapper_output_paths = self.local_path_config.output_paths() + self.path_mapper = PathMapper(pulsar_client, remote_job_config, self.local_path_config.working_directory()) + self._config_directory = remote_job_config[ "configs_directory" ] + self._working_directory = remote_job_config[ "working_directory" ] + self._sep = remote_job_config[ "system_properties" ][ "separator" ] + self._tool_dir = remote_job_config[ "tools_directory" ] + version_path = self.local_path_config.version_path() + new_version_path = self.path_mapper.remote_version_path_rewrite(version_path) + if new_version_path: + version_path = new_version_path + self._version_path = version_path + + def output_paths( self ): + local_output_paths = self._wrapper_output_paths + + results = [] + for local_output_path in local_output_paths: + wrapper_path = str( local_output_path ) + remote_path = self.path_mapper.remote_output_path_rewrite( wrapper_path ) + results.append( self._dataset_path( local_output_path, remote_path ) ) + return results + + def input_paths( self ): + local_input_paths = self._wrapper_input_paths + + results = [] + for local_input_path in local_input_paths: + wrapper_path = str( local_input_path ) + # This will over-copy in some cases. For instance in the case of task + # splitting, this input will be copied even though only the work dir + # input will actually be used. + remote_path = self.path_mapper.remote_input_path_rewrite( wrapper_path ) + results.append( self._dataset_path( local_input_path, remote_path ) ) + return results + + def _dataset_path( self, local_dataset_path, remote_path ): + remote_extra_files_path = None + if remote_path: + remote_extra_files_path = "%s_files" % remote_path[ 0:-len( ".dat" ) ] + return local_dataset_path.with_path_for_job( remote_path, remote_extra_files_path ) + + def working_directory( self ): + return self._working_directory + + def config_directory( self ): + return self._config_directory + + def new_file_path( self ): + return self.working_directory() # Problems with doing this? + + def sep( self ): + return self._sep + + def version_path( self ): + return self._version_path + + def rewriter( self, parameter_value ): + unstructured_path_rewrites = self.unstructured_path_rewrites + if parameter_value in unstructured_path_rewrites: + # Path previously mapped, use previous mapping. + return unstructured_path_rewrites[ parameter_value ] + if parameter_value in unstructured_path_rewrites.itervalues(): + # Path is a rewritten remote path (this might never occur, + # consider dropping check...) + return parameter_value + + rewrite, new_unstructured_path_rewrites = self.path_mapper.check_for_arbitrary_rewrite( parameter_value ) + if rewrite: + unstructured_path_rewrites.update(new_unstructured_path_rewrites) + return rewrite + else: + # Did need to rewrite, use original path or value. + return parameter_value + + def unstructured_path_rewriter( self ): + return self.rewriter diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/jobs/runners/util/__init__.py --- a/lib/galaxy/jobs/runners/util/__init__.py +++ b/lib/galaxy/jobs/runners/util/__init__.py @@ -1,7 +1,7 @@ """ This module and its submodules contains utilities for running external processes and interfacing with job managers. This module should contain -functionality shared between Galaxy and the LWR. +functionality shared between Galaxy and the Pulsar. """ from galaxy.util.bunch import Bunch diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/jobs/runners/util/cli/factory.py --- a/lib/galaxy/jobs/runners/util/cli/factory.py +++ b/lib/galaxy/jobs/runners/util/cli/factory.py @@ -5,7 +5,7 @@ ) code_dir = 'lib' except ImportError: - from lwr.managers.util.cli import ( + from pulsar.managers.util.cli import ( CliInterface, split_params ) diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/jobs/runners/util/cli/job/slurm.py --- a/lib/galaxy/jobs/runners/util/cli/job/slurm.py +++ b/lib/galaxy/jobs/runners/util/cli/job/slurm.py @@ -5,7 +5,7 @@ from galaxy.model import Job job_states = Job.states except ImportError: - # Not in Galaxy, map Galaxy job states to LWR ones. + # Not in Galaxy, map Galaxy job states to Pulsar ones. from galaxy.util import enum job_states = enum(RUNNING='running', OK='complete', QUEUED='queued') diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/jobs/runners/util/cli/job/torque.py --- a/lib/galaxy/jobs/runners/util/cli/job/torque.py +++ b/lib/galaxy/jobs/runners/util/cli/job/torque.py @@ -7,7 +7,7 @@ from galaxy.model import Job job_states = Job.states except ImportError: - # Not in Galaxy, map Galaxy job states to LWR ones. + # Not in Galaxy, map Galaxy job states to Pulsar ones. from galaxy.util import enum job_states = enum(RUNNING='running', OK='complete', QUEUED='queued') diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -623,9 +623,9 @@ elif store == 'irods': from .rods import IRODSObjectStore return IRODSObjectStore(config=config, config_xml=config_xml) - elif store == 'lwr': - from .lwr import LwrObjectStore - return LwrObjectStore(config=config, config_xml=config_xml) + elif store == 'pulsar': + from .pulsar import PulsarObjectStore + return PulsarObjectStore(config=config, config_xml=config_xml) else: log.error("Unrecognized object store definition: {0}".format(store)) diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/objectstore/lwr.py --- a/lib/galaxy/objectstore/lwr.py +++ /dev/null @@ -1,76 +0,0 @@ -from __future__ import absolute_import # Need to import lwr_client absolutely. -from ..objectstore import ObjectStore -try: - from galaxy.jobs.runners.lwr_client.manager import ObjectStoreClientManager -except ImportError: - from lwr.lwr_client.manager import ObjectStoreClientManager - - -class LwrObjectStore(ObjectStore): - """ - Object store implementation that delegates to a remote LWR server. - - This may be more aspirational than practical for now, it would be good to - Galaxy to a point that a handler thread could be setup that doesn't attempt - to access the disk files returned by a (this) object store - just passing - them along to the LWR unmodified. That modification - along with this - implementation and LWR job destinations would then allow Galaxy to fully - manage jobs on remote servers with completely different mount points. - - This implementation should be considered beta and may be dropped from - Galaxy at some future point or significantly modified. - """ - - def __init__(self, config, config_xml): - self.lwr_client = self.__build_lwr_client(config_xml) - - def exists(self, obj, **kwds): - return self.lwr_client.exists(**self.__build_kwds(obj, **kwds)) - - def file_ready(self, obj, **kwds): - return self.lwr_client.file_ready(**self.__build_kwds(obj, **kwds)) - - def create(self, obj, **kwds): - return self.lwr_client.create(**self.__build_kwds(obj, **kwds)) - - def empty(self, obj, **kwds): - return self.lwr_client.empty(**self.__build_kwds(obj, **kwds)) - - def size(self, obj, **kwds): - return self.lwr_client.size(**self.__build_kwds(obj, **kwds)) - - def delete(self, obj, **kwds): - return self.lwr_client.delete(**self.__build_kwds(obj, **kwds)) - - # TODO: Optimize get_data. - def get_data(self, obj, **kwds): - return self.lwr_client.get_data(**self.__build_kwds(obj, **kwds)) - - def get_filename(self, obj, **kwds): - return self.lwr_client.get_filename(**self.__build_kwds(obj, **kwds)) - - def update_from_file(self, obj, **kwds): - return self.lwr_client.update_from_file(**self.__build_kwds(obj, **kwds)) - - def get_store_usage_percent(self): - return self.lwr_client.get_store_usage_percent() - - def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None): - return None - - def __build_kwds(self, obj, **kwds): - kwds['object_id'] = obj.id - return kwds - pass - - def __build_lwr_client(self, config_xml): - url = config_xml.get("url") - private_token = config_xml.get("private_token", None) - transport = config_xml.get("transport", None) - manager_options = dict(transport=transport) - client_options = dict(url=url, private_token=private_token) - lwr_client = ObjectStoreClientManager(**manager_options).get_client(client_options) - return lwr_client - - def shutdown(self): - pass diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/objectstore/pulsar.py --- /dev/null +++ b/lib/galaxy/objectstore/pulsar.py @@ -0,0 +1,73 @@ +from __future__ import absolute_import # Need to import pulsar_client absolutely. +from ..objectstore import ObjectStore +from pulsar.client.manager import ObjectStoreClientManager + + +class PulsarObjectStore(ObjectStore): + """ + Object store implementation that delegates to a remote Pulsar server. + + This may be more aspirational than practical for now, it would be good to + Galaxy to a point that a handler thread could be setup that doesn't attempt + to access the disk files returned by a (this) object store - just passing + them along to the Pulsar unmodified. That modification - along with this + implementation and Pulsar job destinations would then allow Galaxy to fully + manage jobs on remote servers with completely different mount points. + + This implementation should be considered beta and may be dropped from + Galaxy at some future point or significantly modified. + """ + + def __init__(self, config, config_xml): + self.pulsar_client = self.__build_pulsar_client(config_xml) + + def exists(self, obj, **kwds): + return self.pulsar_client.exists(**self.__build_kwds(obj, **kwds)) + + def file_ready(self, obj, **kwds): + return self.pulsar_client.file_ready(**self.__build_kwds(obj, **kwds)) + + def create(self, obj, **kwds): + return self.pulsar_client.create(**self.__build_kwds(obj, **kwds)) + + def empty(self, obj, **kwds): + return self.pulsar_client.empty(**self.__build_kwds(obj, **kwds)) + + def size(self, obj, **kwds): + return self.pulsar_client.size(**self.__build_kwds(obj, **kwds)) + + def delete(self, obj, **kwds): + return self.pulsar_client.delete(**self.__build_kwds(obj, **kwds)) + + # TODO: Optimize get_data. + def get_data(self, obj, **kwds): + return self.pulsar_client.get_data(**self.__build_kwds(obj, **kwds)) + + def get_filename(self, obj, **kwds): + return self.pulsar_client.get_filename(**self.__build_kwds(obj, **kwds)) + + def update_from_file(self, obj, **kwds): + return self.pulsar_client.update_from_file(**self.__build_kwds(obj, **kwds)) + + def get_store_usage_percent(self): + return self.pulsar_client.get_store_usage_percent() + + def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None): + return None + + def __build_kwds(self, obj, **kwds): + kwds['object_id'] = obj.id + return kwds + pass + + def __build_pulsar_client(self, config_xml): + url = config_xml.get("url") + private_token = config_xml.get("private_token", None) + transport = config_xml.get("transport", None) + manager_options = dict(transport=transport) + client_options = dict(url=url, private_token=private_token) + pulsar_client = ObjectStoreClientManager(**manager_options).get_client(client_options) + return pulsar_client + + def shutdown(self): + pass diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/tools/deps/dependencies.py --- a/lib/galaxy/tools/deps/dependencies.py +++ b/lib/galaxy/tools/deps/dependencies.py @@ -8,7 +8,7 @@ related context required to resolve dependencies via the ToolShedPackageDependencyResolver. - This is meant to enable remote resolution of dependencies, by the LWR or + This is meant to enable remote resolution of dependencies, by the Pulsar or other potential remote execution mechanisms. """ @@ -39,7 +39,7 @@ @staticmethod def _toolshed_install_dependency_from_dict(as_dict): - # Rather than requiring full models in LWR, just use simple objects + # Rather than requiring full models in Pulsar, just use simple objects # containing only properties and associations used to resolve # dependencies for tool execution. repository_object = bunch.Bunch( diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/pulsar/client/__init__.py --- /dev/null +++ b/lib/pulsar/client/__init__.py @@ -0,0 +1,62 @@ +""" +pulsar client +====== + +This module contains logic for interfacing with an external Pulsar server. + +------------------ +Configuring Galaxy +------------------ + +Galaxy job runners are configured in Galaxy's ``job_conf.xml`` file. See ``job_conf.xml.sample_advanced`` +in your Galaxy code base or on +`Bitbucket <https://bitbucket.org/galaxy/galaxy-dist/src/tip/job_conf.xml.sample_advanc…>`_ +for information on how to configure Galaxy to interact with the Pulsar. + +Galaxy also supports an older, less rich configuration of job runners directly +in its main ``universe_wsgi.ini`` file. The following section describes how to +configure Galaxy to communicate with the Pulsar in this legacy mode. + +Legacy +------ + +A Galaxy tool can be configured to be executed remotely via Pulsar by +adding a line to the ``universe_wsgi.ini`` file under the +``galaxy:tool_runners`` section with the format:: + + <tool_id> = pulsar://http://<pulsar_host>:<pulsar_port> + +As an example, if a host named remotehost is running the Pulsar server +application on port ``8913``, then the tool with id ``test_tool`` can +be configured to run remotely on remotehost by adding the following +line to ``universe.ini``:: + + test_tool = pulsar://http://remotehost:8913 + +Remember this must be added after the ``[galaxy:tool_runners]`` header +in the ``universe.ini`` file. + + +""" + +from .staging.down import finish_job +from .staging.up import submit_job +from .staging import ClientJobDescription +from .staging import PulsarOutputs +from .staging import ClientOutputs +from .client import OutputNotFoundException +from .manager import build_client_manager +from .destination import url_to_destination_params +from .path_mapper import PathMapper + +__all__ = [ + build_client_manager, + OutputNotFoundException, + url_to_destination_params, + finish_job, + submit_job, + ClientJobDescription, + PulsarOutputs, + ClientOutputs, + PathMapper, +] diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/pulsar/client/action_mapper.py --- /dev/null +++ b/lib/pulsar/client/action_mapper.py @@ -0,0 +1,567 @@ +from json import load +from os import makedirs +from os.path import exists +from os.path import abspath +from os.path import dirname +from os.path import join +from os.path import basename +from os.path import sep +import fnmatch +from re import compile +from re import escape +import galaxy.util +from galaxy.util.bunch import Bunch +from .config_util import read_file +from .util import directory_files +from .util import unique_path_prefix +from .transport import get_file +from .transport import post_file + + +DEFAULT_MAPPED_ACTION = 'transfer' # Not really clear to me what this should be, exception? +DEFAULT_PATH_MAPPER_TYPE = 'prefix' + +STAGING_ACTION_REMOTE = "remote" +STAGING_ACTION_LOCAL = "local" +STAGING_ACTION_NONE = None +STAGING_ACTION_DEFAULT = "default" + +# Poor man's enum. +path_type = Bunch( + # Galaxy input datasets and extra files. + INPUT="input", + # Galaxy config and param files. + CONFIG="config", + # Files from tool's tool_dir (for now just wrapper if available). + TOOL="tool", + # Input work dir files - e.g. metadata files, task-split input files, etc.. + WORKDIR="workdir", + # Galaxy output datasets in their final home. + OUTPUT="output", + # Galaxy from_work_dir output paths and other files (e.g. galaxy.json) + OUTPUT_WORKDIR="output_workdir", + # Other fixed tool parameter paths (likely coming from tool data, but not + # nessecarily). Not sure this is the best name... + UNSTRUCTURED="unstructured", +) + + +ACTION_DEFAULT_PATH_TYPES = [ + path_type.INPUT, + path_type.CONFIG, + path_type.TOOL, + path_type.WORKDIR, + path_type.OUTPUT, + path_type.OUTPUT_WORKDIR, +] +ALL_PATH_TYPES = ACTION_DEFAULT_PATH_TYPES + [path_type.UNSTRUCTURED] + + +class FileActionMapper(object): + """ + Objects of this class define how paths are mapped to actions. + + >>> json_string = r'''{"paths": [ \ + {"path": "/opt/galaxy", "action": "none"}, \ + {"path": "/galaxy/data", "action": "transfer"}, \ + {"path": "/cool/bamfiles/**/*.bam", "action": "copy", "match_type": "glob"}, \ + {"path": ".*/dataset_\\\\d+.dat", "action": "copy", "match_type": "regex"} \ + ]}''' + >>> from tempfile import NamedTemporaryFile + >>> from os import unlink + >>> def mapper_for(default_action, config_contents): + ... f = NamedTemporaryFile(delete=False) + ... f.write(config_contents.encode('UTF-8')) + ... f.close() + ... mock_client = Bunch(default_file_action=default_action, action_config_path=f.name, files_endpoint=None) + ... mapper = FileActionMapper(mock_client) + ... mapper = FileActionMapper(config=mapper.to_dict()) # Serialize and deserialize it to make sure still works + ... unlink(f.name) + ... return mapper + >>> mapper = mapper_for(default_action='none', config_contents=json_string) + >>> # Test first config line above, implicit path prefix mapper + >>> action = mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input') + >>> action.action_type == u'none' + True + >>> action.staging_needed + False + >>> # Test another (2nd) mapper, this one with a different action + >>> action = mapper.action('/galaxy/data/files/000/dataset_1.dat', 'input') + >>> action.action_type == u'transfer' + True + >>> action.staging_needed + True + >>> # Always at least copy work_dir outputs. + >>> action = mapper.action('/opt/galaxy/database/working_directory/45.sh', 'workdir') + >>> action.action_type == u'copy' + True + >>> action.staging_needed + True + >>> # Test glob mapper (matching test) + >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam', 'input').action_type == u'copy' + True + >>> # Test glob mapper (non-matching test) + >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam.bai', 'input').action_type == u'none' + True + >>> # Regex mapper test. + >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'input').action_type == u'copy' + True + >>> # Doesn't map unstructured paths by default + >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'unstructured').action_type == u'none' + True + >>> input_only_mapper = mapper_for(default_action="none", config_contents=r'''{"paths": [ \ + {"path": "/", "action": "transfer", "path_types": "input"} \ + ] }''') + >>> input_only_mapper.action('/dataset_1.dat', 'input').action_type == u'transfer' + True + >>> input_only_mapper.action('/dataset_1.dat', 'output').action_type == u'none' + True + >>> unstructured_mapper = mapper_for(default_action="none", config_contents=r'''{"paths": [ \ + {"path": "/", "action": "transfer", "path_types": "*any*"} \ + ] }''') + >>> unstructured_mapper.action('/old/galaxy/data/dataset_10245.dat', 'unstructured').action_type == u'transfer' + True + """ + + def __init__(self, client=None, config=None): + if config is None and client is None: + message = "FileActionMapper must be constructed from either a client or a config dictionary." + raise Exception(message) + if config is None: + config = self.__client_to_config(client) + self.default_action = config.get("default_action", "transfer") + self.mappers = mappers_from_dicts(config.get("paths", [])) + self.files_endpoint = config.get("files_endpoint", None) + + def action(self, path, type, mapper=None): + mapper = self.__find_mapper(path, type, mapper) + action_class = self.__action_class(path, type, mapper) + file_lister = DEFAULT_FILE_LISTER + action_kwds = {} + if mapper: + file_lister = mapper.file_lister + action_kwds = mapper.action_kwds + action = action_class(path, file_lister=file_lister, **action_kwds) + self.__process_action(action, type) + return action + + def unstructured_mappers(self): + """ Return mappers that will map 'unstructured' files (i.e. go beyond + mapping inputs, outputs, and config files). + """ + return filter(lambda m: path_type.UNSTRUCTURED in m.path_types, self.mappers) + + def to_dict(self): + return dict( + default_action=self.default_action, + files_endpoint=self.files_endpoint, + paths=map(lambda m: m.to_dict(), self.mappers) + ) + + def __client_to_config(self, client): + action_config_path = client.action_config_path + if action_config_path: + config = read_file(action_config_path) + else: + config = dict() + config["default_action"] = client.default_file_action + config["files_endpoint"] = client.files_endpoint + return config + + def __load_action_config(self, path): + config = load(open(path, 'rb')) + self.mappers = mappers_from_dicts(config.get('paths', [])) + + def __find_mapper(self, path, type, mapper=None): + if not mapper: + normalized_path = abspath(path) + for query_mapper in self.mappers: + if query_mapper.matches(normalized_path, type): + mapper = query_mapper + break + return mapper + + def __action_class(self, path, type, mapper): + action_type = self.default_action if type in ACTION_DEFAULT_PATH_TYPES else "none" + if mapper: + action_type = mapper.action_type + if type in ["workdir", "output_workdir"] and action_type == "none": + # We are changing the working_directory relative to what + # Galaxy would use, these need to be copied over. + action_type = "copy" + action_class = actions.get(action_type, None) + if action_class is None: + message_template = "Unknown action_type encountered %s while trying to map path %s" + message_args = (action_type, path) + raise Exception(message_template % message_args) + return action_class + + def __process_action(self, action, file_type): + """ Extension point to populate extra action information after an + action has been created. + """ + if action.action_type == "remote_transfer": + url_base = self.files_endpoint + if not url_base: + raise Exception("Attempted to use remote_transfer action with defining a files_endpoint") + if "?" not in url_base: + url_base = "%s?" % url_base + # TODO: URL encode path. + url = "%s&path=%s&file_type=%s" % (url_base, action.path, file_type) + action.url = url + +REQUIRED_ACTION_KWD = object() + + +class BaseAction(object): + action_spec = {} + + def __init__(self, path, file_lister=None): + self.path = path + self.file_lister = file_lister or DEFAULT_FILE_LISTER + + def unstructured_map(self, path_helper): + unstructured_map = self.file_lister.unstructured_map(self.path) + if self.staging_needed: + # To ensure uniqueness, prepend unique prefix to each name + prefix = unique_path_prefix(self.path) + for path, name in unstructured_map.iteritems(): + unstructured_map[path] = join(prefix, name) + else: + path_rewrites = {} + for path in unstructured_map: + rewrite = self.path_rewrite(path_helper, path) + if rewrite: + path_rewrites[path] = rewrite + unstructured_map = path_rewrites + return unstructured_map + + @property + def staging_needed(self): + return self.staging != STAGING_ACTION_NONE + + @property + def staging_action_local(self): + return self.staging == STAGING_ACTION_LOCAL + + +class NoneAction(BaseAction): + """ This action indicates the corresponding path does not require any + additional action. This should indicate paths that are available both on + the Pulsar client (i.e. Galaxy server) and remote Pulsar server with the same + paths. """ + action_type = "none" + staging = STAGING_ACTION_NONE + + def to_dict(self): + return dict(path=self.path, action_type=self.action_type) + + @classmethod + def from_dict(cls, action_dict): + return NoneAction(path=action_dict["path"]) + + def path_rewrite(self, path_helper, path=None): + return None + + +class RewriteAction(BaseAction): + """ This actin indicates the Pulsar server should simply rewrite the path + to the specified file. + """ + action_spec = dict( + source_directory=REQUIRED_ACTION_KWD, + destination_directory=REQUIRED_ACTION_KWD + ) + action_type = "rewrite" + staging = STAGING_ACTION_NONE + + def __init__(self, path, file_lister=None, source_directory=None, destination_directory=None): + self.path = path + self.file_lister = file_lister or DEFAULT_FILE_LISTER + self.source_directory = source_directory + self.destination_directory = destination_directory + + def to_dict(self): + return dict( + path=self.path, + action_type=self.action_type, + source_directory=self.source_directory, + destination_directory=self.destination_directory, + ) + + @classmethod + def from_dict(cls, action_dict): + return RewriteAction( + path=action_dict["path"], + source_directory=action_dict["source_directory"], + destination_directory=action_dict["destination_directory"], + ) + + def path_rewrite(self, path_helper, path=None): + if not path: + path = self.path + new_path = path_helper.from_posix_with_new_base(self.path, self.source_directory, self.destination_directory) + return None if new_path == self.path else new_path + + +class TransferAction(BaseAction): + """ This actions indicates that the Pulsar client should initiate an HTTP + transfer of the corresponding path to the remote Pulsar server before + launching the job. """ + action_type = "transfer" + staging = STAGING_ACTION_LOCAL + + +class CopyAction(BaseAction): + """ This action indicates that the Pulsar client should execute a file system + copy of the corresponding path to the Pulsar staging directory prior to + launching the corresponding job. """ + action_type = "copy" + staging = STAGING_ACTION_LOCAL + + +class RemoteCopyAction(BaseAction): + """ This action indicates the Pulsar server should copy the file before + execution via direct file system copy. This is like a CopyAction, but + it indicates the action should occur on the Pulsar server instead of on + the client. + """ + action_type = "remote_copy" + staging = STAGING_ACTION_REMOTE + + def to_dict(self): + return dict(path=self.path, action_type=self.action_type) + + @classmethod + def from_dict(cls, action_dict): + return RemoteCopyAction(path=action_dict["path"]) + + def write_to_path(self, path): + galaxy.util.copy_to_path(open(self.path, "rb"), path) + + def write_from_path(self, pulsar_path): + destination = self.path + parent_directory = dirname(destination) + if not exists(parent_directory): + makedirs(parent_directory) + with open(pulsar_path, "rb") as f: + galaxy.util.copy_to_path(f, destination) + + +class RemoteTransferAction(BaseAction): + """ This action indicates the Pulsar server should copy the file before + execution via direct file system copy. This is like a CopyAction, but + it indicates the action should occur on the Pulsar server instead of on + the client. + """ + action_type = "remote_transfer" + staging = STAGING_ACTION_REMOTE + + def __init__(self, path, file_lister=None, url=None): + super(RemoteTransferAction, self).__init__(path, file_lister=file_lister) + self.url = url + + def to_dict(self): + return dict(path=self.path, action_type=self.action_type, url=self.url) + + @classmethod + def from_dict(cls, action_dict): + return RemoteTransferAction(path=action_dict["path"], url=action_dict["url"]) + + def write_to_path(self, path): + get_file(self.url, path) + + def write_from_path(self, pulsar_path): + post_file(self.url, pulsar_path) + + +class MessageAction(object): + """ Sort of pseudo action describing "files" store in memory and + transferred via message (HTTP, Python-call, MQ, etc...) + """ + action_type = "message" + staging = STAGING_ACTION_DEFAULT + + def __init__(self, contents, client=None): + self.contents = contents + self.client = client + + @property + def staging_needed(self): + return True + + @property + def staging_action_local(self): + # Ekkk, cannot be called if created through from_dict. + # Shouldn't be a problem the way it is used - but is an + # object design problem. + return self.client.prefer_local_staging + + def to_dict(self): + return dict(contents=self.contents, action_type=MessageAction.action_type) + + @classmethod + def from_dict(cls, action_dict): + return MessageAction(contents=action_dict["contents"]) + + def write_to_path(self, path): + open(path, "w").write(self.contents) + + +DICTIFIABLE_ACTION_CLASSES = [RemoteCopyAction, RemoteTransferAction, MessageAction] + + +def from_dict(action_dict): + action_type = action_dict.get("action_type", None) + target_class = None + for action_class in DICTIFIABLE_ACTION_CLASSES: + if action_type == action_class.action_type: + target_class = action_class + if not target_class: + message = "Failed to recover action from dictionary - invalid action type specified %s." % action_type + raise Exception(message) + return target_class.from_dict(action_dict) + + +class BasePathMapper(object): + + def __init__(self, config): + action_type = config.get('action', DEFAULT_MAPPED_ACTION) + action_class = actions.get(action_type, None) + action_kwds = action_class.action_spec.copy() + for key, value in action_kwds.items(): + if key in config: + action_kwds[key] = config[key] + elif value is REQUIRED_ACTION_KWD: + message_template = "action_type %s requires key word argument %s" + message = message_template % (action_type, key) + raise Exception(message) + self.action_type = action_type + self.action_kwds = action_kwds + path_types_str = config.get('path_types', "*defaults*") + path_types_str = path_types_str.replace("*defaults*", ",".join(ACTION_DEFAULT_PATH_TYPES)) + path_types_str = path_types_str.replace("*any*", ",".join(ALL_PATH_TYPES)) + self.path_types = path_types_str.split(",") + self.file_lister = FileLister(config) + + def matches(self, path, path_type): + path_type_matches = path_type in self.path_types + return path_type_matches and self._path_matches(path) + + def _extend_base_dict(self, **kwds): + base_dict = dict( + action=self.action_type, + path_types=",".join(self.path_types), + match_type=self.match_type + ) + base_dict.update(self.file_lister.to_dict()) + base_dict.update(self.action_kwds) + base_dict.update(**kwds) + return base_dict + + +class PrefixPathMapper(BasePathMapper): + match_type = 'prefix' + + def __init__(self, config): + super(PrefixPathMapper, self).__init__(config) + self.prefix_path = abspath(config['path']) + + def _path_matches(self, path): + return path.startswith(self.prefix_path) + + def to_pattern(self): + pattern_str = "(%s%s[^\s,\"\']+)" % (escape(self.prefix_path), escape(sep)) + return compile(pattern_str) + + def to_dict(self): + return self._extend_base_dict(path=self.prefix_path) + + +class GlobPathMapper(BasePathMapper): + match_type = 'glob' + + def __init__(self, config): + super(GlobPathMapper, self).__init__(config) + self.glob_path = config['path'] + + def _path_matches(self, path): + return fnmatch.fnmatch(path, self.glob_path) + + def to_pattern(self): + return compile(fnmatch.translate(self.glob_path)) + + def to_dict(self): + return self._extend_base_dict(path=self.glob_path) + + +class RegexPathMapper(BasePathMapper): + match_type = 'regex' + + def __init__(self, config): + super(RegexPathMapper, self).__init__(config) + self.pattern_raw = config['path'] + self.pattern = compile(self.pattern_raw) + + def _path_matches(self, path): + return self.pattern.match(path) is not None + + def to_pattern(self): + return self.pattern + + def to_dict(self): + return self._extend_base_dict(path=self.pattern_raw) + +MAPPER_CLASSES = [PrefixPathMapper, GlobPathMapper, RegexPathMapper] +MAPPER_CLASS_DICT = dict(map(lambda c: (c.match_type, c), MAPPER_CLASSES)) + + +def mappers_from_dicts(mapper_def_list): + return map(lambda m: __mappper_from_dict(m), mapper_def_list) + + +def __mappper_from_dict(mapper_dict): + map_type = mapper_dict.get('match_type', DEFAULT_PATH_MAPPER_TYPE) + return MAPPER_CLASS_DICT[map_type](mapper_dict) + + +class FileLister(object): + + def __init__(self, config): + self.depth = int(config.get("depth", "0")) + + def to_dict(self): + return dict( + depth=self.depth + ) + + def unstructured_map(self, path): + depth = self.depth + if self.depth == 0: + return {path: basename(path)} + else: + while depth > 0: + path = dirname(path) + depth -= 1 + return dict([(join(path, f), f) for f in directory_files(path)]) + +DEFAULT_FILE_LISTER = FileLister(dict(depth=0)) + +ACTION_CLASSES = [ + NoneAction, + RewriteAction, + TransferAction, + CopyAction, + RemoteCopyAction, + RemoteTransferAction, +] +actions = dict([(clazz.action_type, clazz) for clazz in ACTION_CLASSES]) + + +__all__ = [ + FileActionMapper, + path_type, + from_dict, + MessageAction, + RemoteTransferAction, # For testing +] diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/pulsar/client/amqp_exchange.py --- /dev/null +++ b/lib/pulsar/client/amqp_exchange.py @@ -0,0 +1,139 @@ +try: + import kombu + from kombu import pools +except ImportError: + kombu = None + +import socket +import logging +import threading +from time import sleep +log = logging.getLogger(__name__) + + +KOMBU_UNAVAILABLE = "Attempting to bind to AMQP message queue, but kombu dependency unavailable" + +DEFAULT_EXCHANGE_NAME = "pulsar" +DEFAULT_EXCHANGE_TYPE = "direct" +# Set timeout to periodically give up looking and check if polling should end. +DEFAULT_TIMEOUT = 0.2 +DEFAULT_HEARTBEAT = 580 + +DEFAULT_RECONNECT_CONSUMER_WAIT = 1 +DEFAULT_HEARTBEAT_WAIT = 1 + + +class PulsarExchange(object): + """ Utility for publishing and consuming structured Pulsar queues using kombu. + This is shared between the server and client - an exchange should be setup + for each manager (or in the case of the client, each manager one wished to + communicate with.) + + Each Pulsar manager is defined solely by name in the scheme, so only one Pulsar + should target each AMQP endpoint or care should be taken that unique + manager names are used across Pulsar servers targetting same AMQP endpoint - + and in particular only one such Pulsar should define an default manager with + name _default_. + """ + + def __init__( + self, + url, + manager_name, + connect_ssl=None, + timeout=DEFAULT_TIMEOUT, + publish_kwds={}, + ): + """ + """ + if not kombu: + raise Exception(KOMBU_UNAVAILABLE) + self.__url = url + self.__manager_name = manager_name + self.__connect_ssl = connect_ssl + self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE) + self.__timeout = timeout + # Be sure to log message publishing failures. + if publish_kwds.get("retry", False): + if "retry_policy" not in publish_kwds: + publish_kwds["retry_policy"] = {} + if "errback" not in publish_kwds["retry_policy"]: + publish_kwds["retry_policy"]["errback"] = self.__publish_errback + self.__publish_kwds = publish_kwds + + @property + def url(self): + return self.__url + + def consume(self, queue_name, callback, check=True, connection_kwargs={}): + queue = self.__queue(queue_name) + log.debug("Consuming queue '%s'", queue) + while check: + heartbeat_thread = None + try: + with self.connection(self.__url, heartbeat=DEFAULT_HEARTBEAT, **connection_kwargs) as connection: + with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): + heartbeat_thread = self.__start_heartbeat(queue_name, connection) + while check and connection.connected: + try: + connection.drain_events(timeout=self.__timeout) + except socket.timeout: + pass + except (IOError, socket.error), exc: + # In testing, errno is None + log.warning('Got %s, will retry: %s', exc.__class__.__name__, exc) + if heartbeat_thread: + heartbeat_thread.join() + sleep(DEFAULT_RECONNECT_CONSUMER_WAIT) + + def heartbeat(self, connection): + log.debug('AMQP heartbeat thread alive') + while connection.connected: + connection.heartbeat_check() + sleep(DEFAULT_HEARTBEAT_WAIT) + log.debug('AMQP heartbeat thread exiting') + + def publish(self, name, payload): + with self.connection(self.__url) as connection: + with pools.producers[connection].acquire() as producer: + key = self.__queue_name(name) + producer.publish( + payload, + serializer='json', + exchange=self.__exchange, + declare=[self.__exchange], + routing_key=key, + **self.__publish_kwds + ) + + def __publish_errback(self, exc, interval): + log.error("Connection error while publishing: %r", exc, exc_info=1) + log.info("Retrying in %s seconds", interval) + + def connection(self, connection_string, **kwargs): + if "ssl" not in kwargs: + kwargs["ssl"] = self.__connect_ssl + return kombu.Connection(connection_string, **kwargs) + + def __queue(self, name): + queue_name = self.__queue_name(name) + queue = kombu.Queue(queue_name, self.__exchange, routing_key=queue_name) + return queue + + def __queue_name(self, name): + key_prefix = self.__key_prefix() + queue_name = '%s_%s' % (key_prefix, name) + return queue_name + + def __key_prefix(self): + if self.__manager_name == "_default_": + key_prefix = "pulsar_" + else: + key_prefix = "pulsar_%s_" % self.__manager_name + return key_prefix + + def __start_heartbeat(self, queue_name, connection): + thread_name = "consume-heartbeat-%s" % (self.__queue_name(queue_name)) + thread = threading.Thread(name=thread_name, target=self.heartbeat, args=(connection,)) + thread.start() + return thread diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/pulsar/client/amqp_exchange_factory.py --- /dev/null +++ b/lib/pulsar/client/amqp_exchange_factory.py @@ -0,0 +1,41 @@ +from .amqp_exchange import PulsarExchange +from .util import filter_destination_params + + +def get_exchange(url, manager_name, params): + connect_ssl = parse_amqp_connect_ssl_params(params) + exchange_kwds = dict( + manager_name=manager_name, + connect_ssl=connect_ssl, + publish_kwds=parse_amqp_publish_kwds(params) + ) + timeout = params.get('amqp_consumer_timeout', False) + if timeout is not False: + exchange_kwds['timeout'] = timeout + exchange = PulsarExchange(url, **exchange_kwds) + return exchange + + +def parse_amqp_connect_ssl_params(params): + ssl_params = filter_destination_params(params, "amqp_connect_ssl_") + if not ssl_params: + return + + ssl = __import__('ssl') + if 'cert_reqs' in ssl_params: + value = ssl_params['cert_reqs'] + ssl_params['cert_reqs'] = getattr(ssl, value.upper()) + return ssl_params + + +def parse_amqp_publish_kwds(params): + all_publish_params = filter_destination_params(params, "amqp_publish_") + retry_policy_params = {} + for key in all_publish_params.keys(): + if key.startswith("retry_"): + value = all_publish_params[key] + retry_policy_params[key[len("retry_"):]] = value + del all_publish_params[key] + if retry_policy_params: + all_publish_params["retry_policy"] = retry_policy_params + return all_publish_params This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8c569cffa967/ Changeset: 8c569cffa967 User: jmchilton Date: 2014-06-20 07:28:36 Summary: Implement Pulsar job runners. LWR runner and client remains in Galaxy as is and can continue to target old LWR server. But these should be considered deprecated and will likely be dropped at some point. The LWR documentaiton in job_conf.xml.sample_advanced has been replaced with Pulsar documentation to reflect this. Pulsar runners will need to target a Pulsar server (now with a RESTful web interface - MQ option also available). Information on upgrading an LWR instance to pulsar can be found in the [Pulsar docs](http://pulsar.readthedocs.org/en/latest/#upgrading-from-the-lwr). Three new job runners have been added to replace the LWR runner. The `PulsarLegacyJobRunner` more or less has all of the old defaults that the LWR runner had and this one should be easiest to get working for people who are porting over old LWR servers (and will likely be most compatible with remote Windows hosts). The `PulsarRESTJobRunner` targets a remote Pulsar server over HTTP(S) but has newer standard configuration options such as rewriting parameters at tool stage by default, remote dependency evaluation by default, etc.... The `PulsarMQJobRunner` targets a remote Pulsar server via AMQP - and has the newer defaults of the RESTful runner as well as targetting the Galaxy job files API by default. The `url` runner parameter has been renamed `amqp_url` for clarity. These newer runners improve parameter handling in other ways such as warning deployers when ignored parameters are supplied. Affected #: 32 files diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -19,27 +19,30 @@ <param id="drmaa_library_path">/sge/lib/libdrmaa.so</param></plugin> - <plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr:LwrJobRunner"> -  -  + <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> + <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> + <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> +  + <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"> +  -  - </plugin> - <plugin id="amqp_lwr" type="runner" load="galaxy.jobs.runners.lwr:LwrJobRunner"> - <param id="url">amqp://guest:guest@localhost:5672//</param> -  + <plugin id="pulsar_mq" type="runner" load="galaxy.jobs.runners.pulsar:PulsarMQJobRunner"> +  + <param id="amqp_url">amqp://guest:guest@localhost:5672//</param> + <param id="galaxy_url">http://localhost:8080</param> -  + </plugin> - <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> - <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> - <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> + <plugin id="pulsar_legacy" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner"> +  + </plugin></plugins><handlers default="handlers"> @@ -213,87 +224,71 @@ <param id="function">foo</param></destination> - <destination id="secure_lwr" runner="lwr"> - <param id="url">https://windowshost.examle.com:8913/</param> -  + <destination id="secure_pulsar_rest_dest" runner="pulsar_rest"> + <param id="url">https://examle.com:8913/</param> + <param id="private_token">123456789changeme</param> -  -  +  -  -  -  +  -  -  -  +  +  + </destination> - <destination id="amqp_lwr_dest" runner="amqp_lwr" > -  -  - <param id="jobs_directory">/path/to/remote/lwr/lwr_staging/</param> -  - <param id="default_file_action">remote_transfer</param></destination><destination id="ssh_torque" runner="cli"><param id="shell_plugin">SecureShell</param> diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/galaxy/jobs/runners/pulsar.py --- /dev/null +++ b/lib/galaxy/jobs/runners/pulsar.py @@ -0,0 +1,707 @@ +from __future__ import absolute_import # Need to import pulsar_client absolutely. + +import logging + +from galaxy import model +from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner +from galaxy.jobs import ComputeEnvironment +from galaxy.jobs import JobDestination +from galaxy.jobs.command_factory import build_command +from galaxy.tools.deps import dependencies +from galaxy.util import string_as_bool_or_none +from galaxy.util.bunch import Bunch +from galaxy.util import specs + +import errno +from time import sleep +import os + +from pulsar.client import build_client_manager +from pulsar.client import url_to_destination_params +from pulsar.client import finish_job as pulsar_finish_job +from pulsar.client import submit_job as pulsar_submit_job +from pulsar.client import ClientJobDescription +from pulsar.client import PulsarOutputs +from pulsar.client import ClientOutputs +from pulsar.client import PathMapper + +log = logging.getLogger( __name__ ) + +__all__ = [ 'PulsarLegacyJobRunner', 'PulsarRESTJobRunner', 'PulsarMQJobRunner' ] + +NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "Pulsar misconfiguration - Pulsar client configured to set metadata remotely, but remote Pulsar isn't properly configured with a galaxy_home directory." +NO_REMOTE_DATATYPES_CONFIG = "Pulsar client is configured to use remote datatypes configuration when setting metadata externally, but Pulsar is not configured with this information. Defaulting to datatypes_conf.xml." +GENERIC_REMOTE_ERROR = "Failed to communicate with remote job server." + +# Is there a good way to infer some default for this? Can only use +# url_for from web threads. https://gist.github.com/jmchilton/9098762 +DEFAULT_GALAXY_URL = "http://localhost:8080" + +PULSAR_PARAM_SPECS = dict( + transport=dict( + map=specs.to_str_or_none, + valid=specs.is_in("urllib", "curl", None), + default=None + ), + cache=dict( + map=specs.to_bool_or_none, + default=None, + ), + amqp_url=dict( + map=specs.to_str_or_none, + default=None, + ), + galaxy_url=dict( + map=specs.to_str_or_none, + default=DEFAULT_GALAXY_URL, + ), + manager=dict( + map=specs.to_str_or_none, + default=None, + ), + amqp_consumer_timeout=dict( + map=lambda val: None if val == "None" else float(val), + default=None, + ), + amqp_connect_ssl_ca_certs=dict( + map=specs.to_str_or_none, + default=None, + ), + amqp_connect_ssl_keyfile=dict( + map=specs.to_str_or_none, + default=None, + ), + amqp_connect_ssl_certfile=dict( + map=specs.to_str_or_none, + default=None, + ), + amqp_connect_ssl_cert_reqs=dict( + map=specs.to_str_or_none, + default=None, + ), + # http://kombu.readthedocs.org/en/latest/reference/kombu.html#kombu.Producer.… + amqp_publish_retry=dict( + map=specs.to_bool, + default=False, + ), + amqp_publish_priority=dict( + map=int, + valid=lambda x: 0 <= x and x <= 9, + default=0, + ), + # http://kombu.readthedocs.org/en/latest/reference/kombu.html#kombu.Exchange.… + amqp_publish_delivery_mode=dict( + map=str, + valid=specs.is_in("transient", "persistent"), + default="persistent", + ), + amqp_publish_retry_max_retries=dict( + map=int, + default=None, + ), + amqp_publish_retry_interval_start=dict( + map=int, + default=None, + ), + amqp_publish_retry_interval_step=dict( + map=int, + default=None, + ), + amqp_publish_retry_interval_max=dict( + map=int, + default=None, + ), +) + + +PARAMETER_SPECIFICATION_REQUIRED = object() +PARAMETER_SPECIFICATION_IGNORED = object() + + +class PulsarJobRunner( AsynchronousJobRunner ): + """ + Pulsar Job Runner + """ + runner_name = "PulsarJobRunner" + + def __init__( self, app, nworkers, **kwds ): + """Start the job runner """ + super( PulsarJobRunner, self ).__init__( app, nworkers, runner_param_specs=PULSAR_PARAM_SPECS, **kwds ) + self._init_worker_threads() + galaxy_url = self.runner_params.galaxy_url + if galaxy_url: + galaxy_url = galaxy_url.rstrip("/") + self.galaxy_url = galaxy_url + self.__init_client_manager() + self._monitor() + + def _monitor( self ): + # Extension point allow MQ variant to setup callback instead + self._init_monitor_thread() + + def __init_client_manager( self ): + client_manager_kwargs = {} + for kwd in 'manager', 'cache', 'transport': + client_manager_kwargs[ kwd ] = self.runner_params[ kwd ] + for kwd in self.runner_params.keys(): + if kwd.startswith( 'amqp_' ): + client_manager_kwargs[ kwd ] = self.runner_params[ kwd ] + self.client_manager = build_client_manager(**client_manager_kwargs) + + def url_to_destination( self, url ): + """Convert a legacy URL to a job destination""" + return JobDestination( runner="pulsar", params=url_to_destination_params( url ) ) + + def check_watched_item(self, job_state): + try: + client = self.get_client_from_state(job_state) + status = client.get_status() + except Exception: + # An orphaned job was put into the queue at app startup, so remote server went down + # either way we are done I guess. + self.mark_as_finished(job_state) + return None + job_state = self._update_job_state_for_status(job_state, status) + return job_state + + def _update_job_state_for_status(self, job_state, pulsar_status): + if pulsar_status == "complete": + self.mark_as_finished(job_state) + return None + if pulsar_status == "failed": + self.fail_job(job_state) + return None + if pulsar_status == "running" and not job_state.running: + job_state.running = True + job_state.job_wrapper.change_state( model.Job.states.RUNNING ) + return job_state + + def queue_job(self, job_wrapper): + job_destination = job_wrapper.job_destination + self._populate_parameter_defaults( job_destination ) + + command_line, client, remote_job_config, compute_environment = self.__prepare_job( job_wrapper, job_destination ) + + if not command_line: + return + + try: + dependencies_description = PulsarJobRunner.__dependencies_description( client, job_wrapper ) + rewrite_paths = not PulsarJobRunner.__rewrite_parameters( client ) + unstructured_path_rewrites = {} + if compute_environment: + unstructured_path_rewrites = compute_environment.unstructured_path_rewrites + + client_job_description = ClientJobDescription( + command_line=command_line, + input_files=self.get_input_files(job_wrapper), + client_outputs=self.__client_outputs(client, job_wrapper), + working_directory=job_wrapper.working_directory, + tool=job_wrapper.tool, + config_files=job_wrapper.extra_filenames, + dependencies_description=dependencies_description, + env=client.env, + rewrite_paths=rewrite_paths, + arbitrary_files=unstructured_path_rewrites, + ) + job_id = pulsar_submit_job(client, client_job_description, remote_job_config) + log.info("Pulsar job submitted with job_id %s" % job_id) + job_wrapper.set_job_destination( job_destination, job_id ) + job_wrapper.change_state( model.Job.states.QUEUED ) + except Exception: + job_wrapper.fail( "failure running job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + return + + pulsar_job_state = AsynchronousJobState() + pulsar_job_state.job_wrapper = job_wrapper + pulsar_job_state.job_id = job_id + pulsar_job_state.old_state = True + pulsar_job_state.running = False + pulsar_job_state.job_destination = job_destination + self.monitor_job(pulsar_job_state) + + def __prepare_job(self, job_wrapper, job_destination): + """ Build command-line and Pulsar client for this job. """ + command_line = None + client = None + remote_job_config = None + compute_environment = None + try: + client = self.get_client_from_wrapper(job_wrapper) + tool = job_wrapper.tool + remote_job_config = client.setup(tool.id, tool.version) + rewrite_parameters = PulsarJobRunner.__rewrite_parameters( client ) + prepare_kwds = {} + if rewrite_parameters: + compute_environment = PulsarComputeEnvironment( client, job_wrapper, remote_job_config ) + prepare_kwds[ 'compute_environment' ] = compute_environment + job_wrapper.prepare( **prepare_kwds ) + self.__prepare_input_files_locally(job_wrapper) + remote_metadata = PulsarJobRunner.__remote_metadata( client ) + dependency_resolution = PulsarJobRunner.__dependency_resolution( client ) + metadata_kwds = self.__build_metadata_configuration(client, job_wrapper, remote_metadata, remote_job_config) + remote_command_params = dict( + working_directory=remote_job_config['working_directory'], + metadata_kwds=metadata_kwds, + dependency_resolution=dependency_resolution, + ) + remote_working_directory = remote_job_config['working_directory'] + # TODO: Following defs work for Pulsar, always worked for Pulsar but should be + # calculated at some other level. + remote_job_directory = os.path.abspath(os.path.join(remote_working_directory, os.path.pardir)) + remote_tool_directory = os.path.abspath(os.path.join(remote_job_directory, "tool_files")) + container = self._find_container( + job_wrapper, + compute_working_directory=remote_working_directory, + compute_tool_directory=remote_tool_directory, + compute_job_directory=remote_job_directory, + ) + command_line = build_command( + self, + job_wrapper=job_wrapper, + container=container, + include_metadata=remote_metadata, + include_work_dir_outputs=False, + remote_command_params=remote_command_params, + ) + except Exception: + job_wrapper.fail( "failure preparing job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + + # If we were able to get a command line, run the job + if not command_line: + job_wrapper.finish( '', '' ) + + return command_line, client, remote_job_config, compute_environment + + def __prepare_input_files_locally(self, job_wrapper): + """Run task splitting commands locally.""" + prepare_input_files_cmds = getattr(job_wrapper, 'prepare_input_files_cmds', None) + if prepare_input_files_cmds is not None: + for cmd in prepare_input_files_cmds: # run the commands to stage the input files + if 0 != os.system(cmd): + raise Exception('Error running file staging command: %s' % cmd) + job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line + + def _populate_parameter_defaults( self, job_destination ): + updated = False + params = job_destination.params + for key, value in self.destination_defaults.iteritems(): + if key in params: + if value is PARAMETER_SPECIFICATION_IGNORED: + log.warn( "Pulsar runner in selected configuration ignores parameter %s" % key ) + continue + #if self.runner_params.get( key, None ): + # # Let plugin define defaults for some parameters - + # # for instance that way jobs_directory can be + # # configured next to AMQP url (where it belongs). + # params[ key ] = self.runner_params[ key ] + # continue + + if not value: + continue + + if value is PARAMETER_SPECIFICATION_REQUIRED: + raise Exception( "Pulsar destination does not define required parameter %s" % key ) + elif value is not PARAMETER_SPECIFICATION_IGNORED: + params[ key ] = value + updated = True + return updated + + def get_output_files(self, job_wrapper): + output_paths = job_wrapper.get_output_fnames() + return [ str( o ) for o in output_paths ] # Force job_path from DatasetPath objects. + + def get_input_files(self, job_wrapper): + input_paths = job_wrapper.get_input_paths() + return [ str( i ) for i in input_paths ] # Force job_path from DatasetPath objects. + + def get_client_from_wrapper(self, job_wrapper): + job_id = job_wrapper.job_id + if hasattr(job_wrapper, 'task_id'): + job_id = "%s_%s" % (job_id, job_wrapper.task_id) + params = job_wrapper.job_destination.params.copy() + for key, value in params.iteritems(): + if value: + params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) + + env = getattr( job_wrapper.job_destination, "env", [] ) + return self.get_client( params, job_id, env ) + + def get_client_from_state(self, job_state): + job_destination_params = job_state.job_destination.params + job_id = job_state.job_id + return self.get_client( job_destination_params, job_id ) + + def get_client( self, job_destination_params, job_id, env=[] ): + # Cannot use url_for outside of web thread. + #files_endpoint = url_for( controller="job_files", job_id=encoded_job_id ) + + encoded_job_id = self.app.security.encode_id(job_id) + job_key = self.app.security.encode_id( job_id, kind="jobs_files" ) + files_endpoint = "%s/api/jobs/%s/files?job_key=%s" % ( + self.galaxy_url, + encoded_job_id, + job_key + ) + get_client_kwds = dict( + job_id=str( job_id ), + files_endpoint=files_endpoint, + env=env + ) + return self.client_manager.get_client( job_destination_params, **get_client_kwds ) + + def finish_job( self, job_state ): + stderr = stdout = '' + job_wrapper = job_state.job_wrapper + try: + client = self.get_client_from_state(job_state) + run_results = client.full_status() + remote_working_directory = run_results.get("working_directory", None) + stdout = run_results.get('stdout', '') + stderr = run_results.get('stderr', '') + exit_code = run_results.get('returncode', None) + pulsar_outputs = PulsarOutputs.from_status_response(run_results) + # Use Pulsar client code to transfer/copy files back + # and cleanup job if needed. + completed_normally = \ + job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] + cleanup_job = self.app.config.cleanup_job + client_outputs = self.__client_outputs(client, job_wrapper) + finish_args = dict( client=client, + job_completed_normally=completed_normally, + cleanup_job=cleanup_job, + client_outputs=client_outputs, + pulsar_outputs=pulsar_outputs ) + failed = pulsar_finish_job( **finish_args ) + if failed: + job_wrapper.fail("Failed to find or download one or more job outputs from remote server.", exception=True) + except Exception: + message = GENERIC_REMOTE_ERROR + job_wrapper.fail( message, exception=True ) + log.exception("failure finishing job %d" % job_wrapper.job_id) + return + if not PulsarJobRunner.__remote_metadata( client ): + self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) + # Finish the job + try: + job_wrapper.finish( + stdout, + stderr, + exit_code, + remote_working_directory=remote_working_directory + ) + except Exception: + log.exception("Job wrapper finish method failed") + job_wrapper.fail("Unable to finish job", exception=True) + + def fail_job( self, job_state ): + """ + Seperated out so we can use the worker threads for it. + """ + self.stop_job( self.sa_session.query( self.app.model.Job ).get( job_state.job_wrapper.job_id ) ) + job_state.job_wrapper.fail( getattr( job_state, "fail_message", GENERIC_REMOTE_ERROR ) ) + + def check_pid( self, pid ): + try: + os.kill( pid, 0 ) + return True + except OSError, e: + if e.errno == errno.ESRCH: + log.debug( "check_pid(): PID %d is dead" % pid ) + else: + log.warning( "check_pid(): Got errno %s when attempting to check PID %d: %s" % ( errno.errorcode[e.errno], pid, e.strerror ) ) + return False + + def stop_job( self, job ): + #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished + job_ext_output_metadata = job.get_external_output_metadata() + if job_ext_output_metadata: + pid = job_ext_output_metadata[0].job_runner_external_pid # every JobExternalOutputMetadata has a pid set, we just need to take from one of them + if pid in [ None, '' ]: + log.warning( "stop_job(): %s: no PID in database for job, unable to stop" % job.id ) + return + pid = int( pid ) + if not self.check_pid( pid ): + log.warning( "stop_job(): %s: PID %d was already dead or can't be signaled" % ( job.id, pid ) ) + return + for sig in [ 15, 9 ]: + try: + os.killpg( pid, sig ) + except OSError, e: + log.warning( "stop_job(): %s: Got errno %s when attempting to signal %d to PID %d: %s" % ( job.id, errno.errorcode[e.errno], sig, pid, e.strerror ) ) + return # give up + sleep( 2 ) + if not self.check_pid( pid ): + log.debug( "stop_job(): %s: PID %d successfully killed with signal %d" % ( job.id, pid, sig ) ) + return + else: + log.warning( "stop_job(): %s: PID %d refuses to die after signaling TERM/KILL" % ( job.id, pid ) ) + else: + # Remote kill + pulsar_url = job.job_runner_name + job_id = job.job_runner_external_id + log.debug("Attempt remote Pulsar kill of job with url %s and id %s" % (pulsar_url, job_id)) + client = self.get_client(job.destination_params, job_id) + client.kill() + + def recover( self, job, job_wrapper ): + """Recovers jobs stuck in the queued/running state when Galaxy started""" + job_state = self._job_state( job, job_wrapper ) + job_wrapper.command_line = job.get_command_line() + state = job.get_state() + if state in [model.Job.states.RUNNING, model.Job.states.QUEUED]: + log.debug( "(Pulsar/%s) is still in running state, adding to the Pulsar queue" % ( job.get_id()) ) + job_state.old_state = True + job_state.running = state == model.Job.states.RUNNING + self.monitor_queue.put( job_state ) + + def shutdown( self ): + super( PulsarJobRunner, self ).shutdown() + self.client_manager.shutdown() + + def _job_state( self, job, job_wrapper ): + job_state = AsynchronousJobState() + # TODO: Determine why this is set when using normal message queue updates + # but not CLI submitted MQ updates... + raw_job_id = job.get_job_runner_external_id() or job_wrapper.job_id + job_state.job_id = str( raw_job_id ) + job_state.runner_url = job_wrapper.get_job_runner_url() + job_state.job_destination = job_wrapper.job_destination + job_state.job_wrapper = job_wrapper + return job_state + + def __client_outputs( self, client, job_wrapper ): + work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) + output_files = self.get_output_files( job_wrapper ) + client_outputs = ClientOutputs( + working_directory=job_wrapper.working_directory, + work_dir_outputs=work_dir_outputs, + output_files=output_files, + version_file=job_wrapper.get_version_string_path(), + ) + return client_outputs + + @staticmethod + def __dependencies_description( pulsar_client, job_wrapper ): + dependency_resolution = PulsarJobRunner.__dependency_resolution( pulsar_client ) + remote_dependency_resolution = dependency_resolution == "remote" + if not remote_dependency_resolution: + return None + requirements = job_wrapper.tool.requirements or [] + installed_tool_dependencies = job_wrapper.tool.installed_tool_dependencies or [] + return dependencies.DependenciesDescription( + requirements=requirements, + installed_tool_dependencies=installed_tool_dependencies, + ) + + @staticmethod + def __dependency_resolution( pulsar_client ): + dependency_resolution = pulsar_client.destination_params.get( "dependency_resolution", "local" ) + if dependency_resolution not in ["none", "local", "remote"]: + raise Exception("Unknown dependency_resolution value encountered %s" % dependency_resolution) + return dependency_resolution + + @staticmethod + def __remote_metadata( pulsar_client ): + remote_metadata = string_as_bool_or_none( pulsar_client.destination_params.get( "remote_metadata", False ) ) + return remote_metadata + + @staticmethod + def __use_remote_datatypes_conf( pulsar_client ): + """ When setting remote metadata, use integrated datatypes from this + Galaxy instance or use the datatypes config configured via the remote + Pulsar. + + Both options are broken in different ways for same reason - datatypes + may not match. One can push the local datatypes config to the remote + server - but there is no guarentee these datatypes will be defined + there. Alternatively, one can use the remote datatype config - but + there is no guarentee that it will contain all the datatypes available + to this Galaxy. + """ + use_remote_datatypes = string_as_bool_or_none( pulsar_client.destination_params.get( "use_remote_datatypes", False ) ) + return use_remote_datatypes + + @staticmethod + def __rewrite_parameters( pulsar_client ): + return string_as_bool_or_none( pulsar_client.destination_params.get( "rewrite_parameters", False ) ) or False + + def __build_metadata_configuration(self, client, job_wrapper, remote_metadata, remote_job_config): + metadata_kwds = {} + if remote_metadata: + remote_system_properties = remote_job_config.get("system_properties", {}) + remote_galaxy_home = remote_system_properties.get("galaxy_home", None) + if not remote_galaxy_home: + raise Exception(NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE) + metadata_kwds['exec_dir'] = remote_galaxy_home + outputs_directory = remote_job_config['outputs_directory'] + configs_directory = remote_job_config['configs_directory'] + working_directory = remote_job_config['working_directory'] + # For metadata calculation, we need to build a list of of output + # file objects with real path indicating location on Galaxy server + # and false path indicating location on compute server. Since the + # Pulsar disables from_work_dir copying as part of the job command + # line we need to take the list of output locations on the Pulsar + # server (produced by self.get_output_files(job_wrapper)) and for + # each work_dir output substitute the effective path on the Pulsar + # server relative to the remote working directory as the + # false_path to send the metadata command generation module. + work_dir_outputs = self.get_work_dir_outputs(job_wrapper, job_working_directory=working_directory) + outputs = [Bunch(false_path=os.path.join(outputs_directory, os.path.basename(path)), real_path=path) for path in self.get_output_files(job_wrapper)] + for output in outputs: + for pulsar_workdir_path, real_path in work_dir_outputs: + if real_path == output.real_path: + output.false_path = pulsar_workdir_path + metadata_kwds['output_fnames'] = outputs + metadata_kwds['compute_tmp_dir'] = working_directory + metadata_kwds['config_root'] = remote_galaxy_home + default_config_file = os.path.join(remote_galaxy_home, 'universe_wsgi.ini') + metadata_kwds['config_file'] = remote_system_properties.get('galaxy_config_file', default_config_file) + metadata_kwds['dataset_files_path'] = remote_system_properties.get('galaxy_dataset_files_path', None) + if PulsarJobRunner.__use_remote_datatypes_conf( client ): + remote_datatypes_config = remote_system_properties.get('galaxy_datatypes_config_file', None) + if not remote_datatypes_config: + log.warn(NO_REMOTE_DATATYPES_CONFIG) + remote_datatypes_config = os.path.join(remote_galaxy_home, 'datatypes_conf.xml') + metadata_kwds['datatypes_config'] = remote_datatypes_config + else: + integrates_datatypes_config = self.app.datatypes_registry.integrated_datatypes_configs + # Ensure this file gets pushed out to the remote config dir. + job_wrapper.extra_filenames.append(integrates_datatypes_config) + + metadata_kwds['datatypes_config'] = os.path.join(configs_directory, os.path.basename(integrates_datatypes_config)) + return metadata_kwds + + +class PulsarLegacyJobRunner( PulsarJobRunner ): + destination_defaults = dict( + rewrite_parameters="false", + dependency_resolution="local", + ) + + +class PulsarMQJobRunner( PulsarJobRunner ): + destination_defaults = dict( + default_file_action="remote_transfer", + rewrite_parameters="true", + dependency_resolution="remote", + jobs_directory=PARAMETER_SPECIFICATION_REQUIRED, + url=PARAMETER_SPECIFICATION_IGNORED, + private_token=PARAMETER_SPECIFICATION_IGNORED + ) + + def _monitor( self ): + # This is a message queue driven runner, don't monitor + # just setup required callback. + self.client_manager.ensure_has_status_update_callback(self.__async_update) + + def __async_update( self, full_status ): + job_id = None + try: + job_id = full_status[ "job_id" ] + job, job_wrapper = self.app.job_manager.job_handler.job_queue.job_pair_for_id( job_id ) + job_state = self._job_state( job, job_wrapper ) + self._update_job_state_for_status(job_state, full_status[ "status" ] ) + except Exception: + log.exception( "Failed to update Pulsar job status for job_id %s" % job_id ) + raise + # Nothing else to do? - Attempt to fail the job? + + +class PulsarRESTJobRunner( PulsarJobRunner ): + destination_defaults = dict( + default_file_action="transfer", + rewrite_parameters="true", + dependency_resolution="remote", + url=PARAMETER_SPECIFICATION_REQUIRED, + ) + + +class PulsarComputeEnvironment( ComputeEnvironment ): + + def __init__( self, pulsar_client, job_wrapper, remote_job_config ): + self.pulsar_client = pulsar_client + self.job_wrapper = job_wrapper + self.local_path_config = job_wrapper.default_compute_environment() + self.unstructured_path_rewrites = {} + # job_wrapper.prepare is going to expunge the job backing the following + # computations, so precalculate these paths. + self._wrapper_input_paths = self.local_path_config.input_paths() + self._wrapper_output_paths = self.local_path_config.output_paths() + self.path_mapper = PathMapper(pulsar_client, remote_job_config, self.local_path_config.working_directory()) + self._config_directory = remote_job_config[ "configs_directory" ] + self._working_directory = remote_job_config[ "working_directory" ] + self._sep = remote_job_config[ "system_properties" ][ "separator" ] + self._tool_dir = remote_job_config[ "tools_directory" ] + version_path = self.local_path_config.version_path() + new_version_path = self.path_mapper.remote_version_path_rewrite(version_path) + if new_version_path: + version_path = new_version_path + self._version_path = version_path + + def output_paths( self ): + local_output_paths = self._wrapper_output_paths + + results = [] + for local_output_path in local_output_paths: + wrapper_path = str( local_output_path ) + remote_path = self.path_mapper.remote_output_path_rewrite( wrapper_path ) + results.append( self._dataset_path( local_output_path, remote_path ) ) + return results + + def input_paths( self ): + local_input_paths = self._wrapper_input_paths + + results = [] + for local_input_path in local_input_paths: + wrapper_path = str( local_input_path ) + # This will over-copy in some cases. For instance in the case of task + # splitting, this input will be copied even though only the work dir + # input will actually be used. + remote_path = self.path_mapper.remote_input_path_rewrite( wrapper_path ) + results.append( self._dataset_path( local_input_path, remote_path ) ) + return results + + def _dataset_path( self, local_dataset_path, remote_path ): + remote_extra_files_path = None + if remote_path: + remote_extra_files_path = "%s_files" % remote_path[ 0:-len( ".dat" ) ] + return local_dataset_path.with_path_for_job( remote_path, remote_extra_files_path ) + + def working_directory( self ): + return self._working_directory + + def config_directory( self ): + return self._config_directory + + def new_file_path( self ): + return self.working_directory() # Problems with doing this? + + def sep( self ): + return self._sep + + def version_path( self ): + return self._version_path + + def rewriter( self, parameter_value ): + unstructured_path_rewrites = self.unstructured_path_rewrites + if parameter_value in unstructured_path_rewrites: + # Path previously mapped, use previous mapping. + return unstructured_path_rewrites[ parameter_value ] + if parameter_value in unstructured_path_rewrites.itervalues(): + # Path is a rewritten remote path (this might never occur, + # consider dropping check...) + return parameter_value + + rewrite, new_unstructured_path_rewrites = self.path_mapper.check_for_arbitrary_rewrite( parameter_value ) + if rewrite: + unstructured_path_rewrites.update(new_unstructured_path_rewrites) + return rewrite + else: + # Did need to rewrite, use original path or value. + return parameter_value + + def unstructured_path_rewriter( self ): + return self.rewriter diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/galaxy/jobs/runners/util/__init__.py --- a/lib/galaxy/jobs/runners/util/__init__.py +++ b/lib/galaxy/jobs/runners/util/__init__.py @@ -1,7 +1,7 @@ """ This module and its submodules contains utilities for running external processes and interfacing with job managers. This module should contain -functionality shared between Galaxy and the LWR. +functionality shared between Galaxy and the Pulsar. """ from galaxy.util.bunch import Bunch diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/galaxy/jobs/runners/util/cli/factory.py --- a/lib/galaxy/jobs/runners/util/cli/factory.py +++ b/lib/galaxy/jobs/runners/util/cli/factory.py @@ -5,7 +5,7 @@ ) code_dir = 'lib' except ImportError: - from lwr.managers.util.cli import ( + from pulsar.managers.util.cli import ( CliInterface, split_params ) diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/galaxy/jobs/runners/util/cli/job/slurm.py --- a/lib/galaxy/jobs/runners/util/cli/job/slurm.py +++ b/lib/galaxy/jobs/runners/util/cli/job/slurm.py @@ -5,7 +5,7 @@ from galaxy.model import Job job_states = Job.states except ImportError: - # Not in Galaxy, map Galaxy job states to LWR ones. + # Not in Galaxy, map Galaxy job states to Pulsar ones. from galaxy.util import enum job_states = enum(RUNNING='running', OK='complete', QUEUED='queued') diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/galaxy/jobs/runners/util/cli/job/torque.py --- a/lib/galaxy/jobs/runners/util/cli/job/torque.py +++ b/lib/galaxy/jobs/runners/util/cli/job/torque.py @@ -7,7 +7,7 @@ from galaxy.model import Job job_states = Job.states except ImportError: - # Not in Galaxy, map Galaxy job states to LWR ones. + # Not in Galaxy, map Galaxy job states to Pulsar ones. from galaxy.util import enum job_states = enum(RUNNING='running', OK='complete', QUEUED='queued') diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -623,9 +623,9 @@ elif store == 'irods': from .rods import IRODSObjectStore return IRODSObjectStore(config=config, config_xml=config_xml) - elif store == 'lwr': - from .lwr import LwrObjectStore - return LwrObjectStore(config=config, config_xml=config_xml) + elif store == 'pulsar': + from .pulsar import PulsarObjectStore + return PulsarObjectStore(config=config, config_xml=config_xml) else: log.error("Unrecognized object store definition: {0}".format(store)) diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/galaxy/objectstore/lwr.py --- a/lib/galaxy/objectstore/lwr.py +++ /dev/null @@ -1,76 +0,0 @@ -from __future__ import absolute_import # Need to import lwr_client absolutely. -from ..objectstore import ObjectStore -try: - from galaxy.jobs.runners.lwr_client.manager import ObjectStoreClientManager -except ImportError: - from lwr.lwr_client.manager import ObjectStoreClientManager - - -class LwrObjectStore(ObjectStore): - """ - Object store implementation that delegates to a remote LWR server. - - This may be more aspirational than practical for now, it would be good to - Galaxy to a point that a handler thread could be setup that doesn't attempt - to access the disk files returned by a (this) object store - just passing - them along to the LWR unmodified. That modification - along with this - implementation and LWR job destinations would then allow Galaxy to fully - manage jobs on remote servers with completely different mount points. - - This implementation should be considered beta and may be dropped from - Galaxy at some future point or significantly modified. - """ - - def __init__(self, config, config_xml): - self.lwr_client = self.__build_lwr_client(config_xml) - - def exists(self, obj, **kwds): - return self.lwr_client.exists(**self.__build_kwds(obj, **kwds)) - - def file_ready(self, obj, **kwds): - return self.lwr_client.file_ready(**self.__build_kwds(obj, **kwds)) - - def create(self, obj, **kwds): - return self.lwr_client.create(**self.__build_kwds(obj, **kwds)) - - def empty(self, obj, **kwds): - return self.lwr_client.empty(**self.__build_kwds(obj, **kwds)) - - def size(self, obj, **kwds): - return self.lwr_client.size(**self.__build_kwds(obj, **kwds)) - - def delete(self, obj, **kwds): - return self.lwr_client.delete(**self.__build_kwds(obj, **kwds)) - - # TODO: Optimize get_data. - def get_data(self, obj, **kwds): - return self.lwr_client.get_data(**self.__build_kwds(obj, **kwds)) - - def get_filename(self, obj, **kwds): - return self.lwr_client.get_filename(**self.__build_kwds(obj, **kwds)) - - def update_from_file(self, obj, **kwds): - return self.lwr_client.update_from_file(**self.__build_kwds(obj, **kwds)) - - def get_store_usage_percent(self): - return self.lwr_client.get_store_usage_percent() - - def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None): - return None - - def __build_kwds(self, obj, **kwds): - kwds['object_id'] = obj.id - return kwds - pass - - def __build_lwr_client(self, config_xml): - url = config_xml.get("url") - private_token = config_xml.get("private_token", None) - transport = config_xml.get("transport", None) - manager_options = dict(transport=transport) - client_options = dict(url=url, private_token=private_token) - lwr_client = ObjectStoreClientManager(**manager_options).get_client(client_options) - return lwr_client - - def shutdown(self): - pass diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/galaxy/objectstore/pulsar.py --- /dev/null +++ b/lib/galaxy/objectstore/pulsar.py @@ -0,0 +1,73 @@ +from __future__ import absolute_import # Need to import pulsar_client absolutely. +from ..objectstore import ObjectStore +from pulsar.client.manager import ObjectStoreClientManager + + +class PulsarObjectStore(ObjectStore): + """ + Object store implementation that delegates to a remote Pulsar server. + + This may be more aspirational than practical for now, it would be good to + Galaxy to a point that a handler thread could be setup that doesn't attempt + to access the disk files returned by a (this) object store - just passing + them along to the Pulsar unmodified. That modification - along with this + implementation and Pulsar job destinations would then allow Galaxy to fully + manage jobs on remote servers with completely different mount points. + + This implementation should be considered beta and may be dropped from + Galaxy at some future point or significantly modified. + """ + + def __init__(self, config, config_xml): + self.pulsar_client = self.__build_pulsar_client(config_xml) + + def exists(self, obj, **kwds): + return self.pulsar_client.exists(**self.__build_kwds(obj, **kwds)) + + def file_ready(self, obj, **kwds): + return self.pulsar_client.file_ready(**self.__build_kwds(obj, **kwds)) + + def create(self, obj, **kwds): + return self.pulsar_client.create(**self.__build_kwds(obj, **kwds)) + + def empty(self, obj, **kwds): + return self.pulsar_client.empty(**self.__build_kwds(obj, **kwds)) + + def size(self, obj, **kwds): + return self.pulsar_client.size(**self.__build_kwds(obj, **kwds)) + + def delete(self, obj, **kwds): + return self.pulsar_client.delete(**self.__build_kwds(obj, **kwds)) + + # TODO: Optimize get_data. + def get_data(self, obj, **kwds): + return self.pulsar_client.get_data(**self.__build_kwds(obj, **kwds)) + + def get_filename(self, obj, **kwds): + return self.pulsar_client.get_filename(**self.__build_kwds(obj, **kwds)) + + def update_from_file(self, obj, **kwds): + return self.pulsar_client.update_from_file(**self.__build_kwds(obj, **kwds)) + + def get_store_usage_percent(self): + return self.pulsar_client.get_store_usage_percent() + + def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None): + return None + + def __build_kwds(self, obj, **kwds): + kwds['object_id'] = obj.id + return kwds + pass + + def __build_pulsar_client(self, config_xml): + url = config_xml.get("url") + private_token = config_xml.get("private_token", None) + transport = config_xml.get("transport", None) + manager_options = dict(transport=transport) + client_options = dict(url=url, private_token=private_token) + pulsar_client = ObjectStoreClientManager(**manager_options).get_client(client_options) + return pulsar_client + + def shutdown(self): + pass diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/galaxy/tools/deps/dependencies.py --- a/lib/galaxy/tools/deps/dependencies.py +++ b/lib/galaxy/tools/deps/dependencies.py @@ -8,7 +8,7 @@ related context required to resolve dependencies via the ToolShedPackageDependencyResolver. - This is meant to enable remote resolution of dependencies, by the LWR or + This is meant to enable remote resolution of dependencies, by the Pulsar or other potential remote execution mechanisms. """ @@ -39,7 +39,7 @@ @staticmethod def _toolshed_install_dependency_from_dict(as_dict): - # Rather than requiring full models in LWR, just use simple objects + # Rather than requiring full models in Pulsar, just use simple objects # containing only properties and associations used to resolve # dependencies for tool execution. repository_object = bunch.Bunch( diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/pulsar/client/__init__.py --- /dev/null +++ b/lib/pulsar/client/__init__.py @@ -0,0 +1,62 @@ +""" +pulsar client +====== + +This module contains logic for interfacing with an external Pulsar server. + +------------------ +Configuring Galaxy +------------------ + +Galaxy job runners are configured in Galaxy's ``job_conf.xml`` file. See ``job_conf.xml.sample_advanced`` +in your Galaxy code base or on +`Bitbucket <https://bitbucket.org/galaxy/galaxy-dist/src/tip/job_conf.xml.sample_advanc…>`_ +for information on how to configure Galaxy to interact with the Pulsar. + +Galaxy also supports an older, less rich configuration of job runners directly +in its main ``universe_wsgi.ini`` file. The following section describes how to +configure Galaxy to communicate with the Pulsar in this legacy mode. + +Legacy +------ + +A Galaxy tool can be configured to be executed remotely via Pulsar by +adding a line to the ``universe_wsgi.ini`` file under the +``galaxy:tool_runners`` section with the format:: + + <tool_id> = pulsar://http://<pulsar_host>:<pulsar_port> + +As an example, if a host named remotehost is running the Pulsar server +application on port ``8913``, then the tool with id ``test_tool`` can +be configured to run remotely on remotehost by adding the following +line to ``universe.ini``:: + + test_tool = pulsar://http://remotehost:8913 + +Remember this must be added after the ``[galaxy:tool_runners]`` header +in the ``universe.ini`` file. + + +""" + +from .staging.down import finish_job +from .staging.up import submit_job +from .staging import ClientJobDescription +from .staging import PulsarOutputs +from .staging import ClientOutputs +from .client import OutputNotFoundException +from .manager import build_client_manager +from .destination import url_to_destination_params +from .path_mapper import PathMapper + +__all__ = [ + build_client_manager, + OutputNotFoundException, + url_to_destination_params, + finish_job, + submit_job, + ClientJobDescription, + PulsarOutputs, + ClientOutputs, + PathMapper, +] diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/pulsar/client/action_mapper.py --- /dev/null +++ b/lib/pulsar/client/action_mapper.py @@ -0,0 +1,567 @@ +from json import load +from os import makedirs +from os.path import exists +from os.path import abspath +from os.path import dirname +from os.path import join +from os.path import basename +from os.path import sep +import fnmatch +from re import compile +from re import escape +import galaxy.util +from galaxy.util.bunch import Bunch +from .config_util import read_file +from .util import directory_files +from .util import unique_path_prefix +from .transport import get_file +from .transport import post_file + + +DEFAULT_MAPPED_ACTION = 'transfer' # Not really clear to me what this should be, exception? +DEFAULT_PATH_MAPPER_TYPE = 'prefix' + +STAGING_ACTION_REMOTE = "remote" +STAGING_ACTION_LOCAL = "local" +STAGING_ACTION_NONE = None +STAGING_ACTION_DEFAULT = "default" + +# Poor man's enum. +path_type = Bunch( + # Galaxy input datasets and extra files. + INPUT="input", + # Galaxy config and param files. + CONFIG="config", + # Files from tool's tool_dir (for now just wrapper if available). + TOOL="tool", + # Input work dir files - e.g. metadata files, task-split input files, etc.. + WORKDIR="workdir", + # Galaxy output datasets in their final home. + OUTPUT="output", + # Galaxy from_work_dir output paths and other files (e.g. galaxy.json) + OUTPUT_WORKDIR="output_workdir", + # Other fixed tool parameter paths (likely coming from tool data, but not + # nessecarily). Not sure this is the best name... + UNSTRUCTURED="unstructured", +) + + +ACTION_DEFAULT_PATH_TYPES = [ + path_type.INPUT, + path_type.CONFIG, + path_type.TOOL, + path_type.WORKDIR, + path_type.OUTPUT, + path_type.OUTPUT_WORKDIR, +] +ALL_PATH_TYPES = ACTION_DEFAULT_PATH_TYPES + [path_type.UNSTRUCTURED] + + +class FileActionMapper(object): + """ + Objects of this class define how paths are mapped to actions. + + >>> json_string = r'''{"paths": [ \ + {"path": "/opt/galaxy", "action": "none"}, \ + {"path": "/galaxy/data", "action": "transfer"}, \ + {"path": "/cool/bamfiles/**/*.bam", "action": "copy", "match_type": "glob"}, \ + {"path": ".*/dataset_\\\\d+.dat", "action": "copy", "match_type": "regex"} \ + ]}''' + >>> from tempfile import NamedTemporaryFile + >>> from os import unlink + >>> def mapper_for(default_action, config_contents): + ... f = NamedTemporaryFile(delete=False) + ... f.write(config_contents.encode('UTF-8')) + ... f.close() + ... mock_client = Bunch(default_file_action=default_action, action_config_path=f.name, files_endpoint=None) + ... mapper = FileActionMapper(mock_client) + ... mapper = FileActionMapper(config=mapper.to_dict()) # Serialize and deserialize it to make sure still works + ... unlink(f.name) + ... return mapper + >>> mapper = mapper_for(default_action='none', config_contents=json_string) + >>> # Test first config line above, implicit path prefix mapper + >>> action = mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input') + >>> action.action_type == u'none' + True + >>> action.staging_needed + False + >>> # Test another (2nd) mapper, this one with a different action + >>> action = mapper.action('/galaxy/data/files/000/dataset_1.dat', 'input') + >>> action.action_type == u'transfer' + True + >>> action.staging_needed + True + >>> # Always at least copy work_dir outputs. + >>> action = mapper.action('/opt/galaxy/database/working_directory/45.sh', 'workdir') + >>> action.action_type == u'copy' + True + >>> action.staging_needed + True + >>> # Test glob mapper (matching test) + >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam', 'input').action_type == u'copy' + True + >>> # Test glob mapper (non-matching test) + >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam.bai', 'input').action_type == u'none' + True + >>> # Regex mapper test. + >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'input').action_type == u'copy' + True + >>> # Doesn't map unstructured paths by default + >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'unstructured').action_type == u'none' + True + >>> input_only_mapper = mapper_for(default_action="none", config_contents=r'''{"paths": [ \ + {"path": "/", "action": "transfer", "path_types": "input"} \ + ] }''') + >>> input_only_mapper.action('/dataset_1.dat', 'input').action_type == u'transfer' + True + >>> input_only_mapper.action('/dataset_1.dat', 'output').action_type == u'none' + True + >>> unstructured_mapper = mapper_for(default_action="none", config_contents=r'''{"paths": [ \ + {"path": "/", "action": "transfer", "path_types": "*any*"} \ + ] }''') + >>> unstructured_mapper.action('/old/galaxy/data/dataset_10245.dat', 'unstructured').action_type == u'transfer' + True + """ + + def __init__(self, client=None, config=None): + if config is None and client is None: + message = "FileActionMapper must be constructed from either a client or a config dictionary." + raise Exception(message) + if config is None: + config = self.__client_to_config(client) + self.default_action = config.get("default_action", "transfer") + self.mappers = mappers_from_dicts(config.get("paths", [])) + self.files_endpoint = config.get("files_endpoint", None) + + def action(self, path, type, mapper=None): + mapper = self.__find_mapper(path, type, mapper) + action_class = self.__action_class(path, type, mapper) + file_lister = DEFAULT_FILE_LISTER + action_kwds = {} + if mapper: + file_lister = mapper.file_lister + action_kwds = mapper.action_kwds + action = action_class(path, file_lister=file_lister, **action_kwds) + self.__process_action(action, type) + return action + + def unstructured_mappers(self): + """ Return mappers that will map 'unstructured' files (i.e. go beyond + mapping inputs, outputs, and config files). + """ + return filter(lambda m: path_type.UNSTRUCTURED in m.path_types, self.mappers) + + def to_dict(self): + return dict( + default_action=self.default_action, + files_endpoint=self.files_endpoint, + paths=map(lambda m: m.to_dict(), self.mappers) + ) + + def __client_to_config(self, client): + action_config_path = client.action_config_path + if action_config_path: + config = read_file(action_config_path) + else: + config = dict() + config["default_action"] = client.default_file_action + config["files_endpoint"] = client.files_endpoint + return config + + def __load_action_config(self, path): + config = load(open(path, 'rb')) + self.mappers = mappers_from_dicts(config.get('paths', [])) + + def __find_mapper(self, path, type, mapper=None): + if not mapper: + normalized_path = abspath(path) + for query_mapper in self.mappers: + if query_mapper.matches(normalized_path, type): + mapper = query_mapper + break + return mapper + + def __action_class(self, path, type, mapper): + action_type = self.default_action if type in ACTION_DEFAULT_PATH_TYPES else "none" + if mapper: + action_type = mapper.action_type + if type in ["workdir", "output_workdir"] and action_type == "none": + # We are changing the working_directory relative to what + # Galaxy would use, these need to be copied over. + action_type = "copy" + action_class = actions.get(action_type, None) + if action_class is None: + message_template = "Unknown action_type encountered %s while trying to map path %s" + message_args = (action_type, path) + raise Exception(message_template % message_args) + return action_class + + def __process_action(self, action, file_type): + """ Extension point to populate extra action information after an + action has been created. + """ + if action.action_type == "remote_transfer": + url_base = self.files_endpoint + if not url_base: + raise Exception("Attempted to use remote_transfer action with defining a files_endpoint") + if "?" not in url_base: + url_base = "%s?" % url_base + # TODO: URL encode path. + url = "%s&path=%s&file_type=%s" % (url_base, action.path, file_type) + action.url = url + +REQUIRED_ACTION_KWD = object() + + +class BaseAction(object): + action_spec = {} + + def __init__(self, path, file_lister=None): + self.path = path + self.file_lister = file_lister or DEFAULT_FILE_LISTER + + def unstructured_map(self, path_helper): + unstructured_map = self.file_lister.unstructured_map(self.path) + if self.staging_needed: + # To ensure uniqueness, prepend unique prefix to each name + prefix = unique_path_prefix(self.path) + for path, name in unstructured_map.iteritems(): + unstructured_map[path] = join(prefix, name) + else: + path_rewrites = {} + for path in unstructured_map: + rewrite = self.path_rewrite(path_helper, path) + if rewrite: + path_rewrites[path] = rewrite + unstructured_map = path_rewrites + return unstructured_map + + @property + def staging_needed(self): + return self.staging != STAGING_ACTION_NONE + + @property + def staging_action_local(self): + return self.staging == STAGING_ACTION_LOCAL + + +class NoneAction(BaseAction): + """ This action indicates the corresponding path does not require any + additional action. This should indicate paths that are available both on + the Pulsar client (i.e. Galaxy server) and remote Pulsar server with the same + paths. """ + action_type = "none" + staging = STAGING_ACTION_NONE + + def to_dict(self): + return dict(path=self.path, action_type=self.action_type) + + @classmethod + def from_dict(cls, action_dict): + return NoneAction(path=action_dict["path"]) + + def path_rewrite(self, path_helper, path=None): + return None + + +class RewriteAction(BaseAction): + """ This actin indicates the Pulsar server should simply rewrite the path + to the specified file. + """ + action_spec = dict( + source_directory=REQUIRED_ACTION_KWD, + destination_directory=REQUIRED_ACTION_KWD + ) + action_type = "rewrite" + staging = STAGING_ACTION_NONE + + def __init__(self, path, file_lister=None, source_directory=None, destination_directory=None): + self.path = path + self.file_lister = file_lister or DEFAULT_FILE_LISTER + self.source_directory = source_directory + self.destination_directory = destination_directory + + def to_dict(self): + return dict( + path=self.path, + action_type=self.action_type, + source_directory=self.source_directory, + destination_directory=self.destination_directory, + ) + + @classmethod + def from_dict(cls, action_dict): + return RewriteAction( + path=action_dict["path"], + source_directory=action_dict["source_directory"], + destination_directory=action_dict["destination_directory"], + ) + + def path_rewrite(self, path_helper, path=None): + if not path: + path = self.path + new_path = path_helper.from_posix_with_new_base(self.path, self.source_directory, self.destination_directory) + return None if new_path == self.path else new_path + + +class TransferAction(BaseAction): + """ This actions indicates that the Pulsar client should initiate an HTTP + transfer of the corresponding path to the remote Pulsar server before + launching the job. """ + action_type = "transfer" + staging = STAGING_ACTION_LOCAL + + +class CopyAction(BaseAction): + """ This action indicates that the Pulsar client should execute a file system + copy of the corresponding path to the Pulsar staging directory prior to + launching the corresponding job. """ + action_type = "copy" + staging = STAGING_ACTION_LOCAL + + +class RemoteCopyAction(BaseAction): + """ This action indicates the Pulsar server should copy the file before + execution via direct file system copy. This is like a CopyAction, but + it indicates the action should occur on the Pulsar server instead of on + the client. + """ + action_type = "remote_copy" + staging = STAGING_ACTION_REMOTE + + def to_dict(self): + return dict(path=self.path, action_type=self.action_type) + + @classmethod + def from_dict(cls, action_dict): + return RemoteCopyAction(path=action_dict["path"]) + + def write_to_path(self, path): + galaxy.util.copy_to_path(open(self.path, "rb"), path) + + def write_from_path(self, pulsar_path): + destination = self.path + parent_directory = dirname(destination) + if not exists(parent_directory): + makedirs(parent_directory) + with open(pulsar_path, "rb") as f: + galaxy.util.copy_to_path(f, destination) + + +class RemoteTransferAction(BaseAction): + """ This action indicates the Pulsar server should copy the file before + execution via direct file system copy. This is like a CopyAction, but + it indicates the action should occur on the Pulsar server instead of on + the client. + """ + action_type = "remote_transfer" + staging = STAGING_ACTION_REMOTE + + def __init__(self, path, file_lister=None, url=None): + super(RemoteTransferAction, self).__init__(path, file_lister=file_lister) + self.url = url + + def to_dict(self): + return dict(path=self.path, action_type=self.action_type, url=self.url) + + @classmethod + def from_dict(cls, action_dict): + return RemoteTransferAction(path=action_dict["path"], url=action_dict["url"]) + + def write_to_path(self, path): + get_file(self.url, path) + + def write_from_path(self, pulsar_path): + post_file(self.url, pulsar_path) + + +class MessageAction(object): + """ Sort of pseudo action describing "files" store in memory and + transferred via message (HTTP, Python-call, MQ, etc...) + """ + action_type = "message" + staging = STAGING_ACTION_DEFAULT + + def __init__(self, contents, client=None): + self.contents = contents + self.client = client + + @property + def staging_needed(self): + return True + + @property + def staging_action_local(self): + # Ekkk, cannot be called if created through from_dict. + # Shouldn't be a problem the way it is used - but is an + # object design problem. + return self.client.prefer_local_staging + + def to_dict(self): + return dict(contents=self.contents, action_type=MessageAction.action_type) + + @classmethod + def from_dict(cls, action_dict): + return MessageAction(contents=action_dict["contents"]) + + def write_to_path(self, path): + open(path, "w").write(self.contents) + + +DICTIFIABLE_ACTION_CLASSES = [RemoteCopyAction, RemoteTransferAction, MessageAction] + + +def from_dict(action_dict): + action_type = action_dict.get("action_type", None) + target_class = None + for action_class in DICTIFIABLE_ACTION_CLASSES: + if action_type == action_class.action_type: + target_class = action_class + if not target_class: + message = "Failed to recover action from dictionary - invalid action type specified %s." % action_type + raise Exception(message) + return target_class.from_dict(action_dict) + + +class BasePathMapper(object): + + def __init__(self, config): + action_type = config.get('action', DEFAULT_MAPPED_ACTION) + action_class = actions.get(action_type, None) + action_kwds = action_class.action_spec.copy() + for key, value in action_kwds.items(): + if key in config: + action_kwds[key] = config[key] + elif value is REQUIRED_ACTION_KWD: + message_template = "action_type %s requires key word argument %s" + message = message_template % (action_type, key) + raise Exception(message) + self.action_type = action_type + self.action_kwds = action_kwds + path_types_str = config.get('path_types', "*defaults*") + path_types_str = path_types_str.replace("*defaults*", ",".join(ACTION_DEFAULT_PATH_TYPES)) + path_types_str = path_types_str.replace("*any*", ",".join(ALL_PATH_TYPES)) + self.path_types = path_types_str.split(",") + self.file_lister = FileLister(config) + + def matches(self, path, path_type): + path_type_matches = path_type in self.path_types + return path_type_matches and self._path_matches(path) + + def _extend_base_dict(self, **kwds): + base_dict = dict( + action=self.action_type, + path_types=",".join(self.path_types), + match_type=self.match_type + ) + base_dict.update(self.file_lister.to_dict()) + base_dict.update(self.action_kwds) + base_dict.update(**kwds) + return base_dict + + +class PrefixPathMapper(BasePathMapper): + match_type = 'prefix' + + def __init__(self, config): + super(PrefixPathMapper, self).__init__(config) + self.prefix_path = abspath(config['path']) + + def _path_matches(self, path): + return path.startswith(self.prefix_path) + + def to_pattern(self): + pattern_str = "(%s%s[^\s,\"\']+)" % (escape(self.prefix_path), escape(sep)) + return compile(pattern_str) + + def to_dict(self): + return self._extend_base_dict(path=self.prefix_path) + + +class GlobPathMapper(BasePathMapper): + match_type = 'glob' + + def __init__(self, config): + super(GlobPathMapper, self).__init__(config) + self.glob_path = config['path'] + + def _path_matches(self, path): + return fnmatch.fnmatch(path, self.glob_path) + + def to_pattern(self): + return compile(fnmatch.translate(self.glob_path)) + + def to_dict(self): + return self._extend_base_dict(path=self.glob_path) + + +class RegexPathMapper(BasePathMapper): + match_type = 'regex' + + def __init__(self, config): + super(RegexPathMapper, self).__init__(config) + self.pattern_raw = config['path'] + self.pattern = compile(self.pattern_raw) + + def _path_matches(self, path): + return self.pattern.match(path) is not None + + def to_pattern(self): + return self.pattern + + def to_dict(self): + return self._extend_base_dict(path=self.pattern_raw) + +MAPPER_CLASSES = [PrefixPathMapper, GlobPathMapper, RegexPathMapper] +MAPPER_CLASS_DICT = dict(map(lambda c: (c.match_type, c), MAPPER_CLASSES)) + + +def mappers_from_dicts(mapper_def_list): + return map(lambda m: __mappper_from_dict(m), mapper_def_list) + + +def __mappper_from_dict(mapper_dict): + map_type = mapper_dict.get('match_type', DEFAULT_PATH_MAPPER_TYPE) + return MAPPER_CLASS_DICT[map_type](mapper_dict) + + +class FileLister(object): + + def __init__(self, config): + self.depth = int(config.get("depth", "0")) + + def to_dict(self): + return dict( + depth=self.depth + ) + + def unstructured_map(self, path): + depth = self.depth + if self.depth == 0: + return {path: basename(path)} + else: + while depth > 0: + path = dirname(path) + depth -= 1 + return dict([(join(path, f), f) for f in directory_files(path)]) + +DEFAULT_FILE_LISTER = FileLister(dict(depth=0)) + +ACTION_CLASSES = [ + NoneAction, + RewriteAction, + TransferAction, + CopyAction, + RemoteCopyAction, + RemoteTransferAction, +] +actions = dict([(clazz.action_type, clazz) for clazz in ACTION_CLASSES]) + + +__all__ = [ + FileActionMapper, + path_type, + from_dict, + MessageAction, + RemoteTransferAction, # For testing +] diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/pulsar/client/amqp_exchange.py --- /dev/null +++ b/lib/pulsar/client/amqp_exchange.py @@ -0,0 +1,139 @@ +try: + import kombu + from kombu import pools +except ImportError: + kombu = None + +import socket +import logging +import threading +from time import sleep +log = logging.getLogger(__name__) + + +KOMBU_UNAVAILABLE = "Attempting to bind to AMQP message queue, but kombu dependency unavailable" + +DEFAULT_EXCHANGE_NAME = "pulsar" +DEFAULT_EXCHANGE_TYPE = "direct" +# Set timeout to periodically give up looking and check if polling should end. +DEFAULT_TIMEOUT = 0.2 +DEFAULT_HEARTBEAT = 580 + +DEFAULT_RECONNECT_CONSUMER_WAIT = 1 +DEFAULT_HEARTBEAT_WAIT = 1 + + +class PulsarExchange(object): + """ Utility for publishing and consuming structured Pulsar queues using kombu. + This is shared between the server and client - an exchange should be setup + for each manager (or in the case of the client, each manager one wished to + communicate with.) + + Each Pulsar manager is defined solely by name in the scheme, so only one Pulsar + should target each AMQP endpoint or care should be taken that unique + manager names are used across Pulsar servers targetting same AMQP endpoint - + and in particular only one such Pulsar should define an default manager with + name _default_. + """ + + def __init__( + self, + url, + manager_name, + connect_ssl=None, + timeout=DEFAULT_TIMEOUT, + publish_kwds={}, + ): + """ + """ + if not kombu: + raise Exception(KOMBU_UNAVAILABLE) + self.__url = url + self.__manager_name = manager_name + self.__connect_ssl = connect_ssl + self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE) + self.__timeout = timeout + # Be sure to log message publishing failures. + if publish_kwds.get("retry", False): + if "retry_policy" not in publish_kwds: + publish_kwds["retry_policy"] = {} + if "errback" not in publish_kwds["retry_policy"]: + publish_kwds["retry_policy"]["errback"] = self.__publish_errback + self.__publish_kwds = publish_kwds + + @property + def url(self): + return self.__url + + def consume(self, queue_name, callback, check=True, connection_kwargs={}): + queue = self.__queue(queue_name) + log.debug("Consuming queue '%s'", queue) + while check: + heartbeat_thread = None + try: + with self.connection(self.__url, heartbeat=DEFAULT_HEARTBEAT, **connection_kwargs) as connection: + with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): + heartbeat_thread = self.__start_heartbeat(queue_name, connection) + while check and connection.connected: + try: + connection.drain_events(timeout=self.__timeout) + except socket.timeout: + pass + except (IOError, socket.error), exc: + # In testing, errno is None + log.warning('Got %s, will retry: %s', exc.__class__.__name__, exc) + if heartbeat_thread: + heartbeat_thread.join() + sleep(DEFAULT_RECONNECT_CONSUMER_WAIT) + + def heartbeat(self, connection): + log.debug('AMQP heartbeat thread alive') + while connection.connected: + connection.heartbeat_check() + sleep(DEFAULT_HEARTBEAT_WAIT) + log.debug('AMQP heartbeat thread exiting') + + def publish(self, name, payload): + with self.connection(self.__url) as connection: + with pools.producers[connection].acquire() as producer: + key = self.__queue_name(name) + producer.publish( + payload, + serializer='json', + exchange=self.__exchange, + declare=[self.__exchange], + routing_key=key, + **self.__publish_kwds + ) + + def __publish_errback(self, exc, interval): + log.error("Connection error while publishing: %r", exc, exc_info=1) + log.info("Retrying in %s seconds", interval) + + def connection(self, connection_string, **kwargs): + if "ssl" not in kwargs: + kwargs["ssl"] = self.__connect_ssl + return kombu.Connection(connection_string, **kwargs) + + def __queue(self, name): + queue_name = self.__queue_name(name) + queue = kombu.Queue(queue_name, self.__exchange, routing_key=queue_name) + return queue + + def __queue_name(self, name): + key_prefix = self.__key_prefix() + queue_name = '%s_%s' % (key_prefix, name) + return queue_name + + def __key_prefix(self): + if self.__manager_name == "_default_": + key_prefix = "pulsar_" + else: + key_prefix = "pulsar_%s_" % self.__manager_name + return key_prefix + + def __start_heartbeat(self, queue_name, connection): + thread_name = "consume-heartbeat-%s" % (self.__queue_name(queue_name)) + thread = threading.Thread(name=thread_name, target=self.heartbeat, args=(connection,)) + thread.start() + return thread diff -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 -r 8c569cffa9670f765492c8ddc11fb54d9a2ab2f1 lib/pulsar/client/amqp_exchange_factory.py --- /dev/null +++ b/lib/pulsar/client/amqp_exchange_factory.py @@ -0,0 +1,41 @@ +from .amqp_exchange import PulsarExchange +from .util import filter_destination_params + + +def get_exchange(url, manager_name, params): + connect_ssl = parse_amqp_connect_ssl_params(params) + exchange_kwds = dict( + manager_name=manager_name, + connect_ssl=connect_ssl, + publish_kwds=parse_amqp_publish_kwds(params) + ) + timeout = params.get('amqp_consumer_timeout', False) + if timeout is not False: + exchange_kwds['timeout'] = timeout + exchange = PulsarExchange(url, **exchange_kwds) + return exchange + + +def parse_amqp_connect_ssl_params(params): + ssl_params = filter_destination_params(params, "amqp_connect_ssl_") + if not ssl_params: + return + + ssl = __import__('ssl') + if 'cert_reqs' in ssl_params: + value = ssl_params['cert_reqs'] + ssl_params['cert_reqs'] = getattr(ssl, value.upper()) + return ssl_params + + +def parse_amqp_publish_kwds(params): + all_publish_params = filter_destination_params(params, "amqp_publish_") + retry_policy_params = {} + for key in all_publish_params.keys(): + if key.startswith("retry_"): + value = all_publish_params[key] + retry_policy_params[key[len("retry_"):]] = value + del all_publish_params[key] + if retry_policy_params: + all_publish_params["retry_policy"] = retry_policy_params + return all_publish_params This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/566388d62374/ Changeset: 566388d62374 User: jmchilton Date: 2014-06-24 04:27:51 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #422) Implement Pulsar job runners. Affected #: 32 files diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -19,27 +19,30 @@ <param id="drmaa_library_path">/sge/lib/libdrmaa.so</param></plugin> - <plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr:LwrJobRunner"> -  -  + <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> + <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> + <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> +  + <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"> +  -  - </plugin> - <plugin id="amqp_lwr" type="runner" load="galaxy.jobs.runners.lwr:LwrJobRunner"> - <param id="url">amqp://guest:guest@localhost:5672//</param> -  + <plugin id="pulsar_mq" type="runner" load="galaxy.jobs.runners.pulsar:PulsarMQJobRunner"> +  + <param id="amqp_url">amqp://guest:guest@localhost:5672//</param> + <param id="galaxy_url">http://localhost:8080</param> -  + </plugin> - <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> - <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> - <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> + <plugin id="pulsar_legacy" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner"> +  + </plugin></plugins><handlers default="handlers"> @@ -213,87 +224,71 @@ <param id="function">foo</param></destination> - <destination id="secure_lwr" runner="lwr"> - <param id="url">https://windowshost.examle.com:8913/</param> -  + <destination id="secure_pulsar_rest_dest" runner="pulsar_rest"> + <param id="url">https://examle.com:8913/</param> + <param id="private_token">123456789changeme</param> -  -  +  -  -  -  +  -  -  -  +  +  + </destination> - <destination id="amqp_lwr_dest" runner="amqp_lwr" > -  -  - <param id="jobs_directory">/path/to/remote/lwr/lwr_staging/</param> -  - <param id="default_file_action">remote_transfer</param></destination><destination id="ssh_torque" runner="cli"><param id="shell_plugin">SecureShell</param> diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/jobs/runners/pulsar.py --- /dev/null +++ b/lib/galaxy/jobs/runners/pulsar.py @@ -0,0 +1,707 @@ +from __future__ import absolute_import # Need to import pulsar_client absolutely. + +import logging + +from galaxy import model +from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner +from galaxy.jobs import ComputeEnvironment +from galaxy.jobs import JobDestination +from galaxy.jobs.command_factory import build_command +from galaxy.tools.deps import dependencies +from galaxy.util import string_as_bool_or_none +from galaxy.util.bunch import Bunch +from galaxy.util import specs + +import errno +from time import sleep +import os + +from pulsar.client import build_client_manager +from pulsar.client import url_to_destination_params +from pulsar.client import finish_job as pulsar_finish_job +from pulsar.client import submit_job as pulsar_submit_job +from pulsar.client import ClientJobDescription +from pulsar.client import PulsarOutputs +from pulsar.client import ClientOutputs +from pulsar.client import PathMapper + +log = logging.getLogger( __name__ ) + +__all__ = [ 'PulsarLegacyJobRunner', 'PulsarRESTJobRunner', 'PulsarMQJobRunner' ] + +NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "Pulsar misconfiguration - Pulsar client configured to set metadata remotely, but remote Pulsar isn't properly configured with a galaxy_home directory." +NO_REMOTE_DATATYPES_CONFIG = "Pulsar client is configured to use remote datatypes configuration when setting metadata externally, but Pulsar is not configured with this information. Defaulting to datatypes_conf.xml." +GENERIC_REMOTE_ERROR = "Failed to communicate with remote job server." + +# Is there a good way to infer some default for this? Can only use +# url_for from web threads. https://gist.github.com/jmchilton/9098762 +DEFAULT_GALAXY_URL = "http://localhost:8080" + +PULSAR_PARAM_SPECS = dict( + transport=dict( + map=specs.to_str_or_none, + valid=specs.is_in("urllib", "curl", None), + default=None + ), + cache=dict( + map=specs.to_bool_or_none, + default=None, + ), + amqp_url=dict( + map=specs.to_str_or_none, + default=None, + ), + galaxy_url=dict( + map=specs.to_str_or_none, + default=DEFAULT_GALAXY_URL, + ), + manager=dict( + map=specs.to_str_or_none, + default=None, + ), + amqp_consumer_timeout=dict( + map=lambda val: None if val == "None" else float(val), + default=None, + ), + amqp_connect_ssl_ca_certs=dict( + map=specs.to_str_or_none, + default=None, + ), + amqp_connect_ssl_keyfile=dict( + map=specs.to_str_or_none, + default=None, + ), + amqp_connect_ssl_certfile=dict( + map=specs.to_str_or_none, + default=None, + ), + amqp_connect_ssl_cert_reqs=dict( + map=specs.to_str_or_none, + default=None, + ), + # http://kombu.readthedocs.org/en/latest/reference/kombu.html#kombu.Producer.… + amqp_publish_retry=dict( + map=specs.to_bool, + default=False, + ), + amqp_publish_priority=dict( + map=int, + valid=lambda x: 0 <= x and x <= 9, + default=0, + ), + # http://kombu.readthedocs.org/en/latest/reference/kombu.html#kombu.Exchange.… + amqp_publish_delivery_mode=dict( + map=str, + valid=specs.is_in("transient", "persistent"), + default="persistent", + ), + amqp_publish_retry_max_retries=dict( + map=int, + default=None, + ), + amqp_publish_retry_interval_start=dict( + map=int, + default=None, + ), + amqp_publish_retry_interval_step=dict( + map=int, + default=None, + ), + amqp_publish_retry_interval_max=dict( + map=int, + default=None, + ), +) + + +PARAMETER_SPECIFICATION_REQUIRED = object() +PARAMETER_SPECIFICATION_IGNORED = object() + + +class PulsarJobRunner( AsynchronousJobRunner ): + """ + Pulsar Job Runner + """ + runner_name = "PulsarJobRunner" + + def __init__( self, app, nworkers, **kwds ): + """Start the job runner """ + super( PulsarJobRunner, self ).__init__( app, nworkers, runner_param_specs=PULSAR_PARAM_SPECS, **kwds ) + self._init_worker_threads() + galaxy_url = self.runner_params.galaxy_url + if galaxy_url: + galaxy_url = galaxy_url.rstrip("/") + self.galaxy_url = galaxy_url + self.__init_client_manager() + self._monitor() + + def _monitor( self ): + # Extension point allow MQ variant to setup callback instead + self._init_monitor_thread() + + def __init_client_manager( self ): + client_manager_kwargs = {} + for kwd in 'manager', 'cache', 'transport': + client_manager_kwargs[ kwd ] = self.runner_params[ kwd ] + for kwd in self.runner_params.keys(): + if kwd.startswith( 'amqp_' ): + client_manager_kwargs[ kwd ] = self.runner_params[ kwd ] + self.client_manager = build_client_manager(**client_manager_kwargs) + + def url_to_destination( self, url ): + """Convert a legacy URL to a job destination""" + return JobDestination( runner="pulsar", params=url_to_destination_params( url ) ) + + def check_watched_item(self, job_state): + try: + client = self.get_client_from_state(job_state) + status = client.get_status() + except Exception: + # An orphaned job was put into the queue at app startup, so remote server went down + # either way we are done I guess. + self.mark_as_finished(job_state) + return None + job_state = self._update_job_state_for_status(job_state, status) + return job_state + + def _update_job_state_for_status(self, job_state, pulsar_status): + if pulsar_status == "complete": + self.mark_as_finished(job_state) + return None + if pulsar_status == "failed": + self.fail_job(job_state) + return None + if pulsar_status == "running" and not job_state.running: + job_state.running = True + job_state.job_wrapper.change_state( model.Job.states.RUNNING ) + return job_state + + def queue_job(self, job_wrapper): + job_destination = job_wrapper.job_destination + self._populate_parameter_defaults( job_destination ) + + command_line, client, remote_job_config, compute_environment = self.__prepare_job( job_wrapper, job_destination ) + + if not command_line: + return + + try: + dependencies_description = PulsarJobRunner.__dependencies_description( client, job_wrapper ) + rewrite_paths = not PulsarJobRunner.__rewrite_parameters( client ) + unstructured_path_rewrites = {} + if compute_environment: + unstructured_path_rewrites = compute_environment.unstructured_path_rewrites + + client_job_description = ClientJobDescription( + command_line=command_line, + input_files=self.get_input_files(job_wrapper), + client_outputs=self.__client_outputs(client, job_wrapper), + working_directory=job_wrapper.working_directory, + tool=job_wrapper.tool, + config_files=job_wrapper.extra_filenames, + dependencies_description=dependencies_description, + env=client.env, + rewrite_paths=rewrite_paths, + arbitrary_files=unstructured_path_rewrites, + ) + job_id = pulsar_submit_job(client, client_job_description, remote_job_config) + log.info("Pulsar job submitted with job_id %s" % job_id) + job_wrapper.set_job_destination( job_destination, job_id ) + job_wrapper.change_state( model.Job.states.QUEUED ) + except Exception: + job_wrapper.fail( "failure running job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + return + + pulsar_job_state = AsynchronousJobState() + pulsar_job_state.job_wrapper = job_wrapper + pulsar_job_state.job_id = job_id + pulsar_job_state.old_state = True + pulsar_job_state.running = False + pulsar_job_state.job_destination = job_destination + self.monitor_job(pulsar_job_state) + + def __prepare_job(self, job_wrapper, job_destination): + """ Build command-line and Pulsar client for this job. """ + command_line = None + client = None + remote_job_config = None + compute_environment = None + try: + client = self.get_client_from_wrapper(job_wrapper) + tool = job_wrapper.tool + remote_job_config = client.setup(tool.id, tool.version) + rewrite_parameters = PulsarJobRunner.__rewrite_parameters( client ) + prepare_kwds = {} + if rewrite_parameters: + compute_environment = PulsarComputeEnvironment( client, job_wrapper, remote_job_config ) + prepare_kwds[ 'compute_environment' ] = compute_environment + job_wrapper.prepare( **prepare_kwds ) + self.__prepare_input_files_locally(job_wrapper) + remote_metadata = PulsarJobRunner.__remote_metadata( client ) + dependency_resolution = PulsarJobRunner.__dependency_resolution( client ) + metadata_kwds = self.__build_metadata_configuration(client, job_wrapper, remote_metadata, remote_job_config) + remote_command_params = dict( + working_directory=remote_job_config['working_directory'], + metadata_kwds=metadata_kwds, + dependency_resolution=dependency_resolution, + ) + remote_working_directory = remote_job_config['working_directory'] + # TODO: Following defs work for Pulsar, always worked for Pulsar but should be + # calculated at some other level. + remote_job_directory = os.path.abspath(os.path.join(remote_working_directory, os.path.pardir)) + remote_tool_directory = os.path.abspath(os.path.join(remote_job_directory, "tool_files")) + container = self._find_container( + job_wrapper, + compute_working_directory=remote_working_directory, + compute_tool_directory=remote_tool_directory, + compute_job_directory=remote_job_directory, + ) + command_line = build_command( + self, + job_wrapper=job_wrapper, + container=container, + include_metadata=remote_metadata, + include_work_dir_outputs=False, + remote_command_params=remote_command_params, + ) + except Exception: + job_wrapper.fail( "failure preparing job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + + # If we were able to get a command line, run the job + if not command_line: + job_wrapper.finish( '', '' ) + + return command_line, client, remote_job_config, compute_environment + + def __prepare_input_files_locally(self, job_wrapper): + """Run task splitting commands locally.""" + prepare_input_files_cmds = getattr(job_wrapper, 'prepare_input_files_cmds', None) + if prepare_input_files_cmds is not None: + for cmd in prepare_input_files_cmds: # run the commands to stage the input files + if 0 != os.system(cmd): + raise Exception('Error running file staging command: %s' % cmd) + job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line + + def _populate_parameter_defaults( self, job_destination ): + updated = False + params = job_destination.params + for key, value in self.destination_defaults.iteritems(): + if key in params: + if value is PARAMETER_SPECIFICATION_IGNORED: + log.warn( "Pulsar runner in selected configuration ignores parameter %s" % key ) + continue + #if self.runner_params.get( key, None ): + # # Let plugin define defaults for some parameters - + # # for instance that way jobs_directory can be + # # configured next to AMQP url (where it belongs). + # params[ key ] = self.runner_params[ key ] + # continue + + if not value: + continue + + if value is PARAMETER_SPECIFICATION_REQUIRED: + raise Exception( "Pulsar destination does not define required parameter %s" % key ) + elif value is not PARAMETER_SPECIFICATION_IGNORED: + params[ key ] = value + updated = True + return updated + + def get_output_files(self, job_wrapper): + output_paths = job_wrapper.get_output_fnames() + return [ str( o ) for o in output_paths ] # Force job_path from DatasetPath objects. + + def get_input_files(self, job_wrapper): + input_paths = job_wrapper.get_input_paths() + return [ str( i ) for i in input_paths ] # Force job_path from DatasetPath objects. + + def get_client_from_wrapper(self, job_wrapper): + job_id = job_wrapper.job_id + if hasattr(job_wrapper, 'task_id'): + job_id = "%s_%s" % (job_id, job_wrapper.task_id) + params = job_wrapper.job_destination.params.copy() + for key, value in params.iteritems(): + if value: + params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) + + env = getattr( job_wrapper.job_destination, "env", [] ) + return self.get_client( params, job_id, env ) + + def get_client_from_state(self, job_state): + job_destination_params = job_state.job_destination.params + job_id = job_state.job_id + return self.get_client( job_destination_params, job_id ) + + def get_client( self, job_destination_params, job_id, env=[] ): + # Cannot use url_for outside of web thread. + #files_endpoint = url_for( controller="job_files", job_id=encoded_job_id ) + + encoded_job_id = self.app.security.encode_id(job_id) + job_key = self.app.security.encode_id( job_id, kind="jobs_files" ) + files_endpoint = "%s/api/jobs/%s/files?job_key=%s" % ( + self.galaxy_url, + encoded_job_id, + job_key + ) + get_client_kwds = dict( + job_id=str( job_id ), + files_endpoint=files_endpoint, + env=env + ) + return self.client_manager.get_client( job_destination_params, **get_client_kwds ) + + def finish_job( self, job_state ): + stderr = stdout = '' + job_wrapper = job_state.job_wrapper + try: + client = self.get_client_from_state(job_state) + run_results = client.full_status() + remote_working_directory = run_results.get("working_directory", None) + stdout = run_results.get('stdout', '') + stderr = run_results.get('stderr', '') + exit_code = run_results.get('returncode', None) + pulsar_outputs = PulsarOutputs.from_status_response(run_results) + # Use Pulsar client code to transfer/copy files back + # and cleanup job if needed. + completed_normally = \ + job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] + cleanup_job = self.app.config.cleanup_job + client_outputs = self.__client_outputs(client, job_wrapper) + finish_args = dict( client=client, + job_completed_normally=completed_normally, + cleanup_job=cleanup_job, + client_outputs=client_outputs, + pulsar_outputs=pulsar_outputs ) + failed = pulsar_finish_job( **finish_args ) + if failed: + job_wrapper.fail("Failed to find or download one or more job outputs from remote server.", exception=True) + except Exception: + message = GENERIC_REMOTE_ERROR + job_wrapper.fail( message, exception=True ) + log.exception("failure finishing job %d" % job_wrapper.job_id) + return + if not PulsarJobRunner.__remote_metadata( client ): + self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) + # Finish the job + try: + job_wrapper.finish( + stdout, + stderr, + exit_code, + remote_working_directory=remote_working_directory + ) + except Exception: + log.exception("Job wrapper finish method failed") + job_wrapper.fail("Unable to finish job", exception=True) + + def fail_job( self, job_state ): + """ + Seperated out so we can use the worker threads for it. + """ + self.stop_job( self.sa_session.query( self.app.model.Job ).get( job_state.job_wrapper.job_id ) ) + job_state.job_wrapper.fail( getattr( job_state, "fail_message", GENERIC_REMOTE_ERROR ) ) + + def check_pid( self, pid ): + try: + os.kill( pid, 0 ) + return True + except OSError, e: + if e.errno == errno.ESRCH: + log.debug( "check_pid(): PID %d is dead" % pid ) + else: + log.warning( "check_pid(): Got errno %s when attempting to check PID %d: %s" % ( errno.errorcode[e.errno], pid, e.strerror ) ) + return False + + def stop_job( self, job ): + #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished + job_ext_output_metadata = job.get_external_output_metadata() + if job_ext_output_metadata: + pid = job_ext_output_metadata[0].job_runner_external_pid # every JobExternalOutputMetadata has a pid set, we just need to take from one of them + if pid in [ None, '' ]: + log.warning( "stop_job(): %s: no PID in database for job, unable to stop" % job.id ) + return + pid = int( pid ) + if not self.check_pid( pid ): + log.warning( "stop_job(): %s: PID %d was already dead or can't be signaled" % ( job.id, pid ) ) + return + for sig in [ 15, 9 ]: + try: + os.killpg( pid, sig ) + except OSError, e: + log.warning( "stop_job(): %s: Got errno %s when attempting to signal %d to PID %d: %s" % ( job.id, errno.errorcode[e.errno], sig, pid, e.strerror ) ) + return # give up + sleep( 2 ) + if not self.check_pid( pid ): + log.debug( "stop_job(): %s: PID %d successfully killed with signal %d" % ( job.id, pid, sig ) ) + return + else: + log.warning( "stop_job(): %s: PID %d refuses to die after signaling TERM/KILL" % ( job.id, pid ) ) + else: + # Remote kill + pulsar_url = job.job_runner_name + job_id = job.job_runner_external_id + log.debug("Attempt remote Pulsar kill of job with url %s and id %s" % (pulsar_url, job_id)) + client = self.get_client(job.destination_params, job_id) + client.kill() + + def recover( self, job, job_wrapper ): + """Recovers jobs stuck in the queued/running state when Galaxy started""" + job_state = self._job_state( job, job_wrapper ) + job_wrapper.command_line = job.get_command_line() + state = job.get_state() + if state in [model.Job.states.RUNNING, model.Job.states.QUEUED]: + log.debug( "(Pulsar/%s) is still in running state, adding to the Pulsar queue" % ( job.get_id()) ) + job_state.old_state = True + job_state.running = state == model.Job.states.RUNNING + self.monitor_queue.put( job_state ) + + def shutdown( self ): + super( PulsarJobRunner, self ).shutdown() + self.client_manager.shutdown() + + def _job_state( self, job, job_wrapper ): + job_state = AsynchronousJobState() + # TODO: Determine why this is set when using normal message queue updates + # but not CLI submitted MQ updates... + raw_job_id = job.get_job_runner_external_id() or job_wrapper.job_id + job_state.job_id = str( raw_job_id ) + job_state.runner_url = job_wrapper.get_job_runner_url() + job_state.job_destination = job_wrapper.job_destination + job_state.job_wrapper = job_wrapper + return job_state + + def __client_outputs( self, client, job_wrapper ): + work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) + output_files = self.get_output_files( job_wrapper ) + client_outputs = ClientOutputs( + working_directory=job_wrapper.working_directory, + work_dir_outputs=work_dir_outputs, + output_files=output_files, + version_file=job_wrapper.get_version_string_path(), + ) + return client_outputs + + @staticmethod + def __dependencies_description( pulsar_client, job_wrapper ): + dependency_resolution = PulsarJobRunner.__dependency_resolution( pulsar_client ) + remote_dependency_resolution = dependency_resolution == "remote" + if not remote_dependency_resolution: + return None + requirements = job_wrapper.tool.requirements or [] + installed_tool_dependencies = job_wrapper.tool.installed_tool_dependencies or [] + return dependencies.DependenciesDescription( + requirements=requirements, + installed_tool_dependencies=installed_tool_dependencies, + ) + + @staticmethod + def __dependency_resolution( pulsar_client ): + dependency_resolution = pulsar_client.destination_params.get( "dependency_resolution", "local" ) + if dependency_resolution not in ["none", "local", "remote"]: + raise Exception("Unknown dependency_resolution value encountered %s" % dependency_resolution) + return dependency_resolution + + @staticmethod + def __remote_metadata( pulsar_client ): + remote_metadata = string_as_bool_or_none( pulsar_client.destination_params.get( "remote_metadata", False ) ) + return remote_metadata + + @staticmethod + def __use_remote_datatypes_conf( pulsar_client ): + """ When setting remote metadata, use integrated datatypes from this + Galaxy instance or use the datatypes config configured via the remote + Pulsar. + + Both options are broken in different ways for same reason - datatypes + may not match. One can push the local datatypes config to the remote + server - but there is no guarentee these datatypes will be defined + there. Alternatively, one can use the remote datatype config - but + there is no guarentee that it will contain all the datatypes available + to this Galaxy. + """ + use_remote_datatypes = string_as_bool_or_none( pulsar_client.destination_params.get( "use_remote_datatypes", False ) ) + return use_remote_datatypes + + @staticmethod + def __rewrite_parameters( pulsar_client ): + return string_as_bool_or_none( pulsar_client.destination_params.get( "rewrite_parameters", False ) ) or False + + def __build_metadata_configuration(self, client, job_wrapper, remote_metadata, remote_job_config): + metadata_kwds = {} + if remote_metadata: + remote_system_properties = remote_job_config.get("system_properties", {}) + remote_galaxy_home = remote_system_properties.get("galaxy_home", None) + if not remote_galaxy_home: + raise Exception(NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE) + metadata_kwds['exec_dir'] = remote_galaxy_home + outputs_directory = remote_job_config['outputs_directory'] + configs_directory = remote_job_config['configs_directory'] + working_directory = remote_job_config['working_directory'] + # For metadata calculation, we need to build a list of of output + # file objects with real path indicating location on Galaxy server + # and false path indicating location on compute server. Since the + # Pulsar disables from_work_dir copying as part of the job command + # line we need to take the list of output locations on the Pulsar + # server (produced by self.get_output_files(job_wrapper)) and for + # each work_dir output substitute the effective path on the Pulsar + # server relative to the remote working directory as the + # false_path to send the metadata command generation module. + work_dir_outputs = self.get_work_dir_outputs(job_wrapper, job_working_directory=working_directory) + outputs = [Bunch(false_path=os.path.join(outputs_directory, os.path.basename(path)), real_path=path) for path in self.get_output_files(job_wrapper)] + for output in outputs: + for pulsar_workdir_path, real_path in work_dir_outputs: + if real_path == output.real_path: + output.false_path = pulsar_workdir_path + metadata_kwds['output_fnames'] = outputs + metadata_kwds['compute_tmp_dir'] = working_directory + metadata_kwds['config_root'] = remote_galaxy_home + default_config_file = os.path.join(remote_galaxy_home, 'universe_wsgi.ini') + metadata_kwds['config_file'] = remote_system_properties.get('galaxy_config_file', default_config_file) + metadata_kwds['dataset_files_path'] = remote_system_properties.get('galaxy_dataset_files_path', None) + if PulsarJobRunner.__use_remote_datatypes_conf( client ): + remote_datatypes_config = remote_system_properties.get('galaxy_datatypes_config_file', None) + if not remote_datatypes_config: + log.warn(NO_REMOTE_DATATYPES_CONFIG) + remote_datatypes_config = os.path.join(remote_galaxy_home, 'datatypes_conf.xml') + metadata_kwds['datatypes_config'] = remote_datatypes_config + else: + integrates_datatypes_config = self.app.datatypes_registry.integrated_datatypes_configs + # Ensure this file gets pushed out to the remote config dir. + job_wrapper.extra_filenames.append(integrates_datatypes_config) + + metadata_kwds['datatypes_config'] = os.path.join(configs_directory, os.path.basename(integrates_datatypes_config)) + return metadata_kwds + + +class PulsarLegacyJobRunner( PulsarJobRunner ): + destination_defaults = dict( + rewrite_parameters="false", + dependency_resolution="local", + ) + + +class PulsarMQJobRunner( PulsarJobRunner ): + destination_defaults = dict( + default_file_action="remote_transfer", + rewrite_parameters="true", + dependency_resolution="remote", + jobs_directory=PARAMETER_SPECIFICATION_REQUIRED, + url=PARAMETER_SPECIFICATION_IGNORED, + private_token=PARAMETER_SPECIFICATION_IGNORED + ) + + def _monitor( self ): + # This is a message queue driven runner, don't monitor + # just setup required callback. + self.client_manager.ensure_has_status_update_callback(self.__async_update) + + def __async_update( self, full_status ): + job_id = None + try: + job_id = full_status[ "job_id" ] + job, job_wrapper = self.app.job_manager.job_handler.job_queue.job_pair_for_id( job_id ) + job_state = self._job_state( job, job_wrapper ) + self._update_job_state_for_status(job_state, full_status[ "status" ] ) + except Exception: + log.exception( "Failed to update Pulsar job status for job_id %s" % job_id ) + raise + # Nothing else to do? - Attempt to fail the job? + + +class PulsarRESTJobRunner( PulsarJobRunner ): + destination_defaults = dict( + default_file_action="transfer", + rewrite_parameters="true", + dependency_resolution="remote", + url=PARAMETER_SPECIFICATION_REQUIRED, + ) + + +class PulsarComputeEnvironment( ComputeEnvironment ): + + def __init__( self, pulsar_client, job_wrapper, remote_job_config ): + self.pulsar_client = pulsar_client + self.job_wrapper = job_wrapper + self.local_path_config = job_wrapper.default_compute_environment() + self.unstructured_path_rewrites = {} + # job_wrapper.prepare is going to expunge the job backing the following + # computations, so precalculate these paths. + self._wrapper_input_paths = self.local_path_config.input_paths() + self._wrapper_output_paths = self.local_path_config.output_paths() + self.path_mapper = PathMapper(pulsar_client, remote_job_config, self.local_path_config.working_directory()) + self._config_directory = remote_job_config[ "configs_directory" ] + self._working_directory = remote_job_config[ "working_directory" ] + self._sep = remote_job_config[ "system_properties" ][ "separator" ] + self._tool_dir = remote_job_config[ "tools_directory" ] + version_path = self.local_path_config.version_path() + new_version_path = self.path_mapper.remote_version_path_rewrite(version_path) + if new_version_path: + version_path = new_version_path + self._version_path = version_path + + def output_paths( self ): + local_output_paths = self._wrapper_output_paths + + results = [] + for local_output_path in local_output_paths: + wrapper_path = str( local_output_path ) + remote_path = self.path_mapper.remote_output_path_rewrite( wrapper_path ) + results.append( self._dataset_path( local_output_path, remote_path ) ) + return results + + def input_paths( self ): + local_input_paths = self._wrapper_input_paths + + results = [] + for local_input_path in local_input_paths: + wrapper_path = str( local_input_path ) + # This will over-copy in some cases. For instance in the case of task + # splitting, this input will be copied even though only the work dir + # input will actually be used. + remote_path = self.path_mapper.remote_input_path_rewrite( wrapper_path ) + results.append( self._dataset_path( local_input_path, remote_path ) ) + return results + + def _dataset_path( self, local_dataset_path, remote_path ): + remote_extra_files_path = None + if remote_path: + remote_extra_files_path = "%s_files" % remote_path[ 0:-len( ".dat" ) ] + return local_dataset_path.with_path_for_job( remote_path, remote_extra_files_path ) + + def working_directory( self ): + return self._working_directory + + def config_directory( self ): + return self._config_directory + + def new_file_path( self ): + return self.working_directory() # Problems with doing this? + + def sep( self ): + return self._sep + + def version_path( self ): + return self._version_path + + def rewriter( self, parameter_value ): + unstructured_path_rewrites = self.unstructured_path_rewrites + if parameter_value in unstructured_path_rewrites: + # Path previously mapped, use previous mapping. + return unstructured_path_rewrites[ parameter_value ] + if parameter_value in unstructured_path_rewrites.itervalues(): + # Path is a rewritten remote path (this might never occur, + # consider dropping check...) + return parameter_value + + rewrite, new_unstructured_path_rewrites = self.path_mapper.check_for_arbitrary_rewrite( parameter_value ) + if rewrite: + unstructured_path_rewrites.update(new_unstructured_path_rewrites) + return rewrite + else: + # Did need to rewrite, use original path or value. + return parameter_value + + def unstructured_path_rewriter( self ): + return self.rewriter diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/jobs/runners/util/__init__.py --- a/lib/galaxy/jobs/runners/util/__init__.py +++ b/lib/galaxy/jobs/runners/util/__init__.py @@ -1,7 +1,7 @@ """ This module and its submodules contains utilities for running external processes and interfacing with job managers. This module should contain -functionality shared between Galaxy and the LWR. +functionality shared between Galaxy and the Pulsar. """ from galaxy.util.bunch import Bunch diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/jobs/runners/util/cli/factory.py --- a/lib/galaxy/jobs/runners/util/cli/factory.py +++ b/lib/galaxy/jobs/runners/util/cli/factory.py @@ -5,7 +5,7 @@ ) code_dir = 'lib' except ImportError: - from lwr.managers.util.cli import ( + from pulsar.managers.util.cli import ( CliInterface, split_params ) diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/jobs/runners/util/cli/job/slurm.py --- a/lib/galaxy/jobs/runners/util/cli/job/slurm.py +++ b/lib/galaxy/jobs/runners/util/cli/job/slurm.py @@ -5,7 +5,7 @@ from galaxy.model import Job job_states = Job.states except ImportError: - # Not in Galaxy, map Galaxy job states to LWR ones. + # Not in Galaxy, map Galaxy job states to Pulsar ones. from galaxy.util import enum job_states = enum(RUNNING='running', OK='complete', QUEUED='queued') diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/jobs/runners/util/cli/job/torque.py --- a/lib/galaxy/jobs/runners/util/cli/job/torque.py +++ b/lib/galaxy/jobs/runners/util/cli/job/torque.py @@ -7,7 +7,7 @@ from galaxy.model import Job job_states = Job.states except ImportError: - # Not in Galaxy, map Galaxy job states to LWR ones. + # Not in Galaxy, map Galaxy job states to Pulsar ones. from galaxy.util import enum job_states = enum(RUNNING='running', OK='complete', QUEUED='queued') diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -623,9 +623,9 @@ elif store == 'irods': from .rods import IRODSObjectStore return IRODSObjectStore(config=config, config_xml=config_xml) - elif store == 'lwr': - from .lwr import LwrObjectStore - return LwrObjectStore(config=config, config_xml=config_xml) + elif store == 'pulsar': + from .pulsar import PulsarObjectStore + return PulsarObjectStore(config=config, config_xml=config_xml) else: log.error("Unrecognized object store definition: {0}".format(store)) diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/objectstore/lwr.py --- a/lib/galaxy/objectstore/lwr.py +++ /dev/null @@ -1,76 +0,0 @@ -from __future__ import absolute_import # Need to import lwr_client absolutely. -from ..objectstore import ObjectStore -try: - from galaxy.jobs.runners.lwr_client.manager import ObjectStoreClientManager -except ImportError: - from lwr.lwr_client.manager import ObjectStoreClientManager - - -class LwrObjectStore(ObjectStore): - """ - Object store implementation that delegates to a remote LWR server. - - This may be more aspirational than practical for now, it would be good to - Galaxy to a point that a handler thread could be setup that doesn't attempt - to access the disk files returned by a (this) object store - just passing - them along to the LWR unmodified. That modification - along with this - implementation and LWR job destinations would then allow Galaxy to fully - manage jobs on remote servers with completely different mount points. - - This implementation should be considered beta and may be dropped from - Galaxy at some future point or significantly modified. - """ - - def __init__(self, config, config_xml): - self.lwr_client = self.__build_lwr_client(config_xml) - - def exists(self, obj, **kwds): - return self.lwr_client.exists(**self.__build_kwds(obj, **kwds)) - - def file_ready(self, obj, **kwds): - return self.lwr_client.file_ready(**self.__build_kwds(obj, **kwds)) - - def create(self, obj, **kwds): - return self.lwr_client.create(**self.__build_kwds(obj, **kwds)) - - def empty(self, obj, **kwds): - return self.lwr_client.empty(**self.__build_kwds(obj, **kwds)) - - def size(self, obj, **kwds): - return self.lwr_client.size(**self.__build_kwds(obj, **kwds)) - - def delete(self, obj, **kwds): - return self.lwr_client.delete(**self.__build_kwds(obj, **kwds)) - - # TODO: Optimize get_data. - def get_data(self, obj, **kwds): - return self.lwr_client.get_data(**self.__build_kwds(obj, **kwds)) - - def get_filename(self, obj, **kwds): - return self.lwr_client.get_filename(**self.__build_kwds(obj, **kwds)) - - def update_from_file(self, obj, **kwds): - return self.lwr_client.update_from_file(**self.__build_kwds(obj, **kwds)) - - def get_store_usage_percent(self): - return self.lwr_client.get_store_usage_percent() - - def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None): - return None - - def __build_kwds(self, obj, **kwds): - kwds['object_id'] = obj.id - return kwds - pass - - def __build_lwr_client(self, config_xml): - url = config_xml.get("url") - private_token = config_xml.get("private_token", None) - transport = config_xml.get("transport", None) - manager_options = dict(transport=transport) - client_options = dict(url=url, private_token=private_token) - lwr_client = ObjectStoreClientManager(**manager_options).get_client(client_options) - return lwr_client - - def shutdown(self): - pass diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/objectstore/pulsar.py --- /dev/null +++ b/lib/galaxy/objectstore/pulsar.py @@ -0,0 +1,73 @@ +from __future__ import absolute_import # Need to import pulsar_client absolutely. +from ..objectstore import ObjectStore +from pulsar.client.manager import ObjectStoreClientManager + + +class PulsarObjectStore(ObjectStore): + """ + Object store implementation that delegates to a remote Pulsar server. + + This may be more aspirational than practical for now, it would be good to + Galaxy to a point that a handler thread could be setup that doesn't attempt + to access the disk files returned by a (this) object store - just passing + them along to the Pulsar unmodified. That modification - along with this + implementation and Pulsar job destinations would then allow Galaxy to fully + manage jobs on remote servers with completely different mount points. + + This implementation should be considered beta and may be dropped from + Galaxy at some future point or significantly modified. + """ + + def __init__(self, config, config_xml): + self.pulsar_client = self.__build_pulsar_client(config_xml) + + def exists(self, obj, **kwds): + return self.pulsar_client.exists(**self.__build_kwds(obj, **kwds)) + + def file_ready(self, obj, **kwds): + return self.pulsar_client.file_ready(**self.__build_kwds(obj, **kwds)) + + def create(self, obj, **kwds): + return self.pulsar_client.create(**self.__build_kwds(obj, **kwds)) + + def empty(self, obj, **kwds): + return self.pulsar_client.empty(**self.__build_kwds(obj, **kwds)) + + def size(self, obj, **kwds): + return self.pulsar_client.size(**self.__build_kwds(obj, **kwds)) + + def delete(self, obj, **kwds): + return self.pulsar_client.delete(**self.__build_kwds(obj, **kwds)) + + # TODO: Optimize get_data. + def get_data(self, obj, **kwds): + return self.pulsar_client.get_data(**self.__build_kwds(obj, **kwds)) + + def get_filename(self, obj, **kwds): + return self.pulsar_client.get_filename(**self.__build_kwds(obj, **kwds)) + + def update_from_file(self, obj, **kwds): + return self.pulsar_client.update_from_file(**self.__build_kwds(obj, **kwds)) + + def get_store_usage_percent(self): + return self.pulsar_client.get_store_usage_percent() + + def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None): + return None + + def __build_kwds(self, obj, **kwds): + kwds['object_id'] = obj.id + return kwds + pass + + def __build_pulsar_client(self, config_xml): + url = config_xml.get("url") + private_token = config_xml.get("private_token", None) + transport = config_xml.get("transport", None) + manager_options = dict(transport=transport) + client_options = dict(url=url, private_token=private_token) + pulsar_client = ObjectStoreClientManager(**manager_options).get_client(client_options) + return pulsar_client + + def shutdown(self): + pass diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/galaxy/tools/deps/dependencies.py --- a/lib/galaxy/tools/deps/dependencies.py +++ b/lib/galaxy/tools/deps/dependencies.py @@ -8,7 +8,7 @@ related context required to resolve dependencies via the ToolShedPackageDependencyResolver. - This is meant to enable remote resolution of dependencies, by the LWR or + This is meant to enable remote resolution of dependencies, by the Pulsar or other potential remote execution mechanisms. """ @@ -39,7 +39,7 @@ @staticmethod def _toolshed_install_dependency_from_dict(as_dict): - # Rather than requiring full models in LWR, just use simple objects + # Rather than requiring full models in Pulsar, just use simple objects # containing only properties and associations used to resolve # dependencies for tool execution. repository_object = bunch.Bunch( diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/pulsar/client/__init__.py --- /dev/null +++ b/lib/pulsar/client/__init__.py @@ -0,0 +1,62 @@ +""" +pulsar client +====== + +This module contains logic for interfacing with an external Pulsar server. + +------------------ +Configuring Galaxy +------------------ + +Galaxy job runners are configured in Galaxy's ``job_conf.xml`` file. See ``job_conf.xml.sample_advanced`` +in your Galaxy code base or on +`Bitbucket <https://bitbucket.org/galaxy/galaxy-dist/src/tip/job_conf.xml.sample_advanc…>`_ +for information on how to configure Galaxy to interact with the Pulsar. + +Galaxy also supports an older, less rich configuration of job runners directly +in its main ``universe_wsgi.ini`` file. The following section describes how to +configure Galaxy to communicate with the Pulsar in this legacy mode. + +Legacy +------ + +A Galaxy tool can be configured to be executed remotely via Pulsar by +adding a line to the ``universe_wsgi.ini`` file under the +``galaxy:tool_runners`` section with the format:: + + <tool_id> = pulsar://http://<pulsar_host>:<pulsar_port> + +As an example, if a host named remotehost is running the Pulsar server +application on port ``8913``, then the tool with id ``test_tool`` can +be configured to run remotely on remotehost by adding the following +line to ``universe.ini``:: + + test_tool = pulsar://http://remotehost:8913 + +Remember this must be added after the ``[galaxy:tool_runners]`` header +in the ``universe.ini`` file. + + +""" + +from .staging.down import finish_job +from .staging.up import submit_job +from .staging import ClientJobDescription +from .staging import PulsarOutputs +from .staging import ClientOutputs +from .client import OutputNotFoundException +from .manager import build_client_manager +from .destination import url_to_destination_params +from .path_mapper import PathMapper + +__all__ = [ + build_client_manager, + OutputNotFoundException, + url_to_destination_params, + finish_job, + submit_job, + ClientJobDescription, + PulsarOutputs, + ClientOutputs, + PathMapper, +] diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/pulsar/client/action_mapper.py --- /dev/null +++ b/lib/pulsar/client/action_mapper.py @@ -0,0 +1,567 @@ +from json import load +from os import makedirs +from os.path import exists +from os.path import abspath +from os.path import dirname +from os.path import join +from os.path import basename +from os.path import sep +import fnmatch +from re import compile +from re import escape +import galaxy.util +from galaxy.util.bunch import Bunch +from .config_util import read_file +from .util import directory_files +from .util import unique_path_prefix +from .transport import get_file +from .transport import post_file + + +DEFAULT_MAPPED_ACTION = 'transfer' # Not really clear to me what this should be, exception? +DEFAULT_PATH_MAPPER_TYPE = 'prefix' + +STAGING_ACTION_REMOTE = "remote" +STAGING_ACTION_LOCAL = "local" +STAGING_ACTION_NONE = None +STAGING_ACTION_DEFAULT = "default" + +# Poor man's enum. +path_type = Bunch( + # Galaxy input datasets and extra files. + INPUT="input", + # Galaxy config and param files. + CONFIG="config", + # Files from tool's tool_dir (for now just wrapper if available). + TOOL="tool", + # Input work dir files - e.g. metadata files, task-split input files, etc.. + WORKDIR="workdir", + # Galaxy output datasets in their final home. + OUTPUT="output", + # Galaxy from_work_dir output paths and other files (e.g. galaxy.json) + OUTPUT_WORKDIR="output_workdir", + # Other fixed tool parameter paths (likely coming from tool data, but not + # nessecarily). Not sure this is the best name... + UNSTRUCTURED="unstructured", +) + + +ACTION_DEFAULT_PATH_TYPES = [ + path_type.INPUT, + path_type.CONFIG, + path_type.TOOL, + path_type.WORKDIR, + path_type.OUTPUT, + path_type.OUTPUT_WORKDIR, +] +ALL_PATH_TYPES = ACTION_DEFAULT_PATH_TYPES + [path_type.UNSTRUCTURED] + + +class FileActionMapper(object): + """ + Objects of this class define how paths are mapped to actions. + + >>> json_string = r'''{"paths": [ \ + {"path": "/opt/galaxy", "action": "none"}, \ + {"path": "/galaxy/data", "action": "transfer"}, \ + {"path": "/cool/bamfiles/**/*.bam", "action": "copy", "match_type": "glob"}, \ + {"path": ".*/dataset_\\\\d+.dat", "action": "copy", "match_type": "regex"} \ + ]}''' + >>> from tempfile import NamedTemporaryFile + >>> from os import unlink + >>> def mapper_for(default_action, config_contents): + ... f = NamedTemporaryFile(delete=False) + ... f.write(config_contents.encode('UTF-8')) + ... f.close() + ... mock_client = Bunch(default_file_action=default_action, action_config_path=f.name, files_endpoint=None) + ... mapper = FileActionMapper(mock_client) + ... mapper = FileActionMapper(config=mapper.to_dict()) # Serialize and deserialize it to make sure still works + ... unlink(f.name) + ... return mapper + >>> mapper = mapper_for(default_action='none', config_contents=json_string) + >>> # Test first config line above, implicit path prefix mapper + >>> action = mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input') + >>> action.action_type == u'none' + True + >>> action.staging_needed + False + >>> # Test another (2nd) mapper, this one with a different action + >>> action = mapper.action('/galaxy/data/files/000/dataset_1.dat', 'input') + >>> action.action_type == u'transfer' + True + >>> action.staging_needed + True + >>> # Always at least copy work_dir outputs. + >>> action = mapper.action('/opt/galaxy/database/working_directory/45.sh', 'workdir') + >>> action.action_type == u'copy' + True + >>> action.staging_needed + True + >>> # Test glob mapper (matching test) + >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam', 'input').action_type == u'copy' + True + >>> # Test glob mapper (non-matching test) + >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam.bai', 'input').action_type == u'none' + True + >>> # Regex mapper test. + >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'input').action_type == u'copy' + True + >>> # Doesn't map unstructured paths by default + >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'unstructured').action_type == u'none' + True + >>> input_only_mapper = mapper_for(default_action="none", config_contents=r'''{"paths": [ \ + {"path": "/", "action": "transfer", "path_types": "input"} \ + ] }''') + >>> input_only_mapper.action('/dataset_1.dat', 'input').action_type == u'transfer' + True + >>> input_only_mapper.action('/dataset_1.dat', 'output').action_type == u'none' + True + >>> unstructured_mapper = mapper_for(default_action="none", config_contents=r'''{"paths": [ \ + {"path": "/", "action": "transfer", "path_types": "*any*"} \ + ] }''') + >>> unstructured_mapper.action('/old/galaxy/data/dataset_10245.dat', 'unstructured').action_type == u'transfer' + True + """ + + def __init__(self, client=None, config=None): + if config is None and client is None: + message = "FileActionMapper must be constructed from either a client or a config dictionary." + raise Exception(message) + if config is None: + config = self.__client_to_config(client) + self.default_action = config.get("default_action", "transfer") + self.mappers = mappers_from_dicts(config.get("paths", [])) + self.files_endpoint = config.get("files_endpoint", None) + + def action(self, path, type, mapper=None): + mapper = self.__find_mapper(path, type, mapper) + action_class = self.__action_class(path, type, mapper) + file_lister = DEFAULT_FILE_LISTER + action_kwds = {} + if mapper: + file_lister = mapper.file_lister + action_kwds = mapper.action_kwds + action = action_class(path, file_lister=file_lister, **action_kwds) + self.__process_action(action, type) + return action + + def unstructured_mappers(self): + """ Return mappers that will map 'unstructured' files (i.e. go beyond + mapping inputs, outputs, and config files). + """ + return filter(lambda m: path_type.UNSTRUCTURED in m.path_types, self.mappers) + + def to_dict(self): + return dict( + default_action=self.default_action, + files_endpoint=self.files_endpoint, + paths=map(lambda m: m.to_dict(), self.mappers) + ) + + def __client_to_config(self, client): + action_config_path = client.action_config_path + if action_config_path: + config = read_file(action_config_path) + else: + config = dict() + config["default_action"] = client.default_file_action + config["files_endpoint"] = client.files_endpoint + return config + + def __load_action_config(self, path): + config = load(open(path, 'rb')) + self.mappers = mappers_from_dicts(config.get('paths', [])) + + def __find_mapper(self, path, type, mapper=None): + if not mapper: + normalized_path = abspath(path) + for query_mapper in self.mappers: + if query_mapper.matches(normalized_path, type): + mapper = query_mapper + break + return mapper + + def __action_class(self, path, type, mapper): + action_type = self.default_action if type in ACTION_DEFAULT_PATH_TYPES else "none" + if mapper: + action_type = mapper.action_type + if type in ["workdir", "output_workdir"] and action_type == "none": + # We are changing the working_directory relative to what + # Galaxy would use, these need to be copied over. + action_type = "copy" + action_class = actions.get(action_type, None) + if action_class is None: + message_template = "Unknown action_type encountered %s while trying to map path %s" + message_args = (action_type, path) + raise Exception(message_template % message_args) + return action_class + + def __process_action(self, action, file_type): + """ Extension point to populate extra action information after an + action has been created. + """ + if action.action_type == "remote_transfer": + url_base = self.files_endpoint + if not url_base: + raise Exception("Attempted to use remote_transfer action with defining a files_endpoint") + if "?" not in url_base: + url_base = "%s?" % url_base + # TODO: URL encode path. + url = "%s&path=%s&file_type=%s" % (url_base, action.path, file_type) + action.url = url + +REQUIRED_ACTION_KWD = object() + + +class BaseAction(object): + action_spec = {} + + def __init__(self, path, file_lister=None): + self.path = path + self.file_lister = file_lister or DEFAULT_FILE_LISTER + + def unstructured_map(self, path_helper): + unstructured_map = self.file_lister.unstructured_map(self.path) + if self.staging_needed: + # To ensure uniqueness, prepend unique prefix to each name + prefix = unique_path_prefix(self.path) + for path, name in unstructured_map.iteritems(): + unstructured_map[path] = join(prefix, name) + else: + path_rewrites = {} + for path in unstructured_map: + rewrite = self.path_rewrite(path_helper, path) + if rewrite: + path_rewrites[path] = rewrite + unstructured_map = path_rewrites + return unstructured_map + + @property + def staging_needed(self): + return self.staging != STAGING_ACTION_NONE + + @property + def staging_action_local(self): + return self.staging == STAGING_ACTION_LOCAL + + +class NoneAction(BaseAction): + """ This action indicates the corresponding path does not require any + additional action. This should indicate paths that are available both on + the Pulsar client (i.e. Galaxy server) and remote Pulsar server with the same + paths. """ + action_type = "none" + staging = STAGING_ACTION_NONE + + def to_dict(self): + return dict(path=self.path, action_type=self.action_type) + + @classmethod + def from_dict(cls, action_dict): + return NoneAction(path=action_dict["path"]) + + def path_rewrite(self, path_helper, path=None): + return None + + +class RewriteAction(BaseAction): + """ This actin indicates the Pulsar server should simply rewrite the path + to the specified file. + """ + action_spec = dict( + source_directory=REQUIRED_ACTION_KWD, + destination_directory=REQUIRED_ACTION_KWD + ) + action_type = "rewrite" + staging = STAGING_ACTION_NONE + + def __init__(self, path, file_lister=None, source_directory=None, destination_directory=None): + self.path = path + self.file_lister = file_lister or DEFAULT_FILE_LISTER + self.source_directory = source_directory + self.destination_directory = destination_directory + + def to_dict(self): + return dict( + path=self.path, + action_type=self.action_type, + source_directory=self.source_directory, + destination_directory=self.destination_directory, + ) + + @classmethod + def from_dict(cls, action_dict): + return RewriteAction( + path=action_dict["path"], + source_directory=action_dict["source_directory"], + destination_directory=action_dict["destination_directory"], + ) + + def path_rewrite(self, path_helper, path=None): + if not path: + path = self.path + new_path = path_helper.from_posix_with_new_base(self.path, self.source_directory, self.destination_directory) + return None if new_path == self.path else new_path + + +class TransferAction(BaseAction): + """ This actions indicates that the Pulsar client should initiate an HTTP + transfer of the corresponding path to the remote Pulsar server before + launching the job. """ + action_type = "transfer" + staging = STAGING_ACTION_LOCAL + + +class CopyAction(BaseAction): + """ This action indicates that the Pulsar client should execute a file system + copy of the corresponding path to the Pulsar staging directory prior to + launching the corresponding job. """ + action_type = "copy" + staging = STAGING_ACTION_LOCAL + + +class RemoteCopyAction(BaseAction): + """ This action indicates the Pulsar server should copy the file before + execution via direct file system copy. This is like a CopyAction, but + it indicates the action should occur on the Pulsar server instead of on + the client. + """ + action_type = "remote_copy" + staging = STAGING_ACTION_REMOTE + + def to_dict(self): + return dict(path=self.path, action_type=self.action_type) + + @classmethod + def from_dict(cls, action_dict): + return RemoteCopyAction(path=action_dict["path"]) + + def write_to_path(self, path): + galaxy.util.copy_to_path(open(self.path, "rb"), path) + + def write_from_path(self, pulsar_path): + destination = self.path + parent_directory = dirname(destination) + if not exists(parent_directory): + makedirs(parent_directory) + with open(pulsar_path, "rb") as f: + galaxy.util.copy_to_path(f, destination) + + +class RemoteTransferAction(BaseAction): + """ This action indicates the Pulsar server should copy the file before + execution via direct file system copy. This is like a CopyAction, but + it indicates the action should occur on the Pulsar server instead of on + the client. + """ + action_type = "remote_transfer" + staging = STAGING_ACTION_REMOTE + + def __init__(self, path, file_lister=None, url=None): + super(RemoteTransferAction, self).__init__(path, file_lister=file_lister) + self.url = url + + def to_dict(self): + return dict(path=self.path, action_type=self.action_type, url=self.url) + + @classmethod + def from_dict(cls, action_dict): + return RemoteTransferAction(path=action_dict["path"], url=action_dict["url"]) + + def write_to_path(self, path): + get_file(self.url, path) + + def write_from_path(self, pulsar_path): + post_file(self.url, pulsar_path) + + +class MessageAction(object): + """ Sort of pseudo action describing "files" store in memory and + transferred via message (HTTP, Python-call, MQ, etc...) + """ + action_type = "message" + staging = STAGING_ACTION_DEFAULT + + def __init__(self, contents, client=None): + self.contents = contents + self.client = client + + @property + def staging_needed(self): + return True + + @property + def staging_action_local(self): + # Ekkk, cannot be called if created through from_dict. + # Shouldn't be a problem the way it is used - but is an + # object design problem. + return self.client.prefer_local_staging + + def to_dict(self): + return dict(contents=self.contents, action_type=MessageAction.action_type) + + @classmethod + def from_dict(cls, action_dict): + return MessageAction(contents=action_dict["contents"]) + + def write_to_path(self, path): + open(path, "w").write(self.contents) + + +DICTIFIABLE_ACTION_CLASSES = [RemoteCopyAction, RemoteTransferAction, MessageAction] + + +def from_dict(action_dict): + action_type = action_dict.get("action_type", None) + target_class = None + for action_class in DICTIFIABLE_ACTION_CLASSES: + if action_type == action_class.action_type: + target_class = action_class + if not target_class: + message = "Failed to recover action from dictionary - invalid action type specified %s." % action_type + raise Exception(message) + return target_class.from_dict(action_dict) + + +class BasePathMapper(object): + + def __init__(self, config): + action_type = config.get('action', DEFAULT_MAPPED_ACTION) + action_class = actions.get(action_type, None) + action_kwds = action_class.action_spec.copy() + for key, value in action_kwds.items(): + if key in config: + action_kwds[key] = config[key] + elif value is REQUIRED_ACTION_KWD: + message_template = "action_type %s requires key word argument %s" + message = message_template % (action_type, key) + raise Exception(message) + self.action_type = action_type + self.action_kwds = action_kwds + path_types_str = config.get('path_types', "*defaults*") + path_types_str = path_types_str.replace("*defaults*", ",".join(ACTION_DEFAULT_PATH_TYPES)) + path_types_str = path_types_str.replace("*any*", ",".join(ALL_PATH_TYPES)) + self.path_types = path_types_str.split(",") + self.file_lister = FileLister(config) + + def matches(self, path, path_type): + path_type_matches = path_type in self.path_types + return path_type_matches and self._path_matches(path) + + def _extend_base_dict(self, **kwds): + base_dict = dict( + action=self.action_type, + path_types=",".join(self.path_types), + match_type=self.match_type + ) + base_dict.update(self.file_lister.to_dict()) + base_dict.update(self.action_kwds) + base_dict.update(**kwds) + return base_dict + + +class PrefixPathMapper(BasePathMapper): + match_type = 'prefix' + + def __init__(self, config): + super(PrefixPathMapper, self).__init__(config) + self.prefix_path = abspath(config['path']) + + def _path_matches(self, path): + return path.startswith(self.prefix_path) + + def to_pattern(self): + pattern_str = "(%s%s[^\s,\"\']+)" % (escape(self.prefix_path), escape(sep)) + return compile(pattern_str) + + def to_dict(self): + return self._extend_base_dict(path=self.prefix_path) + + +class GlobPathMapper(BasePathMapper): + match_type = 'glob' + + def __init__(self, config): + super(GlobPathMapper, self).__init__(config) + self.glob_path = config['path'] + + def _path_matches(self, path): + return fnmatch.fnmatch(path, self.glob_path) + + def to_pattern(self): + return compile(fnmatch.translate(self.glob_path)) + + def to_dict(self): + return self._extend_base_dict(path=self.glob_path) + + +class RegexPathMapper(BasePathMapper): + match_type = 'regex' + + def __init__(self, config): + super(RegexPathMapper, self).__init__(config) + self.pattern_raw = config['path'] + self.pattern = compile(self.pattern_raw) + + def _path_matches(self, path): + return self.pattern.match(path) is not None + + def to_pattern(self): + return self.pattern + + def to_dict(self): + return self._extend_base_dict(path=self.pattern_raw) + +MAPPER_CLASSES = [PrefixPathMapper, GlobPathMapper, RegexPathMapper] +MAPPER_CLASS_DICT = dict(map(lambda c: (c.match_type, c), MAPPER_CLASSES)) + + +def mappers_from_dicts(mapper_def_list): + return map(lambda m: __mappper_from_dict(m), mapper_def_list) + + +def __mappper_from_dict(mapper_dict): + map_type = mapper_dict.get('match_type', DEFAULT_PATH_MAPPER_TYPE) + return MAPPER_CLASS_DICT[map_type](mapper_dict) + + +class FileLister(object): + + def __init__(self, config): + self.depth = int(config.get("depth", "0")) + + def to_dict(self): + return dict( + depth=self.depth + ) + + def unstructured_map(self, path): + depth = self.depth + if self.depth == 0: + return {path: basename(path)} + else: + while depth > 0: + path = dirname(path) + depth -= 1 + return dict([(join(path, f), f) for f in directory_files(path)]) + +DEFAULT_FILE_LISTER = FileLister(dict(depth=0)) + +ACTION_CLASSES = [ + NoneAction, + RewriteAction, + TransferAction, + CopyAction, + RemoteCopyAction, + RemoteTransferAction, +] +actions = dict([(clazz.action_type, clazz) for clazz in ACTION_CLASSES]) + + +__all__ = [ + FileActionMapper, + path_type, + from_dict, + MessageAction, + RemoteTransferAction, # For testing +] diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/pulsar/client/amqp_exchange.py --- /dev/null +++ b/lib/pulsar/client/amqp_exchange.py @@ -0,0 +1,139 @@ +try: + import kombu + from kombu import pools +except ImportError: + kombu = None + +import socket +import logging +import threading +from time import sleep +log = logging.getLogger(__name__) + + +KOMBU_UNAVAILABLE = "Attempting to bind to AMQP message queue, but kombu dependency unavailable" + +DEFAULT_EXCHANGE_NAME = "pulsar" +DEFAULT_EXCHANGE_TYPE = "direct" +# Set timeout to periodically give up looking and check if polling should end. +DEFAULT_TIMEOUT = 0.2 +DEFAULT_HEARTBEAT = 580 + +DEFAULT_RECONNECT_CONSUMER_WAIT = 1 +DEFAULT_HEARTBEAT_WAIT = 1 + + +class PulsarExchange(object): + """ Utility for publishing and consuming structured Pulsar queues using kombu. + This is shared between the server and client - an exchange should be setup + for each manager (or in the case of the client, each manager one wished to + communicate with.) + + Each Pulsar manager is defined solely by name in the scheme, so only one Pulsar + should target each AMQP endpoint or care should be taken that unique + manager names are used across Pulsar servers targetting same AMQP endpoint - + and in particular only one such Pulsar should define an default manager with + name _default_. + """ + + def __init__( + self, + url, + manager_name, + connect_ssl=None, + timeout=DEFAULT_TIMEOUT, + publish_kwds={}, + ): + """ + """ + if not kombu: + raise Exception(KOMBU_UNAVAILABLE) + self.__url = url + self.__manager_name = manager_name + self.__connect_ssl = connect_ssl + self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE) + self.__timeout = timeout + # Be sure to log message publishing failures. + if publish_kwds.get("retry", False): + if "retry_policy" not in publish_kwds: + publish_kwds["retry_policy"] = {} + if "errback" not in publish_kwds["retry_policy"]: + publish_kwds["retry_policy"]["errback"] = self.__publish_errback + self.__publish_kwds = publish_kwds + + @property + def url(self): + return self.__url + + def consume(self, queue_name, callback, check=True, connection_kwargs={}): + queue = self.__queue(queue_name) + log.debug("Consuming queue '%s'", queue) + while check: + heartbeat_thread = None + try: + with self.connection(self.__url, heartbeat=DEFAULT_HEARTBEAT, **connection_kwargs) as connection: + with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): + heartbeat_thread = self.__start_heartbeat(queue_name, connection) + while check and connection.connected: + try: + connection.drain_events(timeout=self.__timeout) + except socket.timeout: + pass + except (IOError, socket.error), exc: + # In testing, errno is None + log.warning('Got %s, will retry: %s', exc.__class__.__name__, exc) + if heartbeat_thread: + heartbeat_thread.join() + sleep(DEFAULT_RECONNECT_CONSUMER_WAIT) + + def heartbeat(self, connection): + log.debug('AMQP heartbeat thread alive') + while connection.connected: + connection.heartbeat_check() + sleep(DEFAULT_HEARTBEAT_WAIT) + log.debug('AMQP heartbeat thread exiting') + + def publish(self, name, payload): + with self.connection(self.__url) as connection: + with pools.producers[connection].acquire() as producer: + key = self.__queue_name(name) + producer.publish( + payload, + serializer='json', + exchange=self.__exchange, + declare=[self.__exchange], + routing_key=key, + **self.__publish_kwds + ) + + def __publish_errback(self, exc, interval): + log.error("Connection error while publishing: %r", exc, exc_info=1) + log.info("Retrying in %s seconds", interval) + + def connection(self, connection_string, **kwargs): + if "ssl" not in kwargs: + kwargs["ssl"] = self.__connect_ssl + return kombu.Connection(connection_string, **kwargs) + + def __queue(self, name): + queue_name = self.__queue_name(name) + queue = kombu.Queue(queue_name, self.__exchange, routing_key=queue_name) + return queue + + def __queue_name(self, name): + key_prefix = self.__key_prefix() + queue_name = '%s_%s' % (key_prefix, name) + return queue_name + + def __key_prefix(self): + if self.__manager_name == "_default_": + key_prefix = "pulsar_" + else: + key_prefix = "pulsar_%s_" % self.__manager_name + return key_prefix + + def __start_heartbeat(self, queue_name, connection): + thread_name = "consume-heartbeat-%s" % (self.__queue_name(queue_name)) + thread = threading.Thread(name=thread_name, target=self.heartbeat, args=(connection,)) + thread.start() + return thread diff -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee -r 566388d623749dad4259ea04cf44a5d858a56671 lib/pulsar/client/amqp_exchange_factory.py --- /dev/null +++ b/lib/pulsar/client/amqp_exchange_factory.py @@ -0,0 +1,41 @@ +from .amqp_exchange import PulsarExchange +from .util import filter_destination_params + + +def get_exchange(url, manager_name, params): + connect_ssl = parse_amqp_connect_ssl_params(params) + exchange_kwds = dict( + manager_name=manager_name, + connect_ssl=connect_ssl, + publish_kwds=parse_amqp_publish_kwds(params) + ) + timeout = params.get('amqp_consumer_timeout', False) + if timeout is not False: + exchange_kwds['timeout'] = timeout + exchange = PulsarExchange(url, **exchange_kwds) + return exchange + + +def parse_amqp_connect_ssl_params(params): + ssl_params = filter_destination_params(params, "amqp_connect_ssl_") + if not ssl_params: + return + + ssl = __import__('ssl') + if 'cert_reqs' in ssl_params: + value = ssl_params['cert_reqs'] + ssl_params['cert_reqs'] = getattr(ssl, value.upper()) + return ssl_params + + +def parse_amqp_publish_kwds(params): + all_publish_params = filter_destination_params(params, "amqp_publish_") + retry_policy_params = {} + for key in all_publish_params.keys(): + if key.startswith("retry_"): + value = all_publish_params[key] + retry_policy_params[key[len("retry_"):]] = value + del all_publish_params[key] + if retry_policy_params: + all_publish_params["retry_policy"] = retry_policy_params + return all_publish_params This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Merged in jmchilton/galaxy-central-fork-1 (pull request #411)
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4ef50975607e/ Changeset: 4ef50975607e User: jmchilton Date: 2014-06-24 04:15:44 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #411) Allow dynamic job destinations rules to throw `galaxy.jobs.mapper.JobNotReadyException` indicating job not ready. Affected #: 2 files diff -r 5eaeb25bff8f383e54c36bd32e17432e6cafadde -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -13,6 +13,7 @@ from galaxy import model from galaxy.util.sleeper import Sleeper from galaxy.jobs import JobWrapper, TaskWrapper, JobDestination +from galaxy.jobs.mapper import JobNotReadyException log = logging.getLogger( __name__ ) @@ -263,7 +264,7 @@ try: # Check the job's dependencies, requeue if they're not done. # Some of these states will only happen when using the in-memory job queue - job_state = self.__check_if_ready_to_run( job ) + job_state = self.__check_job_state( job ) if job_state == JOB_WAIT: new_waiting_jobs.append( job.id ) elif job_state == JOB_INPUT_ERROR: @@ -304,7 +305,7 @@ # Done with the session self.sa_session.remove() - def __check_if_ready_to_run( self, job ): + def __check_job_state( self, job ): """ Check if a job is ready to run by verifying that each of its input datasets is ready (specifically in the OK state). If any input dataset @@ -314,62 +315,97 @@ job can be dispatched. Otherwise, return JOB_WAIT indicating that input datasets are still being prepared. """ - # If tracking in the database, job.state is guaranteed to be NEW and the inputs are guaranteed to be OK if not self.track_jobs_in_database: - if job.state == model.Job.states.DELETED: - return JOB_DELETED - elif job.state == model.Job.states.ERROR: - return JOB_ADMIN_DELETED - for dataset_assoc in job.input_datasets + job.input_library_datasets: - idata = dataset_assoc.dataset - if not idata: - continue - # don't run jobs for which the input dataset was deleted - if idata.deleted: - self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) ) - return JOB_INPUT_DELETED - # an error in the input data causes us to bail immediately - elif idata.state == idata.states.ERROR: - self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s is in error state" % ( idata.hid ) ) - return JOB_INPUT_ERROR - elif idata.state == idata.states.FAILED_METADATA: - self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s failed to properly set metadata" % ( idata.hid ) ) - return JOB_INPUT_ERROR - elif idata.state != idata.states.OK and not ( idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id ): - # need to requeue - return JOB_WAIT + in_memory_not_ready_state = self.__verify_in_memory_job_inputs( job ) + if in_memory_not_ready_state: + return in_memory_not_ready_state + + # Else, if tracking in the database, job.state is guaranteed to be NEW and + # the inputs are guaranteed to be OK. + # Create the job wrapper so that the destination can be set - if job.id not in self.job_wrappers: - self.job_wrappers[job.id] = self.job_wrapper( job ) - # Cause the job_destination to be set and cached by the mapper + job_id = job.id + job_wrapper = self.job_wrappers.get( job_id, None ) + if not job_wrapper: + job_wrapper = self.job_wrapper( job ) + self.job_wrappers[ job_id ] = job_wrapper + + # If state == JOB_READY, assume job_destination also set - otherwise + # in case of various error or cancelled states do not assume + # destination has been set. + state, job_destination = self.__verify_job_ready( job, job_wrapper ) + + if state == JOB_READY: + # PASS. increase usage by one job (if caching) so that multiple jobs aren't dispatched on this queue iteration + self.increase_running_job_count(job.user_id, job_destination.id ) + return state + + def __verify_job_ready( self, job, job_wrapper ): + """ Compute job destination and verify job is ready at that + destination by checking job limits and quota. If this method + return a job state of JOB_READY - it MUST also return a job + destination. + """ + job_destination = None try: - self.job_wrappers[job.id].job_destination + # Cause the job_destination to be set and cached by the mapper + job_destination = job_wrapper.job_destination + except JobNotReadyException as e: + job_state = e.job_state or JOB_WAIT + return job_state, None except Exception, e: failure_message = getattr( e, 'failure_message', DEFAULT_JOB_PUT_FAILURE_MESSAGE ) if failure_message == DEFAULT_JOB_PUT_FAILURE_MESSAGE: log.exception( 'Failed to generate job destination' ) else: log.debug( "Intentionally failing job with message (%s)" % failure_message ) - self.job_wrappers[job.id].fail( failure_message ) - return JOB_ERROR + job_wrapper.fail( failure_message ) + return JOB_ERROR, job_destination # job is ready to run, check limits # TODO: these checks should be refactored to minimize duplication and made more modular/pluggable - state = self.__check_destination_jobs( job, self.job_wrappers[job.id] ) + state = self.__check_destination_jobs( job, job_wrapper ) if state == JOB_READY: - state = self.__check_user_jobs( job, self.job_wrappers[job.id] ) + state = self.__check_user_jobs( job, job_wrapper ) if state == JOB_READY and self.app.config.enable_quotas: quota = self.app.quota_agent.get_quota( job.user ) if quota is not None: try: usage = self.app.quota_agent.get_usage( user=job.user, history=job.history ) if usage > quota: - return JOB_USER_OVER_QUOTA + return JOB_USER_OVER_QUOTA, job_destination except AssertionError, e: pass # No history, should not happen with an anon user - if state == JOB_READY: - # PASS. increase usage by one job (if caching) so that multiple jobs aren't dispatched on this queue iteration - self.increase_running_job_count(job.user_id, self.job_wrappers[job.id].job_destination.id) - return state + return state, job_destination + + def __verify_in_memory_job_inputs( self, job ): + """ Perform the same checks that happen via SQL for in-memory managed + jobs. + """ + if job.state == model.Job.states.DELETED: + return JOB_DELETED + elif job.state == model.Job.states.ERROR: + return JOB_ADMIN_DELETED + for dataset_assoc in job.input_datasets + job.input_library_datasets: + idata = dataset_assoc.dataset + if not idata: + continue + # don't run jobs for which the input dataset was deleted + if idata.deleted: + self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) ) + return JOB_INPUT_DELETED + # an error in the input data causes us to bail immediately + elif idata.state == idata.states.ERROR: + self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s is in error state" % ( idata.hid ) ) + return JOB_INPUT_ERROR + elif idata.state == idata.states.FAILED_METADATA: + self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s failed to properly set metadata" % ( idata.hid ) ) + return JOB_INPUT_ERROR + elif idata.state != idata.states.OK and not ( idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id ): + # need to requeue + return JOB_WAIT + + # All inputs ready to go. + return None def __clear_job_count( self ): self.user_job_count = None diff -r 5eaeb25bff8f383e54c36bd32e17432e6cafadde -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -16,6 +16,13 @@ self.failure_message = failure_message +class JobNotReadyException( Exception ): + + def __init__( self, job_state=None, message=None ): + self.job_state = job_state + self.message = message + + class JobRunnerMapper( object ): """ This class is responsible to managing the mapping of jobs Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/72a0157988f1/ Changeset: 72a0157988f1 User: jmchilton Date: 2014-06-11 07:19:20 Summary: Refactor to simplify __check_if_ready_to_run. Move checks for in memory managed jobs prior to common path through code into their own helper method. Affected #: 1 file diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 72a0157988f1cf7e9440dc1cb3dc13ca6cdc42ba lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -240,7 +240,7 @@ try: # Check the job's dependencies, requeue if they're not done. # Some of these states will only happen when using the in-memory job queue - job_state = self.__check_if_ready_to_run( job ) + job_state = self.__check_job_state( job ) if job_state == JOB_WAIT: new_waiting_jobs.append( job.id ) elif job_state == JOB_INPUT_ERROR: @@ -281,7 +281,7 @@ # Done with the session self.sa_session.remove() - def __check_if_ready_to_run( self, job ): + def __check_job_state( self, job ): """ Check if a job is ready to run by verifying that each of its input datasets is ready (specifically in the OK state). If any input dataset @@ -293,28 +293,12 @@ """ # If tracking in the database, job.state is guaranteed to be NEW and the inputs are guaranteed to be OK if not self.track_jobs_in_database: - if job.state == model.Job.states.DELETED: - return JOB_DELETED - elif job.state == model.Job.states.ERROR: - return JOB_ADMIN_DELETED - for dataset_assoc in job.input_datasets + job.input_library_datasets: - idata = dataset_assoc.dataset - if not idata: - continue - # don't run jobs for which the input dataset was deleted - if idata.deleted: - self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) ) - return JOB_INPUT_DELETED - # an error in the input data causes us to bail immediately - elif idata.state == idata.states.ERROR: - self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s is in error state" % ( idata.hid ) ) - return JOB_INPUT_ERROR - elif idata.state == idata.states.FAILED_METADATA: - self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s failed to properly set metadata" % ( idata.hid ) ) - return JOB_INPUT_ERROR - elif idata.state != idata.states.OK and not ( idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id ): - # need to requeue - return JOB_WAIT + in_memory_job_state = self.__check_in_memory_job_state( job ) + if in_memory_job_state: + return in_memory_job_state + # If no problems, all inputs ready to go, continue + # with same checks either way. + # Create the job wrapper so that the destination can be set if job.id not in self.job_wrappers: self.job_wrappers[job.id] = self.job_wrapper( job ) @@ -348,6 +332,33 @@ self.increase_running_job_count(job.user_id, self.job_wrappers[job.id].job_destination.id) return state + def __check_in_memory_job_state( self, job ): + if job.state == model.Job.states.DELETED: + return JOB_DELETED + elif job.state == model.Job.states.ERROR: + return JOB_ADMIN_DELETED + for dataset_assoc in job.input_datasets + job.input_library_datasets: + idata = dataset_assoc.dataset + if not idata: + continue + # don't run jobs for which the input dataset was deleted + if idata.deleted: + self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) ) + return JOB_INPUT_DELETED + # an error in the input data causes us to bail immediately + elif idata.state == idata.states.ERROR: + self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s is in error state" % ( idata.hid ) ) + return JOB_INPUT_ERROR + elif idata.state == idata.states.FAILED_METADATA: + self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s failed to properly set metadata" % ( idata.hid ) ) + return JOB_INPUT_ERROR + elif idata.state != idata.states.OK and not ( idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id ): + # need to requeue + return JOB_WAIT + + # All inputs ready to go. + return None + def __clear_job_count( self ): self.user_job_count = None self.user_job_count_per_destination = None https://bitbucket.org/galaxy/galaxy-central/commits/519050ab95d7/ Changeset: 519050ab95d7 User: jmchilton Date: 2014-06-11 07:19:20 Summary: Refactor __check_if_ready_to_run - less code duplication... ... in the sense that it is no longer repeatedly grabbing same values from map, from wrapper, etc. Affected #: 1 file diff -r 72a0157988f1cf7e9440dc1cb3dc13ca6cdc42ba -r 519050ab95d7177abdea8d55bae3b03a3a289476 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -291,33 +291,37 @@ job can be dispatched. Otherwise, return JOB_WAIT indicating that input datasets are still being prepared. """ - # If tracking in the database, job.state is guaranteed to be NEW and the inputs are guaranteed to be OK if not self.track_jobs_in_database: - in_memory_job_state = self.__check_in_memory_job_state( job ) - if in_memory_job_state: - return in_memory_job_state - # If no problems, all inputs ready to go, continue - # with same checks either way. + in_memory_not_ready_state = self.__verify_in_memory_job_inputs( job ) + if in_memory_not_ready_state: + return in_memory_not_ready_state + + # Else, if tracking in the database, job.state is guaranteed to be NEW and + # the inputs are guaranteed to be OK. # Create the job wrapper so that the destination can be set - if job.id not in self.job_wrappers: - self.job_wrappers[job.id] = self.job_wrapper( job ) + job_id = job.id + job_wrapper = self.job_wrappers.get( job_id, None ) + if not job_wrapper: + job_wrapper = self.job_wrapper( job ) + self.job_wrappers[ job_id ] = job_wrapper + # Cause the job_destination to be set and cached by the mapper try: - self.job_wrappers[job.id].job_destination + job_destination = job_wrapper.job_destination except Exception, e: failure_message = getattr( e, 'failure_message', DEFAULT_JOB_PUT_FAILURE_MESSAGE ) if failure_message == DEFAULT_JOB_PUT_FAILURE_MESSAGE: log.exception( 'Failed to generate job destination' ) else: log.debug( "Intentionally failing job with message (%s)" % failure_message ) - self.job_wrappers[job.id].fail( failure_message ) + job_wrapper.fail( failure_message ) return JOB_ERROR # job is ready to run, check limits # TODO: these checks should be refactored to minimize duplication and made more modular/pluggable - state = self.__check_destination_jobs( job, self.job_wrappers[job.id] ) + state = self.__check_destination_jobs( job, job_wrapper ) if state == JOB_READY: - state = self.__check_user_jobs( job, self.job_wrappers[job.id] ) + state = self.__check_user_jobs( job, job_wrapper ) if state == JOB_READY and self.app.config.enable_quotas: quota = self.app.quota_agent.get_quota( job.user ) if quota is not None: @@ -329,10 +333,13 @@ pass # No history, should not happen with an anon user if state == JOB_READY: # PASS. increase usage by one job (if caching) so that multiple jobs aren't dispatched on this queue iteration - self.increase_running_job_count(job.user_id, self.job_wrappers[job.id].job_destination.id) + self.increase_running_job_count(job.user_id, job_destination.id ) return state - def __check_in_memory_job_state( self, job ): + def __verify_in_memory_job_inputs( self, job ): + """ Perform the same checks that happen via SQL for in-memory managed + jobs. + """ if job.state == model.Job.states.DELETED: return JOB_DELETED elif job.state == model.Job.states.ERROR: https://bitbucket.org/galaxy/galaxy-central/commits/8bbb244d339b/ Changeset: 8bbb244d339b User: jmchilton Date: 2014-06-11 07:19:20 Summary: Break up __check_job_state - extract new __verify_job_ready method. Affected #: 1 file diff -r 519050ab95d7177abdea8d55bae3b03a3a289476 -r 8bbb244d339b396c841341faaa9353f4a1c5e5f1 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -306,8 +306,25 @@ job_wrapper = self.job_wrapper( job ) self.job_wrappers[ job_id ] = job_wrapper - # Cause the job_destination to be set and cached by the mapper + # If state == JOB_READY, assume job_destination also set - otherwise + # in case of various error or cancelled states do not assume + # destination has been set. + state, job_destination = self.__verify_job_ready( job, job_wrapper ) + + if state == JOB_READY: + # PASS. increase usage by one job (if caching) so that multiple jobs aren't dispatched on this queue iteration + self.increase_running_job_count(job.user_id, job_destination.id ) + return state + + def __verify_job_ready( self, job, job_wrapper ): + """ Compute job destination and verify job is ready at that + destination by checking job limits and quota. If this method + return a job state of JOB_READY - it MUST also return a job + destination. + """ + job_destination = None try: + # Cause the job_destination to be set and cached by the mapper job_destination = job_wrapper.job_destination except Exception, e: failure_message = getattr( e, 'failure_message', DEFAULT_JOB_PUT_FAILURE_MESSAGE ) @@ -316,7 +333,7 @@ else: log.debug( "Intentionally failing job with message (%s)" % failure_message ) job_wrapper.fail( failure_message ) - return JOB_ERROR + return JOB_ERROR, job_destination # job is ready to run, check limits # TODO: these checks should be refactored to minimize duplication and made more modular/pluggable state = self.__check_destination_jobs( job, job_wrapper ) @@ -328,13 +345,10 @@ try: usage = self.app.quota_agent.get_usage( user=job.user, history=job.history ) if usage > quota: - return JOB_USER_OVER_QUOTA + return JOB_USER_OVER_QUOTA, job_destination except AssertionError, e: pass # No history, should not happen with an anon user - if state == JOB_READY: - # PASS. increase usage by one job (if caching) so that multiple jobs aren't dispatched on this queue iteration - self.increase_running_job_count(job.user_id, job_destination.id ) - return state + return state, job_destination def __verify_in_memory_job_inputs( self, job ): """ Perform the same checks that happen via SQL for in-memory managed https://bitbucket.org/galaxy/galaxy-central/commits/e1c8d892be5d/ Changeset: e1c8d892be5d User: jmchilton Date: 2014-06-11 07:19:20 Summary: Allow dynamic job destinations to throw new JobNotReadyException to indicate delayed decision. Perhaps wait on some deployer defined limit or resource to become available, etc... Affected #: 2 files diff -r 8bbb244d339b396c841341faaa9353f4a1c5e5f1 -r e1c8d892be5de20ed4564a3e467943701dccacd8 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -13,6 +13,7 @@ from galaxy import model from galaxy.util.sleeper import Sleeper from galaxy.jobs import JobWrapper, TaskWrapper, JobDestination +from galaxy.jobs.mapper import JobNotReadyException log = logging.getLogger( __name__ ) @@ -326,6 +327,9 @@ try: # Cause the job_destination to be set and cached by the mapper job_destination = job_wrapper.job_destination + except JobNotReadyException as e: + job_state = e.job_state or JOB_WAIT + return job_state, None except Exception, e: failure_message = getattr( e, 'failure_message', DEFAULT_JOB_PUT_FAILURE_MESSAGE ) if failure_message == DEFAULT_JOB_PUT_FAILURE_MESSAGE: diff -r 8bbb244d339b396c841341faaa9353f4a1c5e5f1 -r e1c8d892be5de20ed4564a3e467943701dccacd8 lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -16,6 +16,13 @@ self.failure_message = failure_message +class JobNotReadyException( Exception ): + + def __init__( self, job_state=None, message=None ): + self.job_state = job_state + self.message = message + + class JobRunnerMapper( object ): """ This class is responsible to managing the mapping of jobs https://bitbucket.org/galaxy/galaxy-central/commits/4ef50975607e/ Changeset: 4ef50975607e User: jmchilton Date: 2014-06-24 04:15:44 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #411) Allow dynamic job destinations rules to throw `galaxy.jobs.mapper.JobNotReadyException` indicating job not ready. Affected #: 2 files diff -r 5eaeb25bff8f383e54c36bd32e17432e6cafadde -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -13,6 +13,7 @@ from galaxy import model from galaxy.util.sleeper import Sleeper from galaxy.jobs import JobWrapper, TaskWrapper, JobDestination +from galaxy.jobs.mapper import JobNotReadyException log = logging.getLogger( __name__ ) @@ -263,7 +264,7 @@ try: # Check the job's dependencies, requeue if they're not done. # Some of these states will only happen when using the in-memory job queue - job_state = self.__check_if_ready_to_run( job ) + job_state = self.__check_job_state( job ) if job_state == JOB_WAIT: new_waiting_jobs.append( job.id ) elif job_state == JOB_INPUT_ERROR: @@ -304,7 +305,7 @@ # Done with the session self.sa_session.remove() - def __check_if_ready_to_run( self, job ): + def __check_job_state( self, job ): """ Check if a job is ready to run by verifying that each of its input datasets is ready (specifically in the OK state). If any input dataset @@ -314,62 +315,97 @@ job can be dispatched. Otherwise, return JOB_WAIT indicating that input datasets are still being prepared. """ - # If tracking in the database, job.state is guaranteed to be NEW and the inputs are guaranteed to be OK if not self.track_jobs_in_database: - if job.state == model.Job.states.DELETED: - return JOB_DELETED - elif job.state == model.Job.states.ERROR: - return JOB_ADMIN_DELETED - for dataset_assoc in job.input_datasets + job.input_library_datasets: - idata = dataset_assoc.dataset - if not idata: - continue - # don't run jobs for which the input dataset was deleted - if idata.deleted: - self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) ) - return JOB_INPUT_DELETED - # an error in the input data causes us to bail immediately - elif idata.state == idata.states.ERROR: - self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s is in error state" % ( idata.hid ) ) - return JOB_INPUT_ERROR - elif idata.state == idata.states.FAILED_METADATA: - self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s failed to properly set metadata" % ( idata.hid ) ) - return JOB_INPUT_ERROR - elif idata.state != idata.states.OK and not ( idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id ): - # need to requeue - return JOB_WAIT + in_memory_not_ready_state = self.__verify_in_memory_job_inputs( job ) + if in_memory_not_ready_state: + return in_memory_not_ready_state + + # Else, if tracking in the database, job.state is guaranteed to be NEW and + # the inputs are guaranteed to be OK. + # Create the job wrapper so that the destination can be set - if job.id not in self.job_wrappers: - self.job_wrappers[job.id] = self.job_wrapper( job ) - # Cause the job_destination to be set and cached by the mapper + job_id = job.id + job_wrapper = self.job_wrappers.get( job_id, None ) + if not job_wrapper: + job_wrapper = self.job_wrapper( job ) + self.job_wrappers[ job_id ] = job_wrapper + + # If state == JOB_READY, assume job_destination also set - otherwise + # in case of various error or cancelled states do not assume + # destination has been set. + state, job_destination = self.__verify_job_ready( job, job_wrapper ) + + if state == JOB_READY: + # PASS. increase usage by one job (if caching) so that multiple jobs aren't dispatched on this queue iteration + self.increase_running_job_count(job.user_id, job_destination.id ) + return state + + def __verify_job_ready( self, job, job_wrapper ): + """ Compute job destination and verify job is ready at that + destination by checking job limits and quota. If this method + return a job state of JOB_READY - it MUST also return a job + destination. + """ + job_destination = None try: - self.job_wrappers[job.id].job_destination + # Cause the job_destination to be set and cached by the mapper + job_destination = job_wrapper.job_destination + except JobNotReadyException as e: + job_state = e.job_state or JOB_WAIT + return job_state, None except Exception, e: failure_message = getattr( e, 'failure_message', DEFAULT_JOB_PUT_FAILURE_MESSAGE ) if failure_message == DEFAULT_JOB_PUT_FAILURE_MESSAGE: log.exception( 'Failed to generate job destination' ) else: log.debug( "Intentionally failing job with message (%s)" % failure_message ) - self.job_wrappers[job.id].fail( failure_message ) - return JOB_ERROR + job_wrapper.fail( failure_message ) + return JOB_ERROR, job_destination # job is ready to run, check limits # TODO: these checks should be refactored to minimize duplication and made more modular/pluggable - state = self.__check_destination_jobs( job, self.job_wrappers[job.id] ) + state = self.__check_destination_jobs( job, job_wrapper ) if state == JOB_READY: - state = self.__check_user_jobs( job, self.job_wrappers[job.id] ) + state = self.__check_user_jobs( job, job_wrapper ) if state == JOB_READY and self.app.config.enable_quotas: quota = self.app.quota_agent.get_quota( job.user ) if quota is not None: try: usage = self.app.quota_agent.get_usage( user=job.user, history=job.history ) if usage > quota: - return JOB_USER_OVER_QUOTA + return JOB_USER_OVER_QUOTA, job_destination except AssertionError, e: pass # No history, should not happen with an anon user - if state == JOB_READY: - # PASS. increase usage by one job (if caching) so that multiple jobs aren't dispatched on this queue iteration - self.increase_running_job_count(job.user_id, self.job_wrappers[job.id].job_destination.id) - return state + return state, job_destination + + def __verify_in_memory_job_inputs( self, job ): + """ Perform the same checks that happen via SQL for in-memory managed + jobs. + """ + if job.state == model.Job.states.DELETED: + return JOB_DELETED + elif job.state == model.Job.states.ERROR: + return JOB_ADMIN_DELETED + for dataset_assoc in job.input_datasets + job.input_library_datasets: + idata = dataset_assoc.dataset + if not idata: + continue + # don't run jobs for which the input dataset was deleted + if idata.deleted: + self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) ) + return JOB_INPUT_DELETED + # an error in the input data causes us to bail immediately + elif idata.state == idata.states.ERROR: + self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s is in error state" % ( idata.hid ) ) + return JOB_INPUT_ERROR + elif idata.state == idata.states.FAILED_METADATA: + self.job_wrappers.pop(job.id, self.job_wrapper( job )).fail( "input data %s failed to properly set metadata" % ( idata.hid ) ) + return JOB_INPUT_ERROR + elif idata.state != idata.states.OK and not ( idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id ): + # need to requeue + return JOB_WAIT + + # All inputs ready to go. + return None def __clear_job_count( self ): self.user_job_count = None diff -r 5eaeb25bff8f383e54c36bd32e17432e6cafadde -r 4ef50975607ee0d3b4490c9e7a5795d6a04802ee lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -16,6 +16,13 @@ self.failure_message = failure_message +class JobNotReadyException( Exception ): + + def __init__( self, job_state=None, message=None ): + self.job_state = job_state + self.message = message + + class JobRunnerMapper( object ): """ This class is responsible to managing the mapping of jobs Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Docfix: Delete diminutive docker doc deficiency.
by commits-noreply＠bitbucket.org 23 Jun '14

23 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5eaeb25bff8f/ Changeset: 5eaeb25bff8f User: jmchilton Date: 2014-06-23 19:49:05 Summary: Docfix: Delete diminutive docker doc deficiency. Affected #: 1 file diff -r 631127bb6c2657140e75f203301abfdf567d82e5 -r 5eaeb25bff8f383e54c36bd32e17432e6cafadde job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -178,7 +178,7 @@ does trust tool's specified container - but also wants tool's not configured to run in a container the following option can provide a fallback. --> -  + </destination><destination id="pbs" runner="pbs" tags="mycluster"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Missed committing a new __init__.py file for Tool Shed dependencies.
by commits-noreply＠bitbucket.org 23 Jun '14

23 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/631127bb6c26/ Changeset: 631127bb6c26 User: greg Date: 2014-06-23 14:58:25 Summary: Missed committing a new __init__.py file for Tool Shed dependencies. Affected #: 1 file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: A bit of repository dependency function re-factoring for Galaxy installs.
by commits-noreply＠bitbucket.org 23 Jun '14

23 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f5589d243d0f/ Changeset: f5589d243d0f User: greg Date: 2014-06-23 02:31:19 Summary: A bit of repository dependency function re-factoring for Galaxy installs. Affected #: 4 files diff -r 344e84a6554ae94604f32e8f62feebd65a6ac358 -r f5589d243d0f920cdd96c3e980762bb1a7cc061b lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1359,9 +1359,8 @@ else: # Entering this else block occurs only if the tool_shed_repository does not include any valid tools. if install_repository_dependencies: - repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans.app, - tool_shed_repository ) + repository_dependencies = rdm.get_repository_dependencies_for_installed_tool_shed_repository( trans.app, + tool_shed_repository ) else: repository_dependencies = None if metadata: @@ -1579,9 +1578,9 @@ raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) readme_files_dict = json.from_json_string( raw_text ) tool_dependencies = metadata.get( 'tool_dependencies', None ) - repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans.app, - tool_shed_repository ) + rdm = RepositoryDependencyManager( trans.app ) + repository_dependencies = rdm.get_repository_dependencies_for_installed_tool_shed_repository( trans.app, + tool_shed_repository ) repo_info_dict = \ repository_maintenance_util.create_repo_info_dict( app=trans.app, repository_clone_url=repository_clone_url, diff -r 344e84a6554ae94604f32e8f62feebd65a6ac358 -r f5589d243d0f920cdd96c3e980762bb1a7cc061b lib/tool_shed/galaxy_install/repair_repository_manager.py --- a/lib/tool_shed/galaxy_install/repair_repository_manager.py +++ b/lib/tool_shed/galaxy_install/repair_repository_manager.py @@ -4,6 +4,7 @@ log = logging.getLogger( __name__ ) from tool_shed.galaxy_install import install_manager +from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager from tool_shed.util import common_util from tool_shed.util import container_util @@ -55,6 +56,7 @@ issues with an installed repository that has installation problems somewhere in its dependency hierarchy. """ + rdm = RepositoryDependencyManager( self.app ) tsr_ids = [] repo_info_dicts = [] tool_panel_section_keys = [] @@ -62,8 +64,8 @@ irm = install_manager.InstallRepositoryManager( self.app ) # Get a dictionary of all repositories upon which the contents of the current repository_metadata #record depend. - repository_dependencies_dict = \ - repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( self.app, repository ) + repository_dependencies_dict = rdm.get_repository_dependencies_for_installed_tool_shed_repository( self.app, + repository ) if repository_dependencies_dict: # Generate the list of installed repositories from the information contained in the # repository_dependencies dictionary. @@ -73,13 +75,15 @@ # repaired in the required order. for installed_repository in installed_repositories: tsr_ids.append( self.app.security.encode_id( installed_repository.id ) ) - repo_info_dict, tool_panel_section_key = self.get_repo_info_dict_for_repair( installed_repository ) + repo_info_dict, tool_panel_section_key = self.get_repo_info_dict_for_repair( rdm, + installed_repository ) tool_panel_section_keys.append( tool_panel_section_key ) repo_info_dicts.append( repo_info_dict ) else: # The received repository has no repository dependencies. tsr_ids.append( self.app.security.encode_id( repository.id ) ) - repo_info_dict, tool_panel_section_key = self.get_repo_info_dict_for_repair( repository ) + repo_info_dict, tool_panel_section_key = self.get_repo_info_dict_for_repair( rdm, + repository ) tool_panel_section_keys.append( tool_panel_section_key ) repo_info_dicts.append( repo_info_dict ) ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \ @@ -91,11 +95,11 @@ repair_dict[ 'ordered_tool_panel_section_keys' ] = ordered_tool_panel_section_keys return repair_dict - def get_repo_info_dict_for_repair( self, repository ): + def get_repo_info_dict_for_repair( self, rdm, repository ): tool_panel_section_key = None repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( self.app, repository ) + repository_dependencies = rdm.get_repository_dependencies_for_installed_tool_shed_repository( self.app, + repository ) metadata = repository.metadata if metadata: tool_dependencies = metadata.get( 'tool_dependencies', None ) diff -r 344e84a6554ae94604f32e8f62feebd65a6ac358 -r f5589d243d0f920cdd96c3e980762bb1a7cc061b lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py --- a/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py +++ b/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py @@ -255,6 +255,29 @@ self.build_repository_dependency_relationships( all_repo_info_dicts, all_created_or_updated_tool_shed_repositories ) return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts + def get_repository_dependencies_for_installed_tool_shed_repository( self, app, repository ): + """ + Send a request to the appropriate tool shed to retrieve the dictionary of repository dependencies defined + for the received repository which is installed into Galaxy. This method is called only from Galaxy. + """ + tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, str( repository.tool_shed ) ) + params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository.name ), + str( repository.owner ), + str( repository.changeset_revision ) ) + url = common_util.url_join( tool_shed_url, + 'repository/get_repository_dependencies%s' % params ) + try: + raw_text = common_util.tool_shed_get( app, tool_shed_url, url ) + except Exception, e: + print "The URL\n%s\nraised the exception:\n%s\n" % ( url, str( e ) ) + return '' + if len( raw_text ) > 2: + encoded_text = json.loads( raw_text ) + text = encoding_util.tool_shed_decode( encoded_text ) + else: + text = '' + return text + def get_repository_dependency_by_repository_id( self, install_model, decoded_repository_id ): return install_model.context.query( install_model.RepositoryDependency ) \ .filter( install_model.RepositoryDependency.table.c.tool_shed_repository_id == decoded_repository_id ) \ diff -r 344e84a6554ae94604f32e8f62feebd65a6ac358 -r f5589d243d0f920cdd96c3e980762bb1a7cc061b lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -147,29 +147,6 @@ prior_installation_required, only_if_compiling_contained_td ) -def get_repository_dependencies_for_installed_tool_shed_repository( app, repository ): - """ - Send a request to the appropriate tool shed to retrieve the dictionary of repository dependencies defined - for the received repository which is installed into Galaxy. This method is called only from Galaxy. - """ - tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, str( repository.tool_shed ) ) - params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository.name ), - str( repository.owner ), - str( repository.changeset_revision ) ) - url = common_util.url_join( tool_shed_url, - 'repository/get_repository_dependencies%s' % params ) - try: - raw_text = common_util.tool_shed_get( app, tool_shed_url, url ) - except Exception, e: - print "The URL\n%s\nraised the exception:\n%s\n" % ( url, str( e ) ) - return '' - if len( raw_text ) > 2: - encoded_text = json.loads( raw_text ) - text = encoding_util.tool_shed_decode( encoded_text ) - else: - text = '' - return text - def get_repository_dependencies_for_changeset_revision( app, repository, repository_metadata, toolshed_base_url, key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None, circular_repository_dependencies=None ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Eliminate the use of trans when exporting repository capsules from the Tool SHed and move the new tag_attribute_haldler.py module where it was meant to be located.
by commits-noreply＠bitbucket.org 23 Jun '14

23 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/344e84a6554a/ Changeset: 344e84a6554a User: greg Date: 2014-06-23 00:25:22 Summary: Eliminate the use of trans when exporting repository capsules from the Tool SHed and move the new tag_attribute_haldler.py module where it was meant to be located. Affected #: 7 files diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -53,7 +53,8 @@ log.debug( error_message ) return None, error_message repository_id = trans.security.encode_id( repository.id ) - return export_util.export_repository( trans, + return export_util.export_repository( trans.app, + trans.user, tool_shed_url, repository_id, str( repository.name ), diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1172,7 +1172,8 @@ file_type = 'gz' export_repository_dependencies = CheckboxField.is_checked( export_repository_dependencies ) tool_shed_url = web.url_for( '/', qualified=True ) - repositories_archive, error_message = export_util.export_repository( trans, + repositories_archive, error_message = export_util.export_repository( trans.app, + trans.user, tool_shed_url, repository_id, str( repository.name ), diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/tool_shed/dependencies/dependency_manager.py --- a/lib/tool_shed/dependencies/dependency_manager.py +++ b/lib/tool_shed/dependencies/dependency_manager.py @@ -5,7 +5,7 @@ from galaxy.util.odict import odict from galaxy.web import url_for -from tool_shed.dependencies import tag_attribute_handler +from tool_shed.dependencies.tool import tag_attribute_handler from tool_shed.repository_types.util import REPOSITORY_DEPENDENCY_DEFINITION_FILENAME from tool_shed.repository_types.util import TOOL_DEPENDENCY_DEFINITION_FILENAME from tool_shed.util import hg_util diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/tool_shed/dependencies/tag_attribute_handler.py --- a/lib/tool_shed/dependencies/tag_attribute_handler.py +++ /dev/null @@ -1,199 +0,0 @@ -import copy -import logging - -log = logging.getLogger( __name__ ) - - -class TagAttributeHandler( object ): - - def __init__( self, app, rdd, unpopulate ): - self.app = app - self.altered = False - self.rdd = rdd - self.unpopulate = unpopulate - - def process_action_tag_set( self, elem, message ): - # Here we're inside of an <actions> tag set. See http://localhost:9009/view/devteam/package_r_2_11_0 . - # <action> - # <repository name="package_readline_6_2" owner="devteam"> - # <package name="readline" version="6.2" /> - # </repository> - # </action> - elem_altered = False - new_elem = copy.deepcopy( elem ) - for sub_index, sub_elem in enumerate( elem ): - altered = False - error_message = '' - if sub_elem.tag == 'repository': - altered, new_sub_elem, error_message = \ - self.process_repository_tag_set( parent_elem=elem, - elem_index=sub_index, - elem=sub_elem, - message=message ) - if error_message: - message += error_message - if altered: - if not self.altered: - self.altered = True - if not elem_altered: - elem_altered = True - new_elem[ sub_index ] = new_sub_elem - return elem_altered, new_elem, message - - def process_actions_tag_set( self, elem, message ): - # <actions> - # <package name="libgtextutils" version="0.6"> - # <repository name="package_libgtextutils_0_6" owner="test" prior_installation_required="True" /> - # </package> - from tool_shed.util import xml_util - elem_altered = False - new_elem = copy.deepcopy( elem ) - for sub_index, sub_elem in enumerate( elem ): - altered = False - error_message = '' - if sub_elem.tag == 'package': - altered, new_sub_elem, error_message = self.process_package_tag_set( elem=sub_elem, - message=message ) - elif sub_elem.tag == 'action': - # <action type="set_environment_for_install"> - # <repository name="package_readline_6_2" owner="devteam""> - # <package name="readline" version="6.2" /> - # </repository> - # </action> - altered, new_sub_elem, error_message = self.process_action_tag_set( elem=sub_elem, - message=message ) - else: - # Inspect the sub elements of elem to locate all <repository> tags and - # populate them with toolshed and changeset_revision attributes if necessary. - altered, new_sub_elem, error_message = self.rdd.handle_sub_elem( parent_elem=elem, - elem_index=sub_index, - elem=sub_elem ) - if error_message: - message += error_message - if altered: - if not self.altered: - self.altered = True - if not elem_altered: - elem_altered = True - new_elem[ sub_index ] = new_sub_elem - return elem_altered, new_elem, message - - def process_actions_group_tag_set( self, elem, message, skip_actions_tags=False ): - # Inspect all entries in the <actions_group> tag set, skipping <actions> - # tag sets that define os and architecture attributes. We want to inspect - # only the last <actions> tag set contained within the <actions_group> tag - # set to see if a complex repository dependency is defined. - elem_altered = False - new_elem = copy.deepcopy( elem ) - for sub_index, sub_elem in enumerate( elem ): - altered = False - error_message = '' - if sub_elem.tag == 'actions': - if skip_actions_tags: - # Skip all actions tags that include os or architecture attributes. - system = sub_elem.get( 'os' ) - architecture = sub_elem.get( 'architecture' ) - if system or architecture: - continue - altered, new_sub_elem, error_message = \ - self.process_actions_tag_set( elem=sub_elem, - message=message ) - if error_message: - message += error_message - if altered: - if not self.altered: - self.altered = True - if not elem_altered: - elem_altered = True - new_elem[ sub_index ] = new_sub_elem - return elem_altered, new_elem, message - - def process_config( self, root ): - error_message = '' - new_root = copy.deepcopy( root ) - if root.tag == 'tool_dependency': - for elem_index, elem in enumerate( root ): - altered = False - if elem.tag == 'package': - # <package name="eigen" version="2.0.17"> - altered, new_elem, error_message = \ - self.process_package_tag_set( elem=elem, - message=error_message ) - if altered: - if not self.altered: - self.altered = True - new_root[ elem_index ] = new_elem - else: - error_message = "Invalid tool_dependencies.xml file." - return self.altered, new_root, error_message - - def process_install_tag_set( self, elem, message ): - # <install version="1.0"> - elem_altered = False - new_elem = copy.deepcopy( elem ) - for sub_index, sub_elem in enumerate( elem ): - altered = False - error_message = '' - if sub_elem.tag == 'actions_group': - altered, new_sub_elem, error_message = \ - self.process_actions_group_tag_set( elem=sub_elem, - message=message, - skip_actions_tags=True ) - elif sub_elem.tag == 'actions': - altered, new_sub_elem, error_message = \ - self.process_actions_tag_set( elem=sub_elem, - message=message ) - else: - package_name = elem.get( 'name', '' ) - package_version = elem.get( 'version', '' ) - error_message += 'Version %s of the %s package cannot be installed because ' % \ - ( str( package_version ), str( package_name ) ) - error_message += 'the recipe for installing the package is missing either an ' - error_message += '<actions> tag set or an <actions_group> tag set.' - if error_message: - message += error_message - if altered: - if not self.altered: - self.altered = True - if not elem_altered: - elem_altered = True - new_elem[ sub_index ] = new_sub_elem - return elem_altered, new_elem, message - - def process_package_tag_set( self, elem, message ): - elem_altered = False - new_elem = copy.deepcopy( elem ) - for sub_index, sub_elem in enumerate( elem ): - altered = False - error_message = '' - if sub_elem.tag == 'install': - altered, new_sub_elem, error_message = \ - self.process_install_tag_set( elem=sub_elem, - message=message ) - elif sub_elem.tag == 'repository': - altered, new_sub_elem, error_message = \ - self.process_repository_tag_set( parent_elem=elem, - elem_index=sub_index, - elem=sub_elem, - message=message ) - if error_message: - message += error_message - if altered: - if not self.altered: - self.altered = True - if not elem_altered: - elem_altered = True - new_elem[ sub_index ] = new_sub_elem - return elem_altered, new_elem, message - - def process_repository_tag_set( self, parent_elem, elem_index, elem, message ): - # We have a complex repository dependency. - altered, new_elem, error_message = self.rdd.handle_complex_dependency_elem( parent_elem=parent_elem, - elem_index=elem_index, - elem=elem ) - if error_message: - message += error_message - if altered: - if not self.altered: - self.altered = True - return altered, new_elem, message diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/tool_shed/dependencies/tool/tag_attribute_handler.py --- /dev/null +++ b/lib/tool_shed/dependencies/tool/tag_attribute_handler.py @@ -0,0 +1,199 @@ +import copy +import logging + +log = logging.getLogger( __name__ ) + + +class TagAttributeHandler( object ): + + def __init__( self, app, rdd, unpopulate ): + self.app = app + self.altered = False + self.rdd = rdd + self.unpopulate = unpopulate + + def process_action_tag_set( self, elem, message ): + # Here we're inside of an <actions> tag set. See http://localhost:9009/view/devteam/package_r_2_11_0 . + # <action> + # <repository name="package_readline_6_2" owner="devteam"> + # <package name="readline" version="6.2" /> + # </repository> + # </action> + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'repository': + altered, new_sub_elem, error_message = \ + self.process_repository_tag_set( parent_elem=elem, + elem_index=sub_index, + elem=sub_elem, + message=message ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_actions_tag_set( self, elem, message ): + # <actions> + # <package name="libgtextutils" version="0.6"> + # <repository name="package_libgtextutils_0_6" owner="test" prior_installation_required="True" /> + # </package> + from tool_shed.util import xml_util + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'package': + altered, new_sub_elem, error_message = self.process_package_tag_set( elem=sub_elem, + message=message ) + elif sub_elem.tag == 'action': + # <action type="set_environment_for_install"> + # <repository name="package_readline_6_2" owner="devteam""> + # <package name="readline" version="6.2" /> + # </repository> + # </action> + altered, new_sub_elem, error_message = self.process_action_tag_set( elem=sub_elem, + message=message ) + else: + # Inspect the sub elements of elem to locate all <repository> tags and + # populate them with toolshed and changeset_revision attributes if necessary. + altered, new_sub_elem, error_message = self.rdd.handle_sub_elem( parent_elem=elem, + elem_index=sub_index, + elem=sub_elem ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_actions_group_tag_set( self, elem, message, skip_actions_tags=False ): + # Inspect all entries in the <actions_group> tag set, skipping <actions> + # tag sets that define os and architecture attributes. We want to inspect + # only the last <actions> tag set contained within the <actions_group> tag + # set to see if a complex repository dependency is defined. + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'actions': + if skip_actions_tags: + # Skip all actions tags that include os or architecture attributes. + system = sub_elem.get( 'os' ) + architecture = sub_elem.get( 'architecture' ) + if system or architecture: + continue + altered, new_sub_elem, error_message = \ + self.process_actions_tag_set( elem=sub_elem, + message=message ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_config( self, root ): + error_message = '' + new_root = copy.deepcopy( root ) + if root.tag == 'tool_dependency': + for elem_index, elem in enumerate( root ): + altered = False + if elem.tag == 'package': + # <package name="eigen" version="2.0.17"> + altered, new_elem, error_message = \ + self.process_package_tag_set( elem=elem, + message=error_message ) + if altered: + if not self.altered: + self.altered = True + new_root[ elem_index ] = new_elem + else: + error_message = "Invalid tool_dependencies.xml file." + return self.altered, new_root, error_message + + def process_install_tag_set( self, elem, message ): + # <install version="1.0"> + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'actions_group': + altered, new_sub_elem, error_message = \ + self.process_actions_group_tag_set( elem=sub_elem, + message=message, + skip_actions_tags=True ) + elif sub_elem.tag == 'actions': + altered, new_sub_elem, error_message = \ + self.process_actions_tag_set( elem=sub_elem, + message=message ) + else: + package_name = elem.get( 'name', '' ) + package_version = elem.get( 'version', '' ) + error_message += 'Version %s of the %s package cannot be installed because ' % \ + ( str( package_version ), str( package_name ) ) + error_message += 'the recipe for installing the package is missing either an ' + error_message += '<actions> tag set or an <actions_group> tag set.' + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_package_tag_set( self, elem, message ): + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'install': + altered, new_sub_elem, error_message = \ + self.process_install_tag_set( elem=sub_elem, + message=message ) + elif sub_elem.tag == 'repository': + altered, new_sub_elem, error_message = \ + self.process_repository_tag_set( parent_elem=elem, + elem_index=sub_index, + elem=sub_elem, + message=message ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_repository_tag_set( self, parent_elem, elem_index, elem, message ): + # We have a complex repository dependency. + altered, new_elem, error_message = self.rdd.handle_complex_dependency_elem( parent_elem=parent_elem, + elem_index=elem_index, + elem=elem ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + return altered, new_elem, message diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ b/lib/tool_shed/util/export_util.py @@ -7,7 +7,6 @@ from time import gmtime from time import strftime import tool_shed.repository_types.util as rt_util -from galaxy import eggs from galaxy import web from galaxy.util.odict import odict from tool_shed.dependencies import dependency_manager @@ -21,11 +20,6 @@ from tool_shed.util import xml_util from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager -eggs.require( 'mercurial' ) - -from mercurial import commands -from mercurial import ui - log = logging.getLogger( __name__ ) CAPSULE_FILENAME = 'capsule' @@ -36,24 +30,9 @@ def __init__( self ): self.exported_repository_elems = [] -def archive_repository_revision( trans, ui, repository, archive_dir, changeset_revision ): - '''Create an un-versioned archive of a repository.''' - repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) - options_dict = hg_util.get_mercurial_default_options_dict( 'archive' ) - options_dict[ 'rev' ] = changeset_revision - error_message = '' - return_code = None - try: - return_code = commands.archive( ui, repo, archive_dir, **options_dict ) - except Exception, e: - error_message = "Error attempting to archive revision <b>%s</b> of repository %s: %s\nReturn code: %s\n" % \ - ( str( changeset_revision ), str( repository.name ), str( e ), str( return_code ) ) - log.exception( error_message ) - return return_code, error_message - -def export_repository( trans, tool_shed_url, repository_id, repository_name, changeset_revision, file_type, +def export_repository( app, user, tool_shed_url, repository_id, repository_name, changeset_revision, file_type, export_repository_dependencies, api=False ): - repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) + repository = suc.get_repository_in_tool_shed( app, repository_id ) repositories_archive_filename = generate_repository_archive_filename( tool_shed_url, str( repository.name ), str( repository.user.username ), @@ -62,16 +41,16 @@ export_repository_dependencies=export_repository_dependencies, use_tmp_archive_dir=True ) if export_repository_dependencies: - repo_info_dicts = get_repo_info_dicts( trans, tool_shed_url, repository_id, changeset_revision ) - repository_ids = get_repository_ids( trans, repo_info_dicts ) + repo_info_dicts = get_repo_info_dicts( app, user, tool_shed_url, repository_id, changeset_revision ) + repository_ids = get_repository_ids( app, repo_info_dicts ) ordered_repository_ids, ordered_repositories, ordered_changeset_revisions = \ - order_components_for_import( trans, repository_id, repository_ids, repo_info_dicts ) + order_components_for_import( app, repository_id, repository_ids, repo_info_dicts ) else: ordered_repository_ids = [] ordered_repositories = [] ordered_changeset_revisions = [] if repository: - repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( trans.app, + repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app, repository, changeset_revision ) if repository_metadata: @@ -89,7 +68,7 @@ work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-export-er" ) ordered_repository = ordered_repositories[ index ] ordered_changeset_revision = ordered_changeset_revisions[ index ] - repository_archive, error_message = generate_repository_archive( trans, + repository_archive, error_message = generate_repository_archive( app, work_dir, tool_shed_url, ordered_repository, @@ -128,12 +107,15 @@ return dict( download_url=download_url, error_messages=error_messages ) return repositories_archive, error_messages -def generate_repository_archive( trans, work_dir, tool_shed_url, repository, changeset_revision, file_type ): - rdah = dependency_manager.RepositoryDependencyAttributeHandler( trans.app, unpopulate=True ) - tdah = dependency_manager.ToolDependencyAttributeHandler( trans.app, unpopulate=True ) +def generate_repository_archive( app, work_dir, tool_shed_url, repository, changeset_revision, file_type ): + rdah = dependency_manager.RepositoryDependencyAttributeHandler( app, unpopulate=True ) + tdah = dependency_manager.ToolDependencyAttributeHandler( app, unpopulate=True ) file_type_str = get_file_type_str( changeset_revision, file_type ) file_name = '%s-%s' % ( repository.name, file_type_str ) - return_code, error_message = archive_repository_revision( trans, ui, repository, work_dir, changeset_revision ) + return_code, error_message = hg_util.archive_repository_revision( app, + repository, + work_dir, + changeset_revision ) if return_code: return None, error_message repository_archive_name = os.path.join( work_dir, file_name ) @@ -195,7 +177,7 @@ sub_elements[ 'exported_via_api' ] = str( api ) return sub_elements -def get_components_from_repo_info_dict( trans, repo_info_dict ): +def get_components_from_repo_info_dict( app, repo_info_dict ): """ Return the repository and the associated latest installable changeset_revision (including updates) for the repository defined by the received repo_info_dict. @@ -204,8 +186,8 @@ # There should only be one entry in the received repo_info_dict. description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tup ) - repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) - repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( trans.app, + repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) + repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app, repository, changeset_revision ) if repository_metadata: @@ -235,30 +217,30 @@ return repo_info_dict return None -def get_repo_info_dicts( trans, tool_shed_url, repository_id, changeset_revision ): +def get_repo_info_dicts( app, user, tool_shed_url, repository_id, changeset_revision ): """ Return a list of dictionaries defining repositories that are required by the repository associated with the received repository_id. """ - rdm = RepositoryDependencyManager( trans.app ) - repository = suc.get_repository_in_tool_shed( trans.app, repository_id ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision ) + rdm = RepositoryDependencyManager( app ) + repository = suc.get_repository_in_tool_shed( app, repository_id ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, repository_id, changeset_revision ) # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=trans.app, + repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=app, repository=repository, repository_metadata=repository_metadata, toolshed_base_url=toolshed_base_url, key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) - repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) + repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = {} # Cast unicode to string. repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), - common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository ), + common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ), str( changeset_revision ), str( ctx.rev() ), str( repository.user.username ), @@ -292,18 +274,24 @@ sub_elements[ 'categories' ] = categories return attributes, sub_elements -def get_repository_ids( trans, repo_info_dicts ): +def get_repository_ids( app, repo_info_dicts ): """Return a list of repository ids associated with each dictionary in the received repo_info_dicts.""" repository_ids = [] for repo_info_dict in repo_info_dicts: for repository_name, repo_info_tup in repo_info_dict.items(): - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tup ) - repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) - repository_ids.append( trans.security.encode_id( repository.id ) ) + description, \ + repository_clone_url, \ + changeset_revision, \ + ctx_rev, \ + repository_owner, \ + repository_dependencies, \ + tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tup ) + repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) + repository_ids.append( app.security.encode_id( repository.id ) ) return repository_ids -def order_components_for_import( trans, primary_repository_id, repository_ids, repo_info_dicts ): +def order_components_for_import( app, primary_repository_id, repository_ids, repo_info_dicts ): """ Some repositories may have repository dependencies that must be imported and have metadata set on them before the dependent repository is imported. This method will inspect the list of repositories @@ -322,7 +310,7 @@ # Create a dictionary whose keys are the received repository_ids and whose values are a list of # repository_ids, each of which is contained in the received list of repository_ids and whose associated # repository must be imported prior to the repository associated with the repository_id key. - prior_import_required_dict = suc.get_prior_import_or_install_required_dict( trans.app, repository_ids, repo_info_dicts ) + prior_import_required_dict = suc.get_prior_import_or_install_required_dict( app, repository_ids, repo_info_dicts ) processed_repository_ids = [] # Process the list of repository dependencies defined for the repository associated with the received # primary_repository_id. @@ -340,20 +328,20 @@ if prior_import_required_id not in ordered_repository_ids: # Import the associated repository dependency first. prior_repo_info_dict = get_repo_info_dict_for_import( prior_import_required_id, repository_ids, repo_info_dicts ) - prior_repository, prior_import_changeset_revision = get_components_from_repo_info_dict( trans, prior_repo_info_dict ) + prior_repository, prior_import_changeset_revision = get_components_from_repo_info_dict( app, prior_repo_info_dict ) if prior_repository and prior_import_changeset_revision: ordered_repository_ids.append( prior_import_required_id ) ordered_repositories.append( prior_repository ) ordered_changeset_revisions.append( prior_import_changeset_revision ) repo_info_dict = get_repo_info_dict_for_import( repository_id, repository_ids, repo_info_dicts ) - repository, changeset_revision = get_components_from_repo_info_dict( trans, repo_info_dict ) + repository, changeset_revision = get_components_from_repo_info_dict( app, repo_info_dict ) if repository and changeset_revision: ordered_repository_ids.append( repository_id ) ordered_repositories.append( repository ) ordered_changeset_revisions.append( changeset_revision ) # Process the repository associated with the received primary_repository_id last. repo_info_dict = get_repo_info_dict_for_import( primary_repository_id, repository_ids, repo_info_dicts ) - repository, changeset_revision = get_components_from_repo_info_dict( trans, repo_info_dict ) + repository, changeset_revision = get_components_from_repo_info_dict( app, repo_info_dict ) if repository and changeset_revision: ordered_repository_ids.append( repository_id ) ordered_repositories.append( repository ) diff -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 -r 344e84a6554ae94604f32e8f62feebd65a6ac358 lib/tool_shed/util/hg_util.py --- a/lib/tool_shed/util/hg_util.py +++ b/lib/tool_shed/util/hg_util.py @@ -28,6 +28,21 @@ def add_changeset( repo_ui, repo, path_to_filename_in_archive ): commands.add( repo_ui, repo, path_to_filename_in_archive ) +def archive_repository_revision( app, repository, archive_dir, changeset_revision ): + '''Create an un-versioned archive of a repository.''' + repo = get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) + options_dict = get_mercurial_default_options_dict( 'archive' ) + options_dict[ 'rev' ] = changeset_revision + error_message = '' + return_code = None + try: + return_code = commands.archive( get_configured_ui, repo, archive_dir, **options_dict ) + except Exception, e: + error_message = "Error attempting to archive revision <b>%s</b> of repository %s: %s\nReturn code: %s\n" % \ + ( str( changeset_revision ), str( repository.name ), str( e ), str( return_code ) ) + log.exception( error_message ) + return return_code, error_message + def bundle_to_json( fh ): """ Convert the received HG10xx data stream (a mercurial 1.0 bundle created using hg push from the Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Move 2 Tool Shed utility functions into the middleware hg class.
by commits-noreply＠bitbucket.org 22 Jun '14

22 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ae53980fad82/ Changeset: ae53980fad82 User: greg Date: 2014-06-22 14:00:57 Summary: Move 2 Tool Shed utility functions into the middleware hg class. Affected #: 3 files diff -r 63919647ca8424a28042ccb79ea2db6e0c68d507 -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 lib/galaxy/webapps/tool_shed/framework/middleware/hg.py --- a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py +++ b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py @@ -11,7 +11,6 @@ from galaxy.util import asbool from galaxy.util.hash_util import new_secure_hash -from tool_shed.util import commit_util from tool_shed.util import hg_util import tool_shed.repository_types.util as rt_util @@ -54,13 +53,15 @@ connection = engine.connect() path_info = environ[ 'PATH_INFO' ].lstrip( '/' ) user_id, repository_name = self.__get_user_id_repository_name_from_path_info( connection, path_info ) - sql_cmd = "SELECT times_downloaded FROM repository WHERE user_id = %d AND name = '%s'" % ( user_id, repository_name.lower() ) + sql_cmd = "SELECT times_downloaded FROM repository WHERE user_id = %d AND name = '%s'" % \ + ( user_id, repository_name.lower() ) result_set = connection.execute( sql_cmd ) for row in result_set: # Should only be 1 row... times_downloaded = row[ 'times_downloaded' ] times_downloaded += 1 - sql_cmd = "UPDATE repository SET times_downloaded = %d WHERE user_id = %d AND name = '%s'" % ( times_downloaded, user_id, repository_name.lower() ) + sql_cmd = "UPDATE repository SET times_downloaded = %d WHERE user_id = %d AND name = '%s'" % \ + ( times_downloaded, user_id, repository_name.lower() ) connection.execute( sql_cmd ) connection.close() elif cmd in [ 'unbundle', 'pushkey' ]: @@ -132,7 +133,7 @@ if filename and isinstance( filename, str ): if filename == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: # Make sure the any complex repository dependency definitions contain valid <repository> tags. - is_valid, error_msg = commit_util.repository_tags_are_valid( filename, change_list ) + is_valid, error_msg = self.repository_tags_are_valid( filename, change_list ) if not is_valid: log.debug( error_msg ) return self.__display_exception_remotely( start_response, error_msg ) @@ -151,7 +152,7 @@ if filename and isinstance( filename, str ): if filename == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: # Make sure the any complex repository dependency definitions contain valid <repository> tags. - is_valid, error_msg = commit_util.repository_tags_are_valid( filename, change_list ) + is_valid, error_msg = self.repository_tags_are_valid( filename, change_list ) if not is_valid: log.debug( error_msg ) return self.__display_exception_remotely( start_response, error_msg ) @@ -174,7 +175,7 @@ rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME ]: # We check both files since tool dependency definitions files can contain complex # repository dependency definitions. - is_valid, error_msg = commit_util.repository_tags_are_valid( filename, change_list ) + is_valid, error_msg = self.repository_tags_are_valid( filename, change_list ) if not is_valid: log.debug( error_msg ) return self.__display_exception_remotely( start_response, error_msg ) @@ -186,6 +187,54 @@ return result.wsgi_application( environ, start_response ) return self.app( environ, start_response ) + def __authenticate( self, username, password ): + db_password = None + # Instantiate a database connection + engine = sqlalchemy.create_engine( self.db_url ) + connection = engine.connect() + result_set = connection.execute( "select email, password from galaxy_user where username = '%s'" % username.lower() ) + for row in result_set: + # Should only be 1 row... + db_email = row[ 'email' ] + db_password = row[ 'password' ] + connection.close() + if db_password: + # Check if password matches db_password when hashed. + return new_secure_hash( text_type=password ) == db_password + return False + + def __authenticate_remote_user( self, environ, username, password ): + """ + Look after a remote user and "authenticate" - upstream server should already have achieved + this for us, but we check that the user exists at least. Hg allow_push = must include username + - some versions of mercurial blow up with 500 errors. + """ + db_username = None + ru_email = environ[ 'HTTP_REMOTE_USER' ].lower() + ## Instantiate a database connection... + engine = sqlalchemy.create_engine( self.db_url ) + connection = engine.connect() + result_set = connection.execute( "select email, username, password from galaxy_user where email = '%s'" % ru_email ) + for row in result_set: + # Should only be 1 row... + db_email = row[ 'email' ] + db_password = row[ 'password' ] + db_username = row[ 'username' ] + connection.close() + if db_username: + # We could check the password here except that the function galaxy.web.framework.get_or_create_remote_user() + # does some random generation of a password - so that no-one knows the password and only the hash is stored... + return db_username == username + return False + + def __basic_authentication( self, environ, username, password ): + """The environ parameter is needed in basic authentication. We also check it if use_remote_user is true.""" + if asbool( self.config.get( 'use_remote_user', False ) ): + assert "HTTP_REMOTE_USER" in environ, "use_remote_user is set but no HTTP_REMOTE_USER variable" + return self.__authenticate_remote_user( environ, username, password ) + else: + return self.__authenticate( username, password ) + def __display_exception_remotely( self, start_response, msg ): # Display the exception to the remote user's command line. status = "500 %s" % msg @@ -213,49 +262,37 @@ user_id = row[ 'id' ] return user_id, repository_name - def __basic_authentication( self, environ, username, password ): - """The environ parameter is needed in basic authentication. We also check it if use_remote_user is true.""" - if asbool( self.config.get( 'use_remote_user', False ) ): - assert "HTTP_REMOTE_USER" in environ, "use_remote_user is set but no HTTP_REMOTE_USER variable" - return self.__authenticate_remote_user( environ, username, password ) - else: - return self.__authenticate( username, password ) - - def __authenticate( self, username, password ): - db_password = None - # Instantiate a database connection - engine = sqlalchemy.create_engine( self.db_url ) - connection = engine.connect() - result_set = connection.execute( "select email, password from galaxy_user where username = '%s'" % username.lower() ) - for row in result_set: - # Should only be 1 row... - db_email = row[ 'email' ] - db_password = row[ 'password' ] - connection.close() - if db_password: - # Check if password matches db_password when hashed. - return new_secure_hash( text_type=password ) == db_password - return False - - def __authenticate_remote_user( self, environ, username, password ): + def repository_tag_is_valid( self, filename, line ): """ - Look after a remote user and "authenticate" - upstream server should already have achieved this for us, but we check that the - user exists at least. Hg allow_push = must include username - some versions of mercurial blow up with 500 errors. + Checks changes made to <repository> tags in a dependency definition file being pushed to the + Tool Shed from the command line to ensure that all required attributes exist. """ - db_username = None - ru_email = environ[ 'HTTP_REMOTE_USER' ].lower() - ## Instantiate a database connection... - engine = sqlalchemy.create_engine( self.db_url ) - connection = engine.connect() - result_set = connection.execute( "select email, username, password from galaxy_user where email = '%s'" % ru_email ) - for row in result_set: - # Should only be 1 row... - db_email = row[ 'email' ] - db_password = row[ 'password' ] - db_username = row[ 'username' ] - connection.close() - if db_username: - # We could check the password here except that the function galaxy.web.framework.get_or_create_remote_user() does some random generation of - # a password - so that no-one knows the password and only the hash is stored... - return db_username == username - return False + required_attributes = [ 'toolshed', 'name', 'owner', 'changeset_revision' ] + defined_attributes = line.split() + for required_attribute in required_attributes: + defined = False + for defined_attribute in defined_attributes: + if defined_attribute.startswith( required_attribute ): + defined = True + break + if not defined: + error_msg = 'The %s file contains a <repository> tag that is missing the required attribute %s. ' % \ + ( filename, required_attribute ) + error_msg += 'Automatically populating dependency definition attributes occurs only when using ' + error_msg += 'the Tool Shed upload utility. ' + return False, error_msg + return True, '' + + def repository_tags_are_valid( self, filename, change_list ): + """ + Make sure the any complex repository dependency definitions contain valid <repository> tags when pushing + changes to the tool shed on the command line. + """ + tag = '<repository' + for change_dict in change_list: + lines = get_change_lines_in_file_for_tag( tag, change_dict ) + for line in lines: + is_valid, error_msg = repository_tag_is_valid( filename, line ) + if not is_valid: + return False, error_msg + return True, '' diff -r 63919647ca8424a28042ccb79ea2db6e0c68d507 -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 lib/tool_shed/dependencies/dependency_manager.py --- a/lib/tool_shed/dependencies/dependency_manager.py +++ b/lib/tool_shed/dependencies/dependency_manager.py @@ -177,6 +177,7 @@ new_root[ index ] = new_elem return root_altered, new_root, error_message + class ToolDependencyAttributeHandler( object ): def __init__( self, app, unpopulate ): diff -r 63919647ca8424a28042ccb79ea2db6e0c68d507 -r ae53980fad820db494c67ddb5ad0ad5f9deb9dd1 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -221,41 +221,6 @@ gzipped_file.close() shutil.move( uncompressed, uploaded_file_name ) -def repository_tag_is_valid( filename, line ): - """ - Checks changes made to <repository> tags in a dependency definition file being pushed to the - Tool Shed from the command line to ensure that all required attributes exist. - """ - required_attributes = [ 'toolshed', 'name', 'owner', 'changeset_revision' ] - defined_attributes = line.split() - for required_attribute in required_attributes: - defined = False - for defined_attribute in defined_attributes: - if defined_attribute.startswith( required_attribute ): - defined = True - break - if not defined: - error_msg = 'The %s file contains a <repository> tag that is missing the required attribute %s. ' % \ - ( filename, required_attribute ) - error_msg += 'Automatically populating dependency definition attributes occurs only when using ' - error_msg += 'the Tool Shed upload utility. ' - return False, error_msg - return True, '' - -def repository_tags_are_valid( filename, change_list ): - """ - Make sure the any complex repository dependency definitions contain valid <repository> tags when pushing - changes to the tool shed on the command line. - """ - tag = '<repository' - for change_dict in change_list: - lines = get_change_lines_in_file_for_tag( tag, change_dict ) - for line in lines: - is_valid, error_msg = repository_tag_is_valid( filename, line ) - if not is_valid: - return False, error_msg - return True, '' - def uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip=False, isbz2=False ): if isgzip: handle_gzip( repository, uploaded_file_name ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add a dependency manager with tag attribute handler classes to manage the process of populating and unpopulating the toolshed and changeset_revision attributes for <repository> tag sets when uploading and importing / exporting repositories from the tool shed.
by commits-noreply＠bitbucket.org 21 Jun '14

21 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/63919647ca84/ Changeset: 63919647ca84 User: greg Date: 2014-06-21 20:15:20 Summary: Add a dependency manager with tag attribute handler classes to manage the process of populating and unpopulating the toolshed and changeset_revision attributes for <repository> tag sets when uploading and importing / exporting repositories from the tool shed. Affected #: 9 files diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -8,13 +8,14 @@ from galaxy import util from galaxy import web from galaxy.datatypes import checkers +from tool_shed.dependencies import dependency_manager import tool_shed.repository_types.util as rt_util -import tool_shed.util.shed_util_common as suc from tool_shed.util import basic_util from tool_shed.util import commit_util from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import repository_dependency_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import xml_util @@ -95,6 +96,8 @@ uploaded_file_filename = os.path.split( file_data.filename )[ -1 ] isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 if uploaded_file or uploaded_directory: + rdah = dependency_manager.RepositoryDependencyAttributeHandler( trans.app, unpopulate=False ) + tdah = dependency_manager.ToolDependencyAttributeHandler( trans.app, unpopulate=False ) ok = True isgzip = False isbz2 = False @@ -124,6 +127,8 @@ if istar: ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ self.upload_tar( trans, + rdah, + tdah, repository, tar, uploaded_file, @@ -134,6 +139,8 @@ elif uploaded_directory: ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ self.upload_directory( trans, + rdah, + tdah, repository, uploaded_directory, upload_point, @@ -164,12 +171,9 @@ full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) ) # Move some version of the uploaded file to the load_point within the repository hierarchy. if uploaded_file_filename in [ rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME ]: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, - # set them appropriately. - altered, root_elem, error_message = \ - commit_util.handle_repository_dependencies_definition( trans.app, - uploaded_file_name, - unpopulate=False ) + # Inspect the contents of the file to see if toolshed or changeset_revision attributes + # are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) if error_message: ok = False message = error_message @@ -179,12 +183,10 @@ shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) - elif uploaded_file_filename in [ rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, - rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME ]: + elif uploaded_file_filename in [ rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME ]: # Inspect the contents of the file to see if changeset_revision values are # missing and if so, set them appropriately. - altered, root_elem, error_message = \ - commit_util.handle_tool_dependencies_definition( trans.app, uploaded_file_name ) + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) if error_message: ok = False message = error_message @@ -333,7 +335,7 @@ message=message, status=status ) - def upload_directory( self, trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, + def upload_directory( self, trans, rdah, tdah, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): repo_dir = repository.repo_path( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) @@ -364,20 +366,18 @@ if ok: uploaded_file_name = os.path.abspath( os.path.join( root, uploaded_file ) ) if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if changeset_revision values are missing and - # if so, set them appropriately. - altered, root_elem, error_message = \ - commit_util.handle_repository_dependencies_definition( trans.app, - uploaded_file_name, - unpopulate=False ) + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) if error_message: return False, error_message, [], '', [], [] elif altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem, error_message = commit_util.handle_tool_dependencies_definition( trans.app, uploaded_file_name ) + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) if error_message: return False, error_message, [], '', [], [] if altered: @@ -406,7 +406,8 @@ undesirable_dirs_removed, undesirable_files_removed ) - def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): + def upload_tar( self, trans, rdah, tdah, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, + commit_message, new_repo_alert ): # Upload a tar archive of files. repo_dir = repository.repo_path( trans.app ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) @@ -442,18 +443,18 @@ for filename in filenames_in_archive: uploaded_file_name = os.path.join( full_path, filename ) if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem, error_message = commit_util.handle_repository_dependencies_definition( trans.app, - uploaded_file_name, - unpopulate=False ) + # Inspect the contents of the file to see if toolshed or changeset_revision attributes + # are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) if error_message: return False, error_message, [], '', [], [] elif altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem, error_message = commit_util.handle_tool_dependencies_definition( trans.app, uploaded_file_name ) + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) if error_message: return False, error_message, [], '', [], [] if altered: diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/tool_shed/dependencies/dependency_manager.py --- /dev/null +++ b/lib/tool_shed/dependencies/dependency_manager.py @@ -0,0 +1,202 @@ +import copy +import logging + +from galaxy.util import asbool +from galaxy.util.odict import odict +from galaxy.web import url_for + +from tool_shed.dependencies import tag_attribute_handler +from tool_shed.repository_types.util import REPOSITORY_DEPENDENCY_DEFINITION_FILENAME +from tool_shed.repository_types.util import TOOL_DEPENDENCY_DEFINITION_FILENAME +from tool_shed.util import hg_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util +log = logging.getLogger( __name__ ) + + +class RepositoryDependencyAttributeHandler( object ): + + def __init__( self, app, unpopulate ): + self.app = app + self.file_name = REPOSITORY_DEPENDENCY_DEFINITION_FILENAME + self.unpopulate = unpopulate + + def check_tag_attributes( self, elem ): + # <repository name="molecule_datatypes" owner="test" /> + error_message = '' + name = elem.get( 'name' ) + if not name: + error_message += 'The tag is missing the required name attribute. ' + owner = elem.get( 'owner' ) + if not owner: + error_message += 'The tag is missing the required owner attribute. ' + log.debug( error_message ) + return error_message + + def handle_complex_dependency_elem( self, parent_elem, elem_index, elem ): + """ + Populate or unpopulate the toolshed and changeset_revision attributes of a + <repository> tag that defines a complex repository dependency. + """ + # <repository name="package_eigen_2_0" owner="test" prior_installation_required="True" /> + altered, new_elem, error_message = self.handle_elem( elem ) + if error_message: + error_message += ' The %s file contains an invalid <repository> tag.' % TOOL_DEPENDENCY_DEFINITION_FILENAME + return altered, new_elem, error_message + + def handle_elem( self, elem ): + """Populate or unpopulate the changeset_revision and toolshed attributes of repository tags.""" + # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> + # <repository changeset_revision="xxx" name="package_xorg_macros_1_17_1" owner="test" toolshed="yyy"> + # <package name="xorg_macros" version="1.17.1" /> + # </repository> + error_message = '' + name = elem.get( 'name' ) + owner = elem.get( 'owner' ) + # The name and owner attributes are always required, so if either are missing, return the error message. + if not name or not owner: + error_message = self.check_tag_attributes( elem ) + return False, elem, error_message + altered = False + toolshed = elem.get( 'toolshed' ) + changeset_revision = elem.get( 'changeset_revision' ) + # Over a short period of time a bug existed which caused the prior_installation_required attribute + # to be set to False and included in the <repository> tag when a repository was exported along with + # its dependencies. The following will eliminate this problematic attribute upon import. + prior_installation_required = elem.get( 'prior_installation_required' ) + if prior_installation_required is not None and not asbool( prior_installation_required ): + del elem.attrib[ 'prior_installation_required' ] + sub_elems = [ child_elem for child_elem in list( elem ) ] + if len( sub_elems ) > 0: + # At this point, a <repository> tag will point only to a package. + # <package name="xorg_macros" version="1.17.1" /> + # Coerce the list to an odict(). + sub_elements = odict() + packages = [] + for sub_elem in sub_elems: + sub_elem_type = sub_elem.tag + sub_elem_name = sub_elem.get( 'name' ) + sub_elem_version = sub_elem.get( 'version' ) + if sub_elem_type and sub_elem_name and sub_elem_version: + packages.append( ( sub_elem_name, sub_elem_version ) ) + sub_elements[ 'packages' ] = packages + else: + # Set to None. + sub_elements = None + if self.unpopulate: + # We're exporting the repository, so eliminate all toolshed and changeset_revision attributes + # from the <repository> tag. + if toolshed or changeset_revision: + attributes = odict() + attributes[ 'name' ] = name + attributes[ 'owner' ] = owner + prior_installation_required = elem.get( 'prior_installation_required' ) + if asbool( prior_installation_required ): + attributes[ 'prior_installation_required' ] = 'True' + new_elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) + altered = True + return altered, new_elem, error_message + # From here on we're populating the toolshed and changeset_revision attributes if necessary. + if not toolshed: + # Default the setting to the current tool shed. + toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) + elem.attrib[ 'toolshed' ] = toolshed + altered = True + if not changeset_revision: + # Populate the changeset_revision attribute with the latest installable metadata revision for + # the defined repository. We use the latest installable revision instead of the latest metadata + # revision to ensure that the contents of the revision are valid. + repository = suc.get_repository_by_name_and_owner( self.app, name, owner ) + if repository: + repo = hg_util.get_repo_for_repository( self.app, + repository=repository, + repo_path=None, + create=False ) + lastest_installable_changeset_revision = \ + suc.get_latest_downloadable_changeset_revision( self.app, repository, repo ) + if lastest_installable_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH: + elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision + altered = True + else: + error_message = 'Invalid latest installable changeset_revision %s ' % \ + str( lastest_installable_changeset_revision ) + error_message += 'retrieved for repository %s owned by %s. ' % ( str( name ), str( owner ) ) + else: + error_message = 'Unable to locate repository with name %s and owner %s. ' % ( str( name ), str( owner ) ) + return altered, elem, error_message + + def handle_sub_elem( self, parent_elem, elem_index, elem ): + """ + Populate or unpopulate the toolshed and changeset_revision attributes for each of + the following tag sets. + <action type="set_environment_for_install"> + <action type="setup_r_environment"> + <action type="setup_ruby_environment"> + """ + sub_elem_altered = False + error_message = '' + for sub_index, sub_elem in enumerate( elem ): + # Make sure to skip comments and tags that are not <repository>. + if sub_elem.tag == 'repository': + altered, new_sub_elem, message = self.handle_elem( sub_elem ) + if message: + error_message += 'The %s file contains an invalid <repository> tag. %s' % \ + ( TOOL_DEPENDENCY_DEFINITION_FILENAME, message ) + if altered: + if not sub_elem_altered: + sub_elem_altered = True + elem[ sub_index ] = new_sub_elem + if sub_elem_altered: + parent_elem[ elem_index ] = elem + return sub_elem_altered, parent_elem, error_message + + def handle_tag_attributes( self, config ): + """ + Populate or unpopulate the toolshed and changeset_revision attributes of a + <repository> tag. Populating will occur when a dependency definition file + is being uploaded to the repository, while unpopulating will occur when the + repository is being exported. + """ + # Make sure we're looking at a valid repository_dependencies.xml file. + tree, error_message = xml_util.parse_xml( config ) + if tree is None: + return False, None, error_message + root = tree.getroot() + root_altered = False + new_root = copy.deepcopy( root ) + for index, elem in enumerate( root ): + if elem.tag == 'repository': + # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> + altered, new_elem, error_message = self.handle_elem( elem ) + if error_message: + error_message = 'The %s file contains an invalid <repository> tag. %s' % ( self.file_name, error_message ) + return False, None, error_message + if altered: + if not root_altered: + root_altered = True + new_root[ index ] = new_elem + return root_altered, new_root, error_message + +class ToolDependencyAttributeHandler( object ): + + def __init__( self, app, unpopulate ): + self.app = app + self.file_name = TOOL_DEPENDENCY_DEFINITION_FILENAME + self.unpopulate = unpopulate + + def handle_tag_attributes( self, tool_dependencies_config ): + """ + Populate or unpopulate the tooshed and changeset_revision attributes of each <repository> + tag defined within a tool_dependencies.xml file. + """ + rdah = RepositoryDependencyAttributeHandler( self.app, self.unpopulate ) + tah = tag_attribute_handler.TagAttributeHandler( self.app, rdah, self.unpopulate ) + altered = False + error_message = '' + # Make sure we're looking at a valid tool_dependencies.xml file. + tree, error_message = xml_util.parse_xml( tool_dependencies_config ) + if tree is None: + return False, None, error_message + root = tree.getroot() + altered, new_root, error_message = tah.process_config( root ) + return altered, new_root, error_message diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/tool_shed/dependencies/tag_attribute_handler.py --- /dev/null +++ b/lib/tool_shed/dependencies/tag_attribute_handler.py @@ -0,0 +1,199 @@ +import copy +import logging + +log = logging.getLogger( __name__ ) + + +class TagAttributeHandler( object ): + + def __init__( self, app, rdd, unpopulate ): + self.app = app + self.altered = False + self.rdd = rdd + self.unpopulate = unpopulate + + def process_action_tag_set( self, elem, message ): + # Here we're inside of an <actions> tag set. See http://localhost:9009/view/devteam/package_r_2_11_0 . + # <action> + # <repository name="package_readline_6_2" owner="devteam"> + # <package name="readline" version="6.2" /> + # </repository> + # </action> + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'repository': + altered, new_sub_elem, error_message = \ + self.process_repository_tag_set( parent_elem=elem, + elem_index=sub_index, + elem=sub_elem, + message=message ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_actions_tag_set( self, elem, message ): + # <actions> + # <package name="libgtextutils" version="0.6"> + # <repository name="package_libgtextutils_0_6" owner="test" prior_installation_required="True" /> + # </package> + from tool_shed.util import xml_util + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'package': + altered, new_sub_elem, error_message = self.process_package_tag_set( elem=sub_elem, + message=message ) + elif sub_elem.tag == 'action': + # <action type="set_environment_for_install"> + # <repository name="package_readline_6_2" owner="devteam""> + # <package name="readline" version="6.2" /> + # </repository> + # </action> + altered, new_sub_elem, error_message = self.process_action_tag_set( elem=sub_elem, + message=message ) + else: + # Inspect the sub elements of elem to locate all <repository> tags and + # populate them with toolshed and changeset_revision attributes if necessary. + altered, new_sub_elem, error_message = self.rdd.handle_sub_elem( parent_elem=elem, + elem_index=sub_index, + elem=sub_elem ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_actions_group_tag_set( self, elem, message, skip_actions_tags=False ): + # Inspect all entries in the <actions_group> tag set, skipping <actions> + # tag sets that define os and architecture attributes. We want to inspect + # only the last <actions> tag set contained within the <actions_group> tag + # set to see if a complex repository dependency is defined. + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'actions': + if skip_actions_tags: + # Skip all actions tags that include os or architecture attributes. + system = sub_elem.get( 'os' ) + architecture = sub_elem.get( 'architecture' ) + if system or architecture: + continue + altered, new_sub_elem, error_message = \ + self.process_actions_tag_set( elem=sub_elem, + message=message ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_config( self, root ): + error_message = '' + new_root = copy.deepcopy( root ) + if root.tag == 'tool_dependency': + for elem_index, elem in enumerate( root ): + altered = False + if elem.tag == 'package': + # <package name="eigen" version="2.0.17"> + altered, new_elem, error_message = \ + self.process_package_tag_set( elem=elem, + message=error_message ) + if altered: + if not self.altered: + self.altered = True + new_root[ elem_index ] = new_elem + else: + error_message = "Invalid tool_dependencies.xml file." + return self.altered, new_root, error_message + + def process_install_tag_set( self, elem, message ): + # <install version="1.0"> + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'actions_group': + altered, new_sub_elem, error_message = \ + self.process_actions_group_tag_set( elem=sub_elem, + message=message, + skip_actions_tags=True ) + elif sub_elem.tag == 'actions': + altered, new_sub_elem, error_message = \ + self.process_actions_tag_set( elem=sub_elem, + message=message ) + else: + package_name = elem.get( 'name', '' ) + package_version = elem.get( 'version', '' ) + error_message += 'Version %s of the %s package cannot be installed because ' % \ + ( str( package_version ), str( package_name ) ) + error_message += 'the recipe for installing the package is missing either an ' + error_message += '<actions> tag set or an <actions_group> tag set.' + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_package_tag_set( self, elem, message ): + elem_altered = False + new_elem = copy.deepcopy( elem ) + for sub_index, sub_elem in enumerate( elem ): + altered = False + error_message = '' + if sub_elem.tag == 'install': + altered, new_sub_elem, error_message = \ + self.process_install_tag_set( elem=sub_elem, + message=message ) + elif sub_elem.tag == 'repository': + altered, new_sub_elem, error_message = \ + self.process_repository_tag_set( parent_elem=elem, + elem_index=sub_index, + elem=sub_elem, + message=message ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + if not elem_altered: + elem_altered = True + new_elem[ sub_index ] = new_sub_elem + return elem_altered, new_elem, message + + def process_repository_tag_set( self, parent_elem, elem_index, elem, message ): + # We have a complex repository dependency. + altered, new_elem, error_message = self.rdd.handle_complex_dependency_elem( parent_elem=parent_elem, + elem_index=elem_index, + elem=elem ) + if error_message: + message += error_message + if altered: + if not self.altered: + self.altered = True + return altered, new_elem, message diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py @@ -20,7 +20,7 @@ class RecipeTag( object ): """Abstract class that defines a standard format for handling recipe tags when installing packages.""" - def process_tag_set( tool_shed_repository, tool_dependency, package_elem, package_name, package_version, + def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version, from_tool_migration_manager=False, tool_dependency_db_records=None ): raise "Unimplemented Method" diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -5,14 +5,10 @@ import shutil import tempfile from galaxy.datatypes import checkers -from galaxy.util import asbool -from galaxy.util.odict import odict -from galaxy.web import url_for -import tool_shed.util.shed_util_common as suc from tool_shed.util import basic_util from tool_shed.util import hg_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util -from tool_shed.util import xml_util import tool_shed.repository_types.util as rt_util log = logging.getLogger( __name__ ) @@ -48,8 +44,8 @@ def check_file_contents_for_email_alerts( app ): """ - See if any admin users have chosen to receive email alerts when a repository is updated. If so, the file contents of the update must be - checked for inappropriate content. + See if any admin users have chosen to receive email alerts when a repository is updated. + If so, the file contents of the update must be checked for inappropriate content. """ sa_session = app.model.context.current admin_users = app.config.get( "admin_users", "" ).split( "," ) @@ -71,8 +67,9 @@ def get_change_lines_in_file_for_tag( tag, change_dict ): """ - The received change_dict is the jsonified version of the changes to a file in a changeset being pushed to the tool shed from the command line. - This method cleans and returns appropriate lines for inspection. + The received change_dict is the jsonified version of the changes to a file in a + changeset being pushed to the Tool Shed from the command line. This method cleans + and returns appropriate lines for inspection. """ cleaned_lines = [] data_list = change_dict.get( 'data', [] ) @@ -108,7 +105,9 @@ return upload_point def handle_bz2( repository, uploaded_file_name ): - fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_bunzip2_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) + fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_bunzip2_' % repository.id, + dir=os.path.dirname( uploaded_file_name ), + text=False ) bzipped_file = bz2.BZ2File( uploaded_file_name, 'rb' ) while 1: try: @@ -125,22 +124,6 @@ bzipped_file.close() shutil.move( uncompressed, uploaded_file_name ) -def handle_complex_repository_dependency_elem( app, elem, sub_elem_index, sub_elem, sub_elem_altered, altered, unpopulate=False ): - """ - Populate or unpopulate the toolshed and changeset_revision attributes of a <repository> tag that defines - a complex repository dependency. - """ - # <repository name="package_eigen_2_0" owner="test" prior_installation_required="True" /> - revised, repository_elem, error_message = handle_repository_dependency_elem( app, sub_elem, unpopulate=unpopulate ) - if error_message: - error_message = 'The tool_dependencies.xml file contains an invalid <repository> tag. %s' % error_message - if revised: - elem[ sub_elem_index ] = repository_elem - sub_elem_altered = True - if not altered: - altered = True - return altered, sub_elem_altered, elem, error_message - def handle_directory_changes( app, host, username, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed ): repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) @@ -218,20 +201,10 @@ admin_only=admin_only ) return True, '', files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed -def handle_missing_repository_attribute( elem ): - # <repository name="molecule_datatypes" owner="test" /> - error_message = '' - name = elem.get( 'name' ) - if not name: - error_message += 'The tag is missing the required name attribute. ' - owner = elem.get( 'owner' ) - if not owner: - error_message += 'The tag is missing the required owner attribute. ' - log.debug( error_message ) - return error_message - def handle_gzip( repository, uploaded_file_name ): - fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_gunzip_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) + fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_gunzip_' % repository.id, + dir=os.path.dirname( uploaded_file_name ), + text=False ) gzipped_file = gzip.GzipFile( uploaded_file_name, 'rb' ) while 1: try: @@ -248,249 +221,6 @@ gzipped_file.close() shutil.move( uncompressed, uploaded_file_name ) -def handle_repository_dependencies_definition( app, repository_dependencies_config, unpopulate=False ): - """ - Populate or unpopulate the toolshed and changeset_revision attributes of a <repository> tag. Populating will occur when a - dependency definition file is being uploaded to the repository, while depopulating will occur when the repository is being - exported. - """ - altered = False - # Make sure we're looking at a valid repository_dependencies.xml file. - tree, error_message = xml_util.parse_xml( repository_dependencies_config ) - if tree is None: - return False, None, error_message - root = tree.getroot() - if root.tag == 'repositories': - for index, elem in enumerate( root ): - if elem.tag == 'repository': - # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> - revised, elem, error_message = handle_repository_dependency_elem( app, elem, unpopulate=unpopulate ) - if error_message: - error_message = 'The repository_dependencies.xml file contains an invalid <repository> tag. %s' % error_message - return False, None, error_message - if revised: - root[ index ] = elem - if not altered: - altered = True - return altered, root, error_message - return False, None, error_message - -def handle_repository_dependency_elem( app, elem, unpopulate=False ): - """Populate or unpopulate repository tags.""" - # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> - # <repository changeset_revision="xxx" name="package_xorg_macros_1_17_1" owner="test" toolshed="yyy"> - # <package name="xorg_macros" version="1.17.1" /> - # </repository> - error_message = '' - name = elem.get( 'name' ) - owner = elem.get( 'owner' ) - # The name and owner attributes are always required, so if either are missing, return the error message. - if not name or not owner: - error_message = handle_missing_repository_attribute( elem ) - return False, elem, error_message - revised = False - toolshed = elem.get( 'toolshed' ) - changeset_revision = elem.get( 'changeset_revision' ) - # Over a short period of time a bug existed which caused the prior_installation_required attribute - # to be set to False and included in the <repository> tag when a repository was exported along with - # its dependencies. The following will eliminate this problematic attribute upon import. - prior_installation_required = elem.get( 'prior_installation_required' ) - if prior_installation_required is not None and not asbool( prior_installation_required ): - del elem.attrib[ 'prior_installation_required' ] - sub_elems = [ child_elem for child_elem in list( elem ) ] - if len( sub_elems ) > 0: - # At this point, a <repository> tag will point only to a package. - # <package name="xorg_macros" version="1.17.1" /> - # Coerce the list to an odict(). - sub_elements = odict() - packages = [] - for sub_elem in sub_elems: - sub_elem_type = sub_elem.tag - sub_elem_name = sub_elem.get( 'name' ) - sub_elem_version = sub_elem.get( 'version' ) - if sub_elem_type and sub_elem_name and sub_elem_version: - packages.append( ( sub_elem_name, sub_elem_version ) ) - sub_elements[ 'packages' ] = packages - else: - # Set to None. - sub_elements = None - if unpopulate: - # We're exporting the repository, so eliminate all toolshed and changeset_revision attributes from the - # <repository> tag. - if toolshed or changeset_revision: - attributes = odict() - attributes[ 'name' ] = name - attributes[ 'owner' ] = owner - prior_installation_required = elem.get( 'prior_installation_required' ) - if asbool( prior_installation_required ): - attributes[ 'prior_installation_required' ] = 'True' - elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) - revised = True - return revised, elem, error_message - # From here on we're populating the toolshed and changeset_revisions if necessary. - if not toolshed: - # Default the setting to the current tool shed. - toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) - elem.attrib[ 'toolshed' ] = toolshed - revised = True - if not changeset_revision: - # Populate the changeset_revision attribute with the latest installable metadata revision for the defined repository. - # We use the latest installable revision instead of the latest metadata revision to ensure that the contents of the - # revision are valid. - repository = suc.get_repository_by_name_and_owner( app, name, owner ) - if repository: - repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) - lastest_installable_changeset_revision = suc.get_latest_downloadable_changeset_revision( app, repository, repo ) - if lastest_installable_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH: - elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision - revised = True - else: - error_message = 'Invalid latest installable changeset_revision %s ' % str( lastest_installable_changeset_revision ) - error_message += 'retrieved for repository %s owned by %s. ' % ( str( name ), str( owner ) ) - else: - error_message = 'Unable to locate repository with name %s and owner %s. ' % ( str( name ), str( owner ) ) - return revised, elem, error_message - -def handle_repository_dependency_sub_elem( app, package_altered, altered, actions_elem, action_index, action_elem, unpopulate=False ): - """ - Populate or unpopulate the toolshed and changeset_revision attributes for each of the following tag sets. - <action type="set_environment_for_install"> - <action type="setup_r_environment"> - <action type="setup_ruby_environment"> - """ - error_message = '' - for repo_index, repo_elem in enumerate( action_elem ): - # Make sure to skip comments and tags that are not <repository>. - if repo_elem.tag == 'repository': - revised, repository_elem, message = handle_repository_dependency_elem( app, repo_elem, unpopulate=unpopulate ) - if message: - error_message += 'The tool_dependencies.xml file contains an invalid <repository> tag. %s' % message - if revised: - action_elem[ repo_index ] = repository_elem - package_altered = True - if not altered: - altered = True - if package_altered: - actions_elem[ action_index ] = action_elem - return package_altered, altered, actions_elem, error_message - -def handle_tool_dependencies_definition( app, tool_dependencies_config, unpopulate=False ): - """ - Populate or unpopulate the tooshed and changeset_revision attributes of each <repository> - tag defined within a tool_dependencies.xml file. - """ - altered = False - error_message = '' - # Make sure we're looking at a valid tool_dependencies.xml file. - tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - if tree is None: - return False, None, error_message - root = tree.getroot() - if root.tag == 'tool_dependency': - package_altered = False - for root_index, root_elem in enumerate( root ): - # <package name="eigen" version="2.0.17"> - package_altered = False - if root_elem.tag == 'package': - for package_index, package_elem in enumerate( root_elem ): - if package_elem.tag == 'repository': - # We have a complex repository dependency. - altered, package_altered, root_elem, message = \ - handle_complex_repository_dependency_elem( app, - root_elem, - package_index, - package_elem, - package_altered, - altered, - unpopulate=unpopulate ) - if message: - error_message += message - if package_altered: - root[ root_index ] = root_elem - elif package_elem.tag == 'install': - # <install version="1.0"> - for actions_index, actions_elem in enumerate( package_elem ): - if actions_elem.tag == 'actions_group': - # Inspect all entries in the <actions_group> tag set, skipping <actions> - # tag sets that define os and architecture attributes. We want to inspect - # only the last <actions> tag set contained within the <actions_group> tag - # set to see if a complex repository dependency is defined. - for actions_group_index, actions_group_elem in enumerate( actions_elem ): - if actions_group_elem.tag == 'actions': - # Skip all actions tags that include os or architecture attributes. - system = actions_group_elem.get( 'os' ) - architecture = actions_group_elem.get( 'architecture' ) - if system or architecture: - continue - # ... - # <actions> - # <package name="libgtextutils" version="0.6"> - # <repository name="package_libgtextutils_0_6" owner="test" prior_installation_required="True" /> - # </package> - # ... - for last_actions_index, last_actions_elem in enumerate( actions_group_elem ): - last_actions_package_altered = False - if last_actions_elem.tag == 'package': - last_actions_elem_package_elem_altered = False - for last_actions_elem_package_index, last_actions_elem_package_elem in enumerate( last_actions_elem ): - if last_actions_elem_package_elem.tag == 'repository': - # We have a complex repository dependency. - last_actions_package_altered, last_actions_elem_package_elem_altered, last_actions_elem, message = \ - handle_complex_repository_dependency_elem( app, - last_actions_elem, - last_actions_elem_package_index, - last_actions_elem_package_elem, - last_actions_elem_package_elem_altered, - last_actions_package_altered, - unpopulate=unpopulate ) - if not altered and last_actions_package_altered: - altered = True - if message: - error_message += message - if last_actions_elem_package_elem_altered: - actions_group_elem[ last_actions_index ] = last_actions_elem - else: - # Inspect the sub elements of last_actions_elem to locate all <repository> tags and - # populate them with toolshed and changeset_revision attributes if necessary. - last_actions_package_altered, altered, last_actions_elem, message = \ - handle_repository_dependency_sub_elem( app, - last_actions_package_altered, - altered, - actions_group_elem, - last_actions_index, - last_actions_elem, - unpopulate=unpopulate ) - if message: - error_message += message - elif actions_elem.tag == 'actions': - # We are not in an <actions_group> tag set, so we must be in an <actions> tag set. - for action_index, action_elem in enumerate( actions_elem ): - # Inspect the sub elements of last_actions_elem to locate all <repository> tags - # and populate them with toolshed and changeset_revision attributes if necessary. - package_altered, altered, actions_elem, message = \ - handle_repository_dependency_sub_elem( app, - package_altered, - altered, - actions_elem, - action_index, - action_elem, - unpopulate=unpopulate ) - if message: - error_message += message - else: - package_name = root_elem.get( 'name', '' ) - package_version = root_elem.get( 'version', '' ) - error_message += 'Version %s of the %s package cannot be installed because ' % \ - ( str( package_version ), str( package_name ) ) - error_message += 'the recipe for installing the package is missing either an ' - error_message += '<actions> tag set or an <actions_group> tag set.' - if package_altered: - package_elem[ actions_index ] = actions_elem - if package_altered: - root[ root_index ] = root_elem - return altered, root, error_message - return False, None, error_message - def repository_tag_is_valid( filename, line ): """ Checks changes made to <repository> tags in a dependency definition file being pushed to the diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ b/lib/tool_shed/util/export_util.py @@ -6,19 +6,19 @@ import threading from time import gmtime from time import strftime -import tool_shed.util.shed_util_common as suc import tool_shed.repository_types.util as rt_util from galaxy import eggs from galaxy import web from galaxy.util.odict import odict +from tool_shed.dependencies import dependency_manager from tool_shed.util import basic_util from tool_shed.util import commit_util from tool_shed.util import common_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import repository_dependency_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import xml_util - from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager eggs.require( 'mercurial' ) @@ -129,6 +129,8 @@ return repositories_archive, error_messages def generate_repository_archive( trans, work_dir, tool_shed_url, repository, changeset_revision, file_type ): + rdah = dependency_manager.RepositoryDependencyAttributeHandler( trans.app, unpopulate=True ) + tdah = dependency_manager.ToolDependencyAttributeHandler( trans.app, unpopulate=True ) file_type_str = get_file_type_str( changeset_revision, file_type ) file_name = '%s-%s' % ( repository.name, file_type_str ) return_code, error_message = archive_repository_revision( trans, ui, repository, work_dir, changeset_revision ) @@ -151,8 +153,7 @@ # See if we have a repository dependencies defined. if name == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. - altered, root_elem, error_message = \ - commit_util.handle_repository_dependencies_definition( trans.app, full_path, unpopulate=True ) + altered, root_elem, error_message = rdah.handle_tag_attributes( full_path ) if error_message: return None, error_message if altered: @@ -160,8 +161,7 @@ shutil.move( tmp_filename, full_path ) elif name == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. - altered, root_elem, error_message = \ - commit_util.handle_tool_dependencies_definition( trans.app, full_path, unpopulate=True ) + altered, root_elem, error_message = tdah.handle_tag_attributes( full_path ) if error_message: return None, error_message if altered: diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 lib/tool_shed/util/import_util.py --- a/lib/tool_shed/util/import_util.py +++ b/lib/tool_shed/util/import_util.py @@ -5,13 +5,14 @@ import tempfile import urllib from galaxy import util +from tool_shed.dependencies import dependency_manager from tool_shed.util import commit_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import repository_maintenance_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import xml_util -import tool_shed.util.shed_util_common as suc import tool_shed.repository_types.util as rt_util log = logging.getLogger( __name__ ) @@ -267,6 +268,8 @@ def import_repository_archive( app, host, user, repository, repository_archive_dict ): """Import a repository archive contained within a repository capsule.""" + rdah = dependency_manager.RepositoryDependencyAttributeHandler( app, unpopulate=False ) + tdah = dependency_manager.ToolDependencyAttributeHandler( app, unpopulate=False ) archive_file_name = repository_archive_dict.get( 'archive_file_name', None ) capsule_file_name = repository_archive_dict[ 'capsule_file_name' ] encoded_file_path = repository_archive_dict[ 'encoded_file_path' ] @@ -303,9 +306,9 @@ for filename in filenames_in_archive: uploaded_file_name = os.path.join( full_path, filename ) if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem, error_message = \ - commit_util.handle_repository_dependencies_definition( app, uploaded_file_name, unpopulate=False ) + # Inspect the contents of the file to see if toolshed or changeset_revision attributes + # are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) if error_message: results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message @@ -313,8 +316,9 @@ tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem, error_message = commit_util.handle_tool_dependencies_definition( app, uploaded_file_name ) + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) if error_message: results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message diff -r e832e466471403d54d788193c938f3c4d139142c -r 63919647ca8424a28042ccb79ea2db6e0c68d507 test/tool_shed/functional/test_0470_tool_dependency_repository_type.py --- a/test/tool_shed/functional/test_0470_tool_dependency_repository_type.py +++ b/test/tool_shed/functional/test_0470_tool_dependency_repository_type.py @@ -169,7 +169,9 @@ commit_message='Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.', strings_displayed=[], strings_not_displayed=[] ) - assert len( package_x11_repository.metadata_revisions ) == 1, 'package_x11_client_1_5_proto_7_0_0470 has incorrect number of metadata revisions' + assert len( package_x11_repository.metadata_revisions ) == 1, \ + 'package_x11_client_1_5_proto_7_0_0470 has incorrect number of metadata revisions, expected 1 but found %d' % \ + len( package_x11_repository.metadata_revisions ) def test_0025_upload_updated_tool_dependency_to_package_emboss( self ): '''Upload a new tool_dependencies.xml to package_emboss_5_0_0_0470.''' @@ -189,7 +191,9 @@ commit_message='Populate package_emboss_5_0_0_0470 with tool dependency definitions.', strings_displayed=[], strings_not_displayed=[] ) - assert len( package_emboss_repository.metadata_revisions ) == 2, 'package_emboss_5_0_0_0470 has incorrect number of metadata revisions' + assert len( package_emboss_repository.metadata_revisions ) == 2, \ + 'package_emboss_5_0_0_0470 has incorrect number of metadata revisions, expected 2 but found %d' % \ + len( package_emboss_repository.metadata_revisions ) def test_0030_upload_updated_tool_dependency_to_emboss_5_repository( self ): '''Upload a new tool_dependencies.xml to emboss_5_0470.''' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Fix for interpreter on version commands (when different from command interpreter).
by commits-noreply＠bitbucket.org 20 Jun '14

20 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e832e4664714/ Changeset: e832e4664714 User: jmchilton Date: 2014-06-20 23:00:38 Summary: Fix for interpreter on version commands (when different from command interpreter). Thanks to Will Holtz for tracking down the problem and Peter Cock for submitting the patch. Affected #: 1 file diff -r c972ce1e3e8840309dceaa40ac6858c3156fdff3 -r e832e466471403d54d788193c938f3c4d139142c lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1264,7 +1264,7 @@ executable = self.version_string_cmd.split()[0] abs_executable = os.path.abspath(os.path.join(self.tool_dir, executable)) command_line = self.version_string_cmd.replace(executable, abs_executable, 1) - self.version_string_cmd = self.interpreter + " " + command_line + self.version_string_cmd = version_cmd_interpreter + " " + command_line # Parallelism for tasks, read from tool config. parallelism = root.find("parallelism") if parallelism is not None and parallelism.get("method"): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Charts: Fix last change
by commits-noreply＠bitbucket.org 20 Jun '14

20 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c972ce1e3e88/ Changeset: c972ce1e3e88 User: guerler Date: 2014-06-20 09:37:10 Summary: Charts: Fix last change Affected #: 1 file diff -r bace76c0aa9b41aa32b793506794cb69e38cf44e -r c972ce1e3e8840309dceaa40ac6858c3156fdff3 config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js @@ -207,11 +207,11 @@ // add tooltip events boxes.selectAll('rect') .on('dblclick', function(d) { - d3.event.stopPropagation(); - var xLabel = self.categories.array.x[d.x]; - var yLabel = self.categories.array.y[d.y]; var url = self.chart.settings.get('url_template').trim(); if (url) { + d3.event.stopPropagation(); + var xLabel = self.categories.array.x[d.x]; + var yLabel = self.categories.array.y[d.y]; window.open(url.replace('__LABEL__', xLabel)); window.open(url.replace('__LABEL__', yLabel)); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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