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m.default.TracksterView(h.extend(t,{header:!1})),this.view.editor=!0,e.when(this.view.load_chroms_deferred).then(function(e){var t=null;if(i){var r=i.chrom,l=i.start,d=i.end;t=i.overview,r&&void 0!==l&&d?o.view.change_chrom(r,l,d):o.view.change_chrom(e[0].chrom)}else o.view.change_chrom(e[0].chrom);if(n)for(var c=0;c"),e("#right-border").click(function(){t.ui.view.resize_window()}),window.force_right_panel("hide"),window.galaxy_config.app.id?this.view_existing():x.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()}},{key:"choose_existing_or_new",value:function(){var e=this,t=x.default.get("dbkey"),i={},n={dbkey:t,dataset_id:x.default.get("dataset_id"),hda_ldda:x.default.get("hda_ldda"),gene_region:x.default.get("gene_region")};t&&(i["f-dbkey"]=t),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"r)return e(this).insertAfter(s),f.remove_drawable(h),void f.container.add_drawable(h)}for(s=null,l=0;l=o&&i.offsetY<=r)return i.offsetY-o0?l-1:l))}).bind("dragstart",function(){e(this).addClass("dragging")}).bind("dragend",function(){e(this).removeClass("dragging")})}function r(e,t){t||(t=0);var i=Math.pow(10,t);return Math.round(e*i)/i}function l(t){var i=e.Deferred();return e.ajax({type:"HEAD",url:t,beforeSend:function(e){e.setRequestHeader("Range","bytes=0-10")},success:function(e,t,n){i.resolve(206===n.status)}}),i}Object.defineProperty(t,"__esModule",{value:!0});var d=i(3),c=a(d),u=i(1),h=n(u),f=i(2),p=n(f),_=i(15),m=a(_),g=i(81),v=a(g),w=i(18),y=a(w),b=i(82),x=a(b),k=i(83),C=a(k),S=i(84),T=a(S),M=i(14),$=a(M),P=i(54),O=a(P),E=i(33),A=a(E),D=i(137),z=a(D);i(19);var I=h.extend,j={},L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G=["Histogram","Line","Filled","Intensity"],R=function e(t,i,n){if(e.id_counter||(e.id_counter=0),this.id=e.id_counter++,this.view=t,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=A.default.ConfigSettingCollection.from_models_and_saved_values(this.build_config_params(),n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new v.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var s=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){s.show()},function(){s.hide()})}};R.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(e){e.config.get_value("content_visible")?(e.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),e.hide_contents(),e.config.set_value("content_visible",!1)):(e.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),e.config.set_value("content_visible",!0),e.show_contents())}},{name:"settings_icon",title:(0,c.default)("Edit settings"),css_class:"gear",on_click_fn:function(e){new A.default.ConfigSettingCollectionView({collection:e.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:(0,c.default)("Remove"),css_class:"remove-icon",on_click_fn:function(t){e(".tooltip").remove(),t.remove()}}],I(R.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],build_config_params:function(){return this.config_params},config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(e){},to_dict:function(){},set_name:function(e){this.old_name=this.config.get_value("name"),this.config.set_value("name",e)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var t=this.view;this.container_div.hide(0,function(){e(this).remove(),t.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var N=function(e,t,i){R.call(this,e,t,i),this.obj_type=i.obj_type,this.drawables=[]};I(N.prototype,R.prototype,{unpack_drawables:function(e){this.drawables=[];for(var t,i=0;i").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),s(this.container_div,this),s(this.content_div,this),o(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new T.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(e("")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new T.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};I(V.prototype,R.prototype,N.prototype,{action_icons_def:[R.prototype.action_icons_def[0],R.prototype.action_icons_def[1],{name:"composite_icon",title:(0,c.default)("Show composite track"),css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_composite_track()}},{name:"filters_icon",title:(0,c.default)("Filters"),css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?(e.filters_manager.clear_filters(),e._restore_filter_managers()):(e.setup_multitrack_filtering(),e.request_draw({clear_tile_cache:!0})),e.filters_manager.toggle()}},R.prototype.action_icons_def[2]],build_container_div:function(){var t=e("").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(t),t},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var t=this.drawables.length;if(0===t)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===t)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof Z),this.action_icons.filters_icon.hide();else{var i,n,a,s=this.drawables[0].get_type(),o=0;for(i=0;i1&&o===this.drawables.length){var r,l={};for(a=this.drawables[0],n=0;n0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var e=0;e0){this.saved_filters_managers=[];for(var e=0;e").addClass("top-container").appendTo(t),this.browser_content_div=e("").addClass("content").appendTo(t),this.bottom_container=e("").addClass("bottom-container").appendTo(t),this.top_labeltrack=e("").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=e("").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,s(this.viewport_container,i),this.intro_div=e("").addClass("intro").appendTo(this.viewport_container),e("").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){m.default.select_datasets({dbkey:i.dbkey},function(e){h.each(e,function(e){i.add_drawable(re(e,i,i))})})}),this.nav_container=e("").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=e("").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=e("").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=e("").addClass("overview-viewport").appendTo(this.overview),this.overview_close=e("").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=e("").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=e("").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=e("").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=e("").addClass("nav-controls").appendTo(this.nav),this.chrom_select=e("").attr({name:"chrom"}).addClass("chrom-nav").append("").appendTo(this.nav_controls);var n=function(t){"focusout"!==t.type&&13!==(t.keyCode||t.which)&&27!==(t.keyCode||t.which)||(27!==(t.keyCode||t.which)&&i.go_to(e(this).val()),e(this).hide(),e(this).val(""),i.location_span.show(),i.chrom_select.show()),t.stopPropagation()};this.nav_input=e("").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=e("").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(t,n){var a=[],s=e.map(i.get_tracks(ne),function(e){return e.data_manager.search_features(t.term).success(function(e){a=a.concat(e)})});e.when.apply(e,s).done(function(){n(e.map(a,function(e){return{label:e[0],value:e[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=e("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=e("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=e("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(t){e(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(e){i.zoom_in(e.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(e,t){this.current_x=t.offsetX}).bind("drag",function(e,t){var n=t.offsetX-this.current_x;this.current_x=t.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(e,t){if(e.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(e,t){t.original_low=i.low,t.current_height=e.clientY,t.current_x=t.offsetX}).bind("drag",function(t,n){var a=e(this),s=n.offsetX-n.current_x,o=a.scrollTop()-(t.clientY-n.current_height);a.scrollTop(o),n.current_height=t.clientY,n.current_x=n.offsetX;var r=Math.round(s/i.viewport_container.width()*(i.high-i.low));i.move_delta(r)}),this.top_labeltrack.bind("dragstart",function(t,n){return e("").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(e(this))}).bind("drag",function(t,n){e(n.proxy).css({left:Math.min(t.pageX,n.startX)-i.container.offset().left,width:Math.abs(t.pageX-n.startX)});var a=Math.min(t.pageX,n.startX)-i.container.offset().left,s=Math.max(t.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,r=i.viewport_container.width();i.update_location(Math.round(a/r*o)+i.low,Math.round(s/r*o)+i.low)}).bind("dragend",function(t,n){var a=Math.min(t.pageX,n.startX),s=Math.max(t.pageX,n.startX),o=i.high-i.low,r=i.viewport_container.width(),l=i.low;i.low=Math.round(a/r*o)+l,i.high=Math.round(s/r*o)+l,e(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new Q(this,{content_div:this.top_labeltrack})),e(window).bind("resize",function(){this.resize_timer&&window.clearTimeout(this.resize_timer),this.resize_timer=window.setTimeout(function(){i.resize_window()},500)}),e(document).bind("redraw",function(){i.redraw()}),this.reset(),e(window).trigger("resize")},get_base_color:function(e){return this.config.get_value(e.toLowerCase()+"_color")||this.config.get_value("n_color")}});I(H.prototype,N.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(e,t,i,n){var a=this;this.timer&&window.clearTimeout(this.timer),n?this.timer=window.setTimeout(function(){a.trigger("navigate",e+":"+t+"-"+i)},500):this.trigger("navigate",e+":"+t+"-"+i)},update_location:function(e,t){this.location_span.text(y.default.commatize(e)+" - "+y.default.commatize(t)),this.nav_input.val(this.chrom+":"+y.default.commatize(e)+"-"+y.default.commatize(t));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(t){var i=this;t.num=100;var n=e.Deferred();return e.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:t,dataType:"json",success:function(t){if(0!==t.chrom_info.length){if(t.reference){var a=new ee(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=t.chrom_info,i.chrom_select.html(""),i.chrom_select.append(e(''));for(var s=0,o=i.chrom_data.length;s");l.text(r),l.val(r),i.chrom_select.append(l)}t.prev_chroms&&i.chrom_select.append(e('')),t.next_chroms&&i.chrom_select.append(e('')),i.chrom_start_index=t.start_index,n.resolve(t.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+this.dbkey)}}),n},change_chrom:function(t,i,n){var a=this;if(!a.chrom_data)return void a.load_chroms_deferred.then(function(){a.change_chrom(t,i,n)});if(t&&"None"!==t){if("previous"===t)return void a.load_chroms({low:this.chrom_start_index-100});if("next"===t)return void a.load_chroms({low:this.chrom_start_index+100});var s=e.grep(a.chrom_data,function(e,i){return e.chrom===t})[0];if(void 0===s)return void a.load_chroms({chrom:t},function(){a.change_chrom(t,i,n)});if(t!==a.chrom){a.chrom=t,a.chrom_select.val(a.chrom),a.max_high=s.len-1,a.reset();for(var o=0,r=a.drawables.length;ot.max_high?(t.high=t.max_high,t.low=t.max_high-i):(t.high-=e,t.low-=e),t.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&window.clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=window.setTimeout(function(){t.request_redraw()},200);var n=t.chrom_select.val();this.trigger_navigate(n,t.low,t.high,!0)},add_drawable:function(e){N.prototype.add_drawable.call(this,e),e.init(),this.changed(),this.update_intro_div();var t=this;e.config.on("change",function(){t.changed()})},add_label_track:function(e){e.view=this,e.init(),this.label_tracks.push(e)},remove_drawable:function(t,i){if(N.prototype.remove_drawable.call(this,t),i){var n=this;t.container_div.hide(0,function(){e(this).remove(),n.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(e,t){var i=this,n=t?[t]:i.drawables;h.each(n,function(t){var n=h.find(i.tracks_to_be_redrawn,function(e){return e[0]===t});n?n[1]=e:i.tracks_to_be_redrawn.push([t,e])}),this.requested_redraw||(window.requestAnimationFrame(function(){i._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var e=this.low,t=this.high;ethis.max_high&&(t=this.max_high);var i=this.high-this.low;0!==this.high&&i").addClass("param-label").text(i.get("label")).appendTo(t),e("").addClass("param-input").html(i.get("html")).appendTo(t).find(":input").val(i.get("value")),e("").appendTo(t)},update_value:function(t){this.model.set_value(e(t.target).val())}}),q=p.View.extend({initialize:function(e){this.model.on("change:hidden",this.set_visible,this)},render:function(){var t=this,i=this.model,n=this.$el.addClass("dynamic-tool").hide();n.bind("drag",function(e){e.stopPropagation()}).click(function(e){e.stopPropagation()}).bind("dblclick",function(e){e.stopPropagation()}).keydown(function(e){e.stopPropagation()}),e("
<%- tool.name %> (version <%- tool.version %>)
','',"<% _.each( tool.inputs, function( input ){ %>",'
",'','','
","<% }); %>","',"<%= input.html %>","
",'',"<%- input.help %>","
",'',"','',"
",'','
"].join(""),{variable:"tool"})});t.default={ToolParameter:f,IntegerToolParameter:m,SelectToolParameter:v,Tool:w,ToolCollection:y,ToolSearch:k,ToolPanel:C,ToolPanelView:O,ToolFormView:E}}).call(t,i(2),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=a(s),r=i(5),l=(a(r),i(152)),d=a(l),c=i(10),u=a(c),h=i(26),f=a(h),p=i(25),_=a(p),m=i(66),g=a(m),v=i(40),w=a(v);t.default=f.default.extend({initialize:function(e){var t=this;this.deferred=new d.default,f.default.prototype.initialize.call(this,e),this._update(this.model.get("initialmodel")),this.model.get("listen_to_history")&&parent.Galaxy&&parent.Galaxy.currHistoryPanel&&this.listenTo(parent.Galaxy.currHistoryPanel.collection,"change",function(){t.model.get("onchange")()}),this.$el.on("remove",function(){t._destroy()})},_update:function(e){var t=this;e=e||this.model.get("buildmodel"),e?(this.deferred.reset(),this.deferred.execute(function(i){e(i,t),i.then(function(){t._render()})})):this._render()},_destroy:function(){var e=this;this.$el.off().hide(),this.deferred.execute(function(){f.default.prototype.remove.call(e),Galaxy.emit.debug("tool-form-base::_destroy()","Destroy view.")})},_render:function(){var t=this,i=this.model.attributes;this.model.set({title:i.fixed_title||""+i.name+" "+i.description+" (Galaxy Version "+i.version+")",operations:!i.hide_operations&&this._operations(),onchange:function(){t.deferred.reset(),t.deferred.execute(function(e){t.model.get("postchange")(e,t)})}}),this.render(),this.model.get("collapsible")||this.$el.append(e("").addClass("ui-margin-top-large").append(this._footer())),this.show_message&&this.message.update({status:"success",message:"Now you are using '"+i.name+"' version "+i.version+", id '"+i.id+"'.",persistent:!1}),this.show_message=!0},_operations:function(){var e=this,t=this.model.attributes,i=new u.default.ButtonMenu({icon:"fa-cubes",title:!t.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!t.sustain_version&&t.versions&&t.versions.length>1)for(var n in t.versions){var a=t.versions[n];a!=t.version&&i.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){e.model.set("id",t.id.replace(t.version,this.version)),e.model.set("version",this.version),e._update()}})}else i.$el.hide();var s=new u.default.ButtonMenu({id:"options",icon:"fa-caret-down",title:!t.narrow&&"Options"||null,tooltip:"View available options"});return t.biostar_url&&(s.addMenu({icon:"fa-question-circle",title:"Question?",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}}),s.addMenu({icon:"fa-search",title:(0,o.default)("Search"),onclick:function(){window.open(t.biostar_url+"/local/search/page/?q="+t.name)}})),s.addMenu({icon:"fa-share",title:(0,o.default)("Share"),onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+t.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&s.addMenu({icon:"fa-download",title:(0,o.default)("Download"),onclick:function(){window.location.href=Galaxy.root+"api/tools/"+t.id+"/download"}}),t.requirements&&t.requirements.length>0&&s.addMenu({icon:"fa-info-circle",title:(0,o.default)("Requirements"),onclick:function(){!this.requirements_visible||e.portlet.collapsed?(this.requirements_visible=!0,e.portlet.expand(),e.message.update({persistent:!0,message:e._templateRequirements(t),status:"info"})):(this.requirements_visible=!1,e.message.update({message:""}))}}),t.sharable_url&&s.addMenu({icon:"fa-external-link",title:(0,o.default)("See in Tool Shed"),onclick:function(){window.open(t.sharable_url)}}),_.default.load({type:"tool-menu",callback:function(e){e.each(function(e){var i=e.toJSON();i.activate&&i.config.function&&s.addMenu({icon:i.config.icon,title:i.config.title,onclick:function(){new Function("options",i.config.function)(t)}})})}}),{menu:s,versions:i}},_footer:function(){var t=this.model.attributes,i=e("").append(this._templateHelp(t));if(t.citations){var n=w.default.extend(g.default),a=document.createElement("div");i.append(a),new n({propsData:{id:t.id,source:"tools"}}).$mount(a)}return i},_templateHelp:function(t){var i=e("").addClass("ui-form-help").append(t.help);return i.find("a").attr("target","_blank"),i.find("img").each(function(){var t=e(this).attr("src");-1!==t.indexOf("admin_toolshed")&&e(this).attr("src",Galaxy.root+t)}),i},_templateRequirements:function(t){var i=t.requirements.length;if(i>0){var a="This tool requires ";n.each(t.requirements,function(e,t){a+=e.name+(e.version?" (Version "+e.version+")":"")+(t<% tool.help %>
',"\n \n \n \n
")},_renderNametags:function(){return e.template(["<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>",'<% if (tag.indexOf("name:") == 0){ %>','<%- tag.slice(5) %>',"<% } %>","<% }); %>"].join(""))({tags:this.model.get("tags")})},events:e.extend(e.clone(g.prototype.events),{"click .display-btn":function(e){this.trigger("display",this,e)},"click .params-btn":function(e){this.trigger("params",this,e)},"click .download-btn":function(e){this.trigger("download",this,e)}}),toString:function(){return"DatasetListItemView("+(this.model?""+this.model:"(no model)")+")"}});v.prototype.templates=function(){var t=e.extend({},g.prototype.templates.warnings,{failed_metadata:p.default.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','- \n
- \n \n '+(0,m.default)("Download dataset")+"\n \n \n "+e.map(this.model.get("meta_files"),function(e){return'
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t.cyrillicUnicodeChart[e]}},function(e,t,i){"use strict";function n(e){return t.specialCharacters.hasOwnProperty(e)}Object.defineProperty(t,"__esModule",{value:!0}),t.specialCharacters={i:"ı",j:"ȷ",oe:"œ",OE:"Œ",ae:"æ",AE:"Æ",aa:"å",AA:"Å",o:"ø",O:"Ø",ss:"ß",l:"ł",L:"Ł"},t.isSpecialCharacter=n,t.specialCharacter=function(e){return n(e)?t.specialCharacters[e]:void 0}},function(e,t,i){"use strict";function n(e,t){switch(e){case"cyrchar":var i=o.translateCharToCyrillic(t);if(i)return i;break;default:for(var n=0,r=[a.diacriticUnicode,s.formattingUnicode];n=t}),u=function(e,t){if(a.bwg.instrument&&console.log("level="+t+"; offset="+e+"; time="+(0|Date.now())),d+=e.length,1==e.length&&e[0]-a.cirTreeOffset==48&&a.cachedCirRoot)return _(a.cachedCirRoot,0,t),void(0===--d&&n.when(a.fetchFeatures(c,l)).then(function(e){s.resolve(e)}));for(var i,o=4+32*a.cirBlockSize,r=0;re||v==e&&w>=t)&&l.push({offset:y,size:b}),a+=32}else{for(var 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n([]);this.getFirstAdjacentById(a,t,i,n)},d.prototype.getFirstAdjacentById=function(e,t,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(s){a.cirHeader=s;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(e,t,i,n)});var s=null,o=-1,l=-1,d=0,c=(Date.now(),function(e,t){d+=e.length;for(var i,n=4+32*a.cirBlockSize,s=0;s0&&(0!=e||t>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(e!=a.bwg.maxID||t<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,s,o){return i<0&&(n0&&(n>e||a>t)},[s],function(e){for(var t=null,a=-1,s=-1,o=0;oa||c>s)||i>0&&(l0&&(b>e||b==e&&x>=t))&&(/_random/.exec(a.bwg.idsToChroms[w])||(null==s||i<0&&(b>o||b==o&&x>l)||i>0&&(w=e||i>0&&(b>e||b==e&&x>=t)&&w<=e)&&(S<0||x>T)&&(S=k,T=i<0?x:y,i<0?b:w),d+=24}S>=0&&c([S],u+1)}};c([a.cirTreeOffset+48],1)},l.prototype.readWigData=function(e,t,i){var n,a=i-t;if(a<=25e3||0===this.zoomLevels.length)n=this.getUnzoomedView();else for(var s=0;s=this.zoomLevels.length-1)){var o;return o=e<0?this.getUnzoomedView():this.getZoomedView(e),o.readWigDataById(t,i,n,a)}if(this.topLevelReductionCache){for(var r=[],l=this.topLevelReductionCache,d=0;d0?0:3e8;e.fromRef&&(r=t);for(var d=0;d0){if(c>n)if(e.zoom<0){if(u.min>r)return a(u)}else u.max>r&&l.push({chr:e.chr,chrOrd:e.chrOrd,zoom:e.zoom-2,min:u.min,max:u.max,fromRef:e.fromRef})}else if(c>n)if(e.zoom<0){if(u.maxi.field-3)return s[i.field-3]==e},[{offset:v,size:w}],t)}f+=u}return t([])}for(var y=null,p=0;pn._max&&(n._max=e._max):(i.push(n),n=e)}),i.push(n),this._ranges=i}function i(e,i){return e instanceof t||(e instanceof Array||(e=[e]),e=new t(e)),i&&e.insertRange(i),e}function n(i,n){for(var a=i.ranges(),s=n.ranges(),o=a.length,r=s.length,l=0,d=0,c=[];l=u&&c.push(new e(u,h)),i.max()>n.max()?++d:++l}return 0==c.length?null:1==c.length?c[0]:new t(c)}function a(e){for(var t=0,i=e.ranges(),n=0;nt.min()?1:e.max()e.max()?1:0}function o(e,t){return e._mint._min?1:e._maxe._max?1:0}return e.prototype.min=function(){return this._min},e.prototype.max=function(){return this._max},e.prototype.contains=function(e){return e>=this._min&&e<=this._max},e.prototype.isContiguous=function(){return!0},e.prototype.ranges=function(){return[this]},e.prototype._pushRanges=function(e){e.push(this)},e.prototype.toString=function(){return"["+this._min+"-"+this._max+"]"},t.prototype.min=function(){return this._ranges[0].min()},t.prototype.max=function(){return this._ranges[this._ranges.length-1].max()},t.prototype.lower_bound=function(e){var t=this.ranges();if(e>this.max())return t.length;if(et[a]._max)i=a+1;else{if(!(ee._max&&(e._max=i[n]._max),this._ranges.splice(t,n-t+1,e)},t.prototype.isContiguous=function(){return this._ranges.length>1},t.prototype.ranges=function(){return this._ranges},t.prototype._pushRanges=function(e){for(var t=0;t0&&(e+=","),e+=this._ranges[t].toString();return e},{Range:e,union:i,intersection:n,coverage:a,rangeOver:s,_rangeOrder:o}}.apply(t,n))&&(e.exports=a)},function(e,t,i){var n,a;n=[],void 0!==(a=function(){function e(){}function t(){this.was=[0]}function i(e,t,i){this.hufts=new Int32Array(3*u),this.window=new Uint8Array(i),this.end=i,this.checkfn=t,this.mode=g,this.reset(e,null),this.left=0,this.table=0,this.index=0,this.blens=null,this.bb=new Int32Array(1),this.tb=new Int32Array(1),this.codes=new n,this.last=0,this.bitk=0,this.bitb=0,this.read=0,this.write=0,this.check=0,this.inftree=new a}function n(){}function a(){}function s(e,t,i,n,a){return e[0]=v,t[0]=w,i[0]=y,n[0]=b,f}function o(e,t,i,n,a){if(0!=a){if(!e)throw"Undef src";if(!i)throw"Undef dest";0==t&&a==e.length?l(e,i,n):P?l(e.subarray(t,t+a),i,n):1==e.BYTES_PER_ELEMENT&&a>100?l(new Uint8Array(e.buffer,e.byteOffset+t,a),i,n):r(e,t,i,n,a)}}function r(e,t,i,n,a){for(var s=0;s15?(this.inflateEnd(e),-2):(this.wbits=t,e.istate.blocks=new i(e,0!=e.istate.nowrap?null:this,1<>4)>e.istate.wbits){e.istate.mode=13,e.msg="invalid window size",e.istate.marker=5;break}e.istate.mode=1;case 1:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,n=255&e.next_in[e.next_in_index++],((e.istate.method<<8)+n)%31!=0){e.istate.mode=13,e.msg="incorrect header check",e.istate.marker=5;break}if(0==(32&n)){e.istate.mode=7;break}e.istate.mode=2;case 2:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need=(255&e.next_in[e.next_in_index++])<<24&4278190080,e.istate.mode=3;case 3:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<16&16711680,e.istate.mode=4;case 4:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<8&65280,e.istate.mode=5;case 5:return 0==e.avail_in?i:(i=t,e.avail_in--,e.total_in++,e.istate.need+=255&e.next_in[e.next_in_index++],e.adler=e.istate.need,e.istate.mode=6,2);case 6:return e.istate.mode=13,e.msg="need dictionary",e.istate.marker=0,-2;case 7:if(-3==(i=e.istate.blocks.proc(e,i))){e.istate.mode=13,e.istate.marker=0;break}if(i==f&&(i=t),i!=p)return i;if(i=t,e.istate.blocks.reset(e,e.istate.was),0!=e.istate.nowrap){e.istate.mode=12;break}e.istate.mode=8;case 8:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need=(255&e.next_in[e.next_in_index++])<<24&4278190080,e.istate.mode=9;case 9:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<16&16711680,e.istate.mode=10;case 10:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<8&65280,e.istate.mode=11;case 11:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,e.istate.need+=255&e.next_in[e.next_in_index++],e.istate.was[0]!=e.istate.need){e.istate.mode=13,e.msg="incorrect data check",e.istate.marker=5;break}e.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},t.prototype.inflateSetDictionary=function(e,t,i){var n=0,a=i;return null==e||null==e.istate||6!=e.istate.mode?-2:e._adler.adler32(1,t,0,i)!=e.adler?-3:(e.adler=e._adler.adler32(0,null,0,0),a>=1<>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],v=[];s(u,h,_,v,e),this.codes.init(u[0],h[0],_[0],0,v[0],0,e),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,e.msg="invalid block type",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<>>16&65535)!=(65535&n))return this.mode=13,e.msg="invalid stored block lengths",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,write=d,this.inflate_flush(e,t);if(0==c&&(d==end&&0!=read&&(d=0,c=dl&&(i=l),i>c&&(i=c),o(e.next_in,r,this.window,d,i),r+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<29||(i>>5&31)>29)return this.mode=9,e.msg="too many length or distance symbols",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<>>=3,a-=3}for(;this.index<19;)this.blens[M[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,e))!=f)return t=i,-3==t&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,write=d,this.inflate_flush(e,t);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var w,y,b;for(i=this.bb[0];a>>=i,a-=i,this.blens[this.index++]=b;else{for(w=18==b?7:b-14,y=18==b?11:3;a>>=i,a-=i,y+=n&m[w],n>>>=w,a-=w,w=this.index,i=this.table,w+y>258+(31&i)+(i>>5&31)||16==b&&w<1)return this.blens=null,this.mode=9,e.msg="invalid bit length repeat",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);b=16==b?this.blens[w-1]:0;do{this.blens[w++]=b}while(0!=--y);this.index=w}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,v,this.hufts,e))!=f)return-3==i&&(this.blens=null,this.mode=13),t=i,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,v[0],e),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,(t=this.codes.proc(this,e,t))!=p)return this.inflate_flush(e,t);if(t=f,this.codes.free(e),r=e.next_in_index,l=e.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=de.avail_out&&(i=e.avail_out),0!=i&&t==_&&(t=f),e.avail_out-=i,e.total_out+=i,null!=this.checkfn&&(e.adler=this.check=e._adler.adler32(this.check,this.window,a,i)),o(this.window,a,e.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>e.avail_out&&(i=e.avail_out),0!=i&&t==_&&(t=f),e.avail_out-=i,e.total_out+=i,null!=this.checkfn&&(e.adler=this.check=e._adler.adler32(this.check,this.window,a,i)),o(this.window,a,e.next_out,n,i),n+=i,a+=i),e.next_out_index=n,this.read=a,t};n.prototype.init=function(e,t,i,n,a,s,o){this.mode=0,this.lbits=e,this.dbits=t,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=s,this.tree=null},n.prototype.proc=function(e,t,i){var n,a,s,o,r,l,d,c=0,u=0,h=0;for(h=t.next_in_index,o=t.avail_in,c=e.bitb,u=e.bitk,r=e.write,l=r=258&&o>=10&&(e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,e,t),h=t.next_in_index,o=t.avail_in,c=e.bitb,u=e.bitk,r=e.write,l=r>>=this.tree[a+1],u-=this.tree[a+1],0==(s=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&s)){this.get=15&s,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&s)){this.need=s,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&s)){this.mode=7;break}return this.mode=9,t.msg="invalid literal/length code",i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 2:for(n=this.get;u>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(s=this.tree[a]))){this.get=15&s,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&s)){this.need=s,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,t.msg="invalid distance code",i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 4:for(n=this.get;u>=n,u-=n,this.mode=5;case 5:for(d=r-this.dist;d<0;)d+=e.end;for(;0!=this.len;){if(0==l&&(r==e.end&&0!=e.read&&(r=0,l=r7&&(u-=8,o++,h--),e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r>=c[M+1],g-=c[M+1],0!=(16&h)){for(h&=15,C=c[M+2]+(_&m[h]),_>>=h,g-=h;g<15;)w--,_|=(255&l.next_in[v++])<>=c[M+1],g-=c[M+1],0!=(16&h)){for(h&=15;g>=h,g-=h,b-=C,y>=S)T=y-S,r.window[y++]=r.window[T++],r.window[y++]=r.window[T++],C-=2;else{T=y-S;do{T+=r.end}while(T<0);if(h=r.end-T,C>h){if(C-=h,y-T>0&&h>y-T)do{r.window[y++]=r.window[T++]}while(0!=--h);else o(r.window,T,r.window,y,h),y+=h,T+=h,h=0;T=0}}do{r.window[y++]=r.window[T++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-w,C=g>>3>3:C,w+=C,v-=C,g-=C<<3,r.bitb=_,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=y,-3;d+=c[M+2],d+=_&m[h],M=3*(u+d),h=c[M]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-w,C=g>>3>3:C,w+=C,v-=C,g-=C<<3,r.bitb=_,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=y,p):(l.msg="invalid literal/length code",C=l.avail_in-w,C=g>>3>3:C,w+=C,v-=C,g-=C<<3,r.bitb=_,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=y,-3);if(d+=c[M+2],d+=_&m[h],M=3*(u+d),0==(h=c[M])){_>>=c[M+1],g-=c[M+1],r.window[y++]=c[M+2],b--;break}}else _>>=c[M+1],g-=c[M+1],r.window[y++]=c[M+2],b--}while(b>=258&&w>=10);return C=l.avail_in-w,C=g>>3>3:C,w+=C,v-=C,g-=C<<3,r.bitb=_,r.bitk=g,l.avail_in=w,l.total_in+=v-l.next_in_index,l.next_in_index=v,r.write=y,f},a.prototype.huft_build=function(e,t,i,n,a,s,r,l,d,c,h){var p,m,g,v,w,y,b,x,k,C,S,T,M,$,P;C=0,w=i;do{this.c[e[t+C]]++,C++,w--}while(0!=w);if(this.c[0]==i)return r[0]=-1,l[0]=0,f;for(x=l[0],y=1;y<=15&&0==this.c[y];y++);for(b=y,xw&&(x=w),l[0]=x,$=1<T+x;){if(v++,T+=x,P=g-T,P=P>x?x:P,(m=1<<(y=b-T))>p+1&&(m-=p+1,M=b,yu)return-3;this.u[v]=S=this.hn[0],this.hn[0]+=P,0!=v?(this.x[v]=w,this.r[0]=y,this.r[1]=x,y=w>>>T-x,this.r[2]=S-this.u[v-1]-y,o(this.r,0,d,3*(this.u[v-1]+y),3)):r[0]=S}for(this.r[1]=b-T,C>=i?this.r[0]=192:h[C]>>T;y>>=1)w^=y;for(w^=y,k=(1<257?(-3==d?l.msg="oversubscribed distance tree":d==_?(l.msg="incomplete distance tree",d=-3):-4!=d&&(l.msg="empty distance tree with lengths",d=-3),d):f)},a.prototype.initWorkArea=function(e){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(e),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length=this.options.errorAtPercent},_render_quota:function(){var t=this.model.toJSON(),i=t.quota_percent,n=e(this._templateQuotaMeter(t)),a=n.find(".progress-bar");return this.isOverQuota()?(a.attr("class","progress-bar bg-danger"),n.find(".quota-meter-text").css("color","white"),this.trigger("quota:over",t)):i>=this.options.warnAtPercent?(a.attr("class","progress-bar bg-warning"),this.trigger("quota:under quota:under:approaching",t)):(a.attr("class","progress-bar bg-success"),this.trigger("quota:under quota:under:ok",t)),n},_render_usage:function(){var t=e(this._templateUsage(this.model.toJSON()));return this.log(this+".rendering usage:",t),t},render:function(){var e=null;return this.log(this+".model.quota_percent:",this.model.get("quota_percent")),e=null===this.model.get("quota_percent")||void 0===this.model.get("quota_percent")?this._render_usage():this._render_quota(),this.$el.html(e),this.$el.find(".quota-meter-text").tooltip(),this},_templateQuotaMeter:function(e){return['',e.html," "].join("");return a(t).click(function(t){return t.preventDefault(),e.func(t)})});return n.find("ul").append(s),t.replaceWith(n),n},multiselectActions:function(){return[]},$scrollContainer:function(e){return(e||this.$el).parent().parent()},$controls:function(e){return(e||this.$el).find("> .controls")},$list:function(e){return(e||this.$el).find("> .list-items")},$messages:function(e){return(e||this.$el).find("> .controls .messages")},$emptyMessage:function(e){return(e||this.$el).find("> .empty-message")},renderItems:function(e){e=e||this.$el;var t=this;t.log(this+".renderItems",e);var i=t.$list(e);t.freeViews();var n=t._filterCollection();return t.views=n.map(function(e){return t._createItemView(e)}),i.empty(),t.views.length&&t._attachItems(e),t._renderEmptyMessage(e).toggle(!t.views.length),t.trigger("views:ready",t.views),t.views},_filterCollection:function(){var e=this;return e.collection.filter(n.bind(e._filterItem,e))},_filterItem:function(e){var t=this;return n.every(t.filters.map(function(t){return t.call(e)}))&&(!t.searchFor||e.matchesAll(t.searchFor))},_createItemView:function(e){var t=this._getItemViewClass(e),i=n.extend(this._getItemViewOptions(e),{model:e}),a=new t(i);return this._setUpItemViewListeners(a),a},_destroyItemView:function(e){this.stopListening(e),this.views=n.without(this.views,e)},_destroyItemViews:function(e){var t=this;return t.views.forEach(function(e){t.stopListening(e)}),t.views=[],t},freeViews:function(){return this._destroyItemViews()},_getItemViewClass:function(e){return this.viewClass},_getItemViewOptions:function(e){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:n.contains(this.selected,e.id),draggable:this.dragItems}},_setUpItemViewListeners:function(e){var t=this;return this.listenTo(e,"all",function(){var e=Array.prototype.slice.call(arguments,0);e[0]="view:"+e[0],t.trigger.apply(t,e)}),this.listenTo(e,"draggable:dragstart",function(e,t){var i={},n=this.getSelectedModels();i=n.length?n.toJSON():[t.model.toJSON()],e.dataTransfer.setData("text",JSON.stringify(i))},this),t},_attachItems:function(e){var t=this;return this.$list(e).append(this.views.map(function(e){return t._renderItemView$el(e)})),this},_renderItemView$el:function(e){return e.render(0).$el},_renderEmptyMessage:function(e){this.debug("_renderEmptyMessage",e,this.searchFor);var t=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(e).text(t)},expandAll:function(){n.each(this.views,function(e){e.expand()})},collapseAll:function(){n.each(this.views,function(e){e.collapse()})},addItemView:function(e,t,i){var n=this,s=n._filterCollection().indexOf(e);if(-1!==s){var o=n._createItemView(e);return a(o).queue("fx",[function(e){n.$emptyMessage().is(":visible")?n.$emptyMessage().fadeOut(n.fxSpeed,e):e()},function(e){n._attachView(o,s),e()}]),o}},_attachView:function(e,t,i){i=!!n.isUndefined(i)||i,t=t||0;var a=this;return a.views.splice(t,0,e),a._insertIntoListAt(t,a._renderItemView$el(e).hide()),a.trigger("view:attached",e),i?e.$el.slideDown(a.fxSpeed,function(){a.trigger("view:attached:rendered")}):(e.$el.show(),a.trigger("view:attached:rendered")),e},_insertIntoListAt:function(e,t){var i=this.$list();return 0===e?i.prepend(t):i.children().eq(e-1).after(t),t},removeItemView:function(e,t,i){var s=this,o=n.find(s.views,function(t){return t.model===e});if(o)return s.views=n.without(s.views,o),s.trigger("view:removed",o),a({}).queue("fx",[function(e){o.$el.fadeOut(s.fxSpeed,e)},function(e){o.remove(),s.trigger("view:removed:rendered"),s.views.length?e():s._renderEmptyMessage().fadeIn(s.fxSpeed,e)}]),o},viewFromModelId:function(e){return n.find(this.views,function(t){return t.model.id===e})},viewFromModel:function(e){return e?this.viewFromModelId(e.id):void 0},viewsWhereModel:function(e){return this.views.filter(function(t){return n.isMatch(t.model.attributes,e)})},viewRange:function(e,t){if(e===t)return e?[e]:[];var i=this.views.indexOf(e),n=this.views.indexOf(t);return-1===i||-1===n?i===n?[]:-1===i?[t]:[e]:i .controls .search-query");return i.val()!==e&&i.val(e),this},clearSearch:function(e){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTOR_FX_AT:20,showSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.showSelector(e)})},hideSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.hideSelector(e)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(e){n.each(this.views,function(t){t.select(e)})},deselectAll:function(e){this.lastSelected=null,n.each(this.views,function(t){t.deselect(e)})},selectRange:function(e,t){var i=this.viewRange(e,t);return n.each(i,function(e){e.select()}),i},getSelectedViews:function(){return n.filter(this.views,function(e){return e.selected})},getSelectedModels:function(){return new this.collection.constructor(n.map(this.getSelectedViews(),function(e){return e.model}))},_showLoadingIndicator:function(e,t,i){this.debug("_showLoadingIndicator",this.indicator,e,t,i),t=void 0!==t?t:this.fxSpeed,this.indicator||(this.indicator=new d.default.LoadingIndicator(this.$el),this.debug("\t created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(t),this.indicator.show(e,t,i)):this.indicator.show(0,i)},_hideLoadingIndicator:function(e,t){this.debug("_hideLoadingIndicator",this.indicator,e,t),e=void 0!==e?e:this.fxSpeed,this.indicator&&this.indicator.hide(e,t)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(e,t){return t=t||0,this.$scrollContainer().animate({scrollTop:e},t),this},scrollToTop:function(e){return this.scrollTo(0,e)},scrollToItem:function(e,t){return this},scrollToId:function(e,t){return this.scrollToItem(this.viewFromModelId(e),t)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});p.prototype.templates=function(){return{el:u.default.wrapTemplate(["
\n Dataset:"+t.config.get_value("name")+'
\n Region(s):\n \n ',n=function(){Galaxy.modal.hide(),e(window).unbind("keypress.check_enter_esc")},a=function(){var i,n=e('select[name="regions"] option:selected').val(),a=new m.default.GenomeRegion({chrom:(void 0).view.chrom,start:(void 0).view.low,end:(void 0).view.high}),s=h.map(e(".bookmark"),function(t){return new m.default.GenomeRegion({from_str:e(t).children(".position").text()})});i="cur"===n?[a]:"bookmarks"===n?s:[a].concat(s),Galaxy.modal.hide(),window.top.location.href=Galaxy.root+"visualization/sweepster?"+e.param({dataset_id:t.dataset.id,hda_ldda:t.dataset.get("hda_ldda"),regions:JSON.stringify(new p.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:n,Yes:a}})}},R.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&R.prototype.can_draw.call(this)},build_container_div:function(){return e("").addClass("track").attr("id","track_"+this.id)},set_dataset:function(e){this.dataset=e,this.data_manager.set("dataset",e)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var t=this,i=!1,n=!1,a=e("
");e(t.container_div).hover(function(){t.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=e(t.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,t.min_height_px),t.max_height_px);e(t.tiles_div).css("height",a),t.visible_height_px=t.max_height_px===a?0:a,t.on_resize()}).bind("dragend",function(e,s){t.tile_cache.clear(),n=!1,i||a.hide(),t.config.set_value("height",t.visible_height_px),t.changed()}).appendTo(t.container_div)},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(){return this instanceof Q?"LabelTrack":this instanceof ee?"ReferenceTrack":this instanceof te?"LineTrack":this instanceof se?"ReadTrack":this instanceof ae?"VariantTrack":this instanceof Z?"CompositeTrack":this instanceof ne?"FeatureTrack":""},show_message:function(t){return this.tiles_div.remove(),e("").addClass("message").html(t).appendTo(this.content_div)},init:function(t){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=e("").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=e.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:t};return e.getJSON(this.dataset.url(),a,function(t){if(t&&"error"!==t&&"error"!==t.kind)"no converter"===t?(i.container_div.addClass("error"),i.show_message(L)):"no data"===t||void 0!==t.data&&(null===t.data||0===t.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===t?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),window.setTimeout(function(){i.init()},i.data_query_wait)):"data"!==t&&"data"!==t.status||(t.valid_chroms&&(i.valid_chroms=t.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,e.when.apply(e,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");t.message&&(a.append(e("").text("View error").click(function(){Galaxy.modal.show({title:(0,c.default)("Trackster Error"),body:"").text(d).make_text_editable({num_cols:12,on_finish:function(t){e(".tooltip").remove(),this.config.set_value(o,r(t,1)),i()},help_text:"Set "+s+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(e,t,i,n){var a=this;h.filter(e,function(e){return e instanceof J}).length>0?(this.max_height_px=0,h.each(e,function(e){e instanceof J||(e.html_elt.remove(),a.draw_helper(e.region,i,{force:!0,mode:"Coverage"}))}),this._add_yaxis_label("max")):(this.container_div.find(".yaxislabel").remove(),h.find(e,function(e){return e.has_icons})&&h.each(e,function(e){e.has_icons||e.html_elt.css("padding-top",20)}))},get_mode:function(e){return this.mode},update_auto_mode:function(e){},_get_drawables:function(){return[this]},draw_helper:function(t,i,n){var a=this;n||(n={});var s=n.force,o=n.mode||this.mode,r=1/i,l=this._get_drawables(),d=this._gen_tile_cache_key(i,t),c=s?void 0:this.tile_cache.get_elt(d);if(c)return function(e){return e&&"track"in e}(c)&&this.show_tile(c,i),c;if(!1===n.data_fetch)return null;var u=function(){var e=h.find(G,function(e){return e===o})?"Coverage":o,i=h.map(l,function(i){return i.data_manager.get_data(t,e,r,a.data_url_extra_params)});return a.view.reference_track&&i.push(a.view.reference_track.data_manager.get_data(t,o,r,a.view.reference_track.data_url_extra_params)),i},f=e.Deferred();return this.tile_cache.set_elt(d,f),e.when.apply(e,u()).then(function(){var s,o=u(),r=o;if(h.find(o,function(e){return y.default.is_deferred(e)}))return a.tile_cache.set_elt(d,void 0),void e.when(a.draw_helper(t,i,n)).then(function(e){f.resolve(e)});a.view.reference_track&&(s=a.view.reference_track.data_manager.subset_entry(o.pop(),t));var c=[],p=[];h.each(l,function(e,t){var n=r[t];"Auto"===e.mode&&(e.mode=e.get_mode(n),e.update_auto_mode(e.mode)),c.push(e.mode),p.push(e.get_canvas_height(n,e.mode,i,w))});var _,m=a.view.canvas_manager.new_canvas(),g=t.get("start"),v=t.get("end"),w=Math.ceil((v-g)*i)+a.left_offset,b=h.max(p);m.width=w,m.height=n.height||b;var x=m.getContext("2d");x.translate(a.left_offset,0),l.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),h.each(l,function(e,n){_=e.draw_tile(r[n],x,c[n],t,i,s)}),void 0!==_&&(a.tile_cache.set_elt(d,_),a.show_tile(_,i)),f.resolve(_)}),f},get_canvas_height:function(e,t,i,n){return this.visible_height_px},_draw_line_track_tile:function(e,t,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",h.max(h.map(e.data,function(e){return e[1]}))||0);var s=t.canvas;return new C.default.LinePainter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(t,s.width,s.height,a),new J(this,n,a,s,e.data)},draw_tile:function(e,t,i,n,a,s){},show_tile:function(e,t){var i=e.html_elt;e.predisplay_actions();var n=Math.round((e.low-(this.is_overview?this.view.max_low:this.view.low))*t);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(e){var t=this;return" - region=["+(void 0!==e?e.toString():"all")+"], parameters=["+h.values(t.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(e,t){return"Auto"===t||("Coverage"===t?"bigwig"===e.dataset_type:"bigwig"!==e.dataset_type&&"no_detail"!==e.extra_info)},can_subset:function(e){return!e.message&&"no_detail"!==e.extra_info&&("bigwig"!==e.dataset_type||e.data[1][0]-e.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var Q=function(e,t){X.call(this,e,t,{resize:!1,header:!1}),this.container_div.addClass("label-track")};I(Q.prototype,X.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(t){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),s=Math.floor(i.low/a)*a,o=this.view.container.width(),r=e("").addClass("label-container");s").addClass("pos-label").text(y.default.commatize(s)).css({left:l})),s+=a}this.content_div.children(":first").remove(),this.content_div.append(r)}});var Z=function(e,t,i){if(K.call(this,e,t,i),this.drawables=[],"drawables"in i){for(var n,a=0;athis.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}h.each(this.drawables,function(e){(e instanceof ne||e instanceof se)&&e.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};I(Z.prototype,K.prototype,{display_modes:G,build_config_params:function(){return h.union(R.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:(0,c.default)("Show individual tracks"),css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_group()}}].concat(K.prototype.action_icons_def),to_dict:N.prototype.to_dict,add_drawable:N.prototype.add_drawable,unpack_drawables:N.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var e=this.visible_height_px;h.each(this.drawables,function(t){t.visible_height_px=e}),X.prototype.on_resize.call(this)},change_mode:function(e){K.prototype.change_mode.call(this,e);for(var t=0;ts&&(s=o)}for(a=0;athis.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,s=K.prototype.draw_helper.call(this,e,t,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),s},can_subset:function(e){return!0},draw_tile:function(e,t,i,n,a){var s=this.data_manager.subset_entry(e,n),o=s.data,r=t.canvas;t.font=t.canvas.manager.default_font,t.textAlign="center";for(var l=0,d=o.length;l12e3?"Squish":"Pack"},get_canvas_height:function(e,t,i,n){if("Coverage"===t||"bigwig"===e.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,e.data,t),s=new this.painter(null,null,null,this.config.to_key_value_dict(),t);return Math.max(this.min_height_px,s.get_required_height(a,n))},draw_tile:function(e,t,i,n,a,s,o){var r=this,l=t.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===e.dataset_type)return this._draw_line_track_tile(e,t,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(e.data)for(var _=this.filters_manager.filters,m=0,g=e.data.length;m1){var r;if(0===this.container_div.find(".yaxislabel.variant").length&&(r=this.config.get_value("summary_height")/2,this.tiles_div.prepend(e("").text("Summary").addClass("yaxislabel variant top").css({"font-size":r+"px",top:(this.config.get_value("summary_height")-r)/2+"px"})),this.config.get_value("show_sample_data"))){var l=o.join("
");this.tiles_div.prepend(e("").html(l).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}r=("Squish"===this.mode?5:10)+"px",e(this.tiles_div).find(".sample").css({"font-size":r,"line-height":r}),e(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var se=function(e,t,i){ne.call(this,e,t,i),this.painter=C.default.ReadPainter,this.update_icons()};I(se.prototype,R.prototype,K.prototype,ne.prototype,{build_config_params:function(){return h.union(R.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:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var oe={CompositeTrack:Z,DrawableGroup:V,DiagonalHeatmapTrack:ie,FeatureTrack:ne,LineTrack:te,ReadTrack:se,VariantTrack:ae,VcfTrack:ae},re=function(e,t,i){if("copy"in e)return e.copy(i);var n=e.obj_type;return n||(n=e.track_type),new oe[n](t,i,e)};t.default={TracksterView:H,DrawableGroup:V,LineTrack:te,FeatureTrack:ne,DiagonalHeatmapTrack:ie,ReadTrack:se,VariantTrack:ae,CompositeTrack:Z,object_from_template:re}}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(5),d=s(l),c=i(10),u=s(c),h=i(17),f=s(h),p=i(55),_=s(p),m=i(25),g=s(m),v=e.View.extend({initialize:function(e){var t=this;this.modal=parent.Galaxy.modal||new f.default.View,this.form=new _.default(d.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(e,i){var a=i.model.attributes,s="",o={},l=a.job_id;l?s=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(s=Galaxy.root+"api/tools/"+a.id+"/build",o=n.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),a.version&&(o.tool_version=a.version),d.default.get({url:s,data:o,success:function(n){if(!n.display)return void(window.location=Galaxy.root);i.model.set(n),t._customize(i),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",n),e.resolve()},error:function(t,s){var o=t&&t.err_msg||"Uncaught error.";401==s?window.location=Galaxy.root+"user/login?"+n.param({redirect:Galaxy.root+"?tool_id="+a.id}):i.$el.is(":empty")?i.$el.prepend(new u.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:(0,r.default)("Tool request failed"),body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",t),e.reject()}})},postchange:function(e,t){var i={tool_id:t.model.get("id"),tool_version:t.model.get("version"),inputs:n.extend(!0,{},t.data.create())};t.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),d.default.request({type:"POST",url:Galaxy.root+"api/tools/"+t.model.get("id")+"/build",data:i,success:function(i){t.update(i),t.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",t),e.reject()}})}},e)),this.deferred=this.form.deferred,this.setElement(""),this.$el.append(this.form.$el)},_customize:function(e){var t=this,i=e.model.attributes,n=new u.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:(0,r.default)("Execute"),cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),e.portlet.disable(),t.submit(i,function(){n.unwait(),e.portlet.enable()})}});if(i.buttons={execute:n},i.job_id&&i.job_remap){if("job_produced_collection_elements"===i.job_remap)var a="Replace elements in collection ?",s="The previous run of this tool failed. Use this option to replace the failed element(s) in the dataset collectio that were produced during the previous tool run.";else var a="Resume dependencies from this job ?",s="The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.";i.inputs.push({label:a,name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:s})}var o={};Galaxy.user.attributes.preferences&&"extra_user_preferences"in Galaxy.user.attributes.preferences&&(o=JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences)),"true"===("use_cached_job|use_cached_job_checkbox"in o&&o["use_cached_job|use_cached_job_checkbox"])&&i.inputs.push({label:"BETA: Attempt to re-use jobs with identical parameters ?",help:"This may skip executing jobs that you have already run",name:"use_cached_job",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["No",!1],["Yes",!0]]})},submit:function(e,t){var i=this,s={tool_id:e.id,tool_version:e.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(s))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(t&&t());if(e.action!==Galaxy.root+"tool_runner/index"){var o=n("").attr({action:e.action,method:e.method,enctype:e.enctype});return a.each(s.inputs,function(e,t){o.append(n("").attr({name:t,value:e}))}),o.hide().appendTo("body").submit().remove(),void(t&&t())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",s),d.default.request({type:"POST",url:Galaxy.root+"api/tools",data:s,success:function(e){if(t&&t(),i.$el.children().hide(),i.$el.append(i._templateSuccess(e)),e.jobs&&e.jobs.length>0){i.$el.append(n("",{id:"webhook-view"}));new g.default.WebhookView({type:"tool",toolId:s.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(e){t&&t(),Galaxy.emit.debug("tool-form::submit","Submission failed.",e);var n=!1;if(e&&e.err_data){var a=i.form.data.matchResponse(e.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:(0,r.default)("Job submission failed"),body:i._templateError(s,e&&e.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(e){var t=this,i=e.inputs,n=-1,a=null;for(var s in i){var o=i[s],r=this.form.data.match(s),l=this.form.field_list[r],d=this.form.input_list[r];if(r&&d&&l){if(!d.optional&&null==o)return this.form.highlight(r),!1;if(l.validate){var c=function(){t.form.trigger("reset")},u=l.validate(c);if(!u.valid)return this.form.highlight(r,u.message),!1}if(o&&o.batch){var h=o.values.length,f=h>0&&o.values[0]&&o.values[0].src;if(f)if(null===a)a=f;else if(a!==f)return this.form.highlight(r,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===n)n=h;else if(n!==h)return this.form.highlight(r,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+h+" selection(s) while a previous field contains "+n+"."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(e){if(e.jobs&&e.jobs.length>0){var t=e.jobs.length,i=1==t?"1 job has":t+" jobs have",s=n("").addClass("donemessagelarge").append(n("").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(e.outputs,function(e){s.append(n("").addClass("messagerow").append(n("").text(e.hid+": "+e.name)))}),s.append(n("").append("").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),s}return this._templateError(e,"Invalid success response. No jobs found.")},_templateError:function(e,t){return n("").addClass("errormessagelarge").append(n("").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. 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t=l.defaults(t||{},{title:"",url:"",target:"_parent",noscratchbook:!1}),t.url=this._formatUrl(t.url),e("").addClass("dropdown-item").attr("href",t.url).attr("target",t.target).html(t.title).on("click",function(e){e.preventDefault(),i.model.set("show_menu",!1),t.onclick?t.onclick():Galaxy.frame.add(t)})},buildLink:function(t,i){return e("").append(e("").attr("href",Galaxy.root+i).html(t)).html()},_toggleClick:function(t){var i=this,n=this.model;t.preventDefault(),e(".tooltip").hide(),n.trigger("dispatch",function(e){n.id!==e.id&&e.get("menu")&&e.set("show_menu",!1)}),n.get("disabled")?(this.$link.popover&&this.$link.popover("dispose"),this.$link.popover({html:!0,placement:"bottom",content:"Please "+this.buildLink("login","user/login?use_panels=True")+" or "+this.buildLink("register","user/create?use_panels=True")+" to use this 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s=i(9),o=a(s),r=i(1),l=a(r),d=i(77),c=n(d),u=i(14),h=n(u),f=i(15),p=n(f),_=i(61),m=n(_),g=i(3),v=n(g);t.default=o.View.extend({initialize:function(e){var t=this;e=e||{},this.frames=new c.default.View({visible:!1}),this.setElement(this.frames.$el),this.buttonActive=e.collection.add({id:"enable-scratchbook",icon:"fa-th",tooltip:(0,v.default)("Enable/Disable Scratchbook"),onclick:function(){t.active=!t.active,t.buttonActive.set({toggle:t.active,show_note:t.active,note_cls:t.active&&"fa fa-check"}),t.active||t.frames.hide()},onbeforeunload:function(){if(t.frames.length()>0)return"You opened "+t.frames.length()+" frame(s) which will be lost."}}),this.buttonLoad=e.collection.add({id:"show-scratchbook",icon:"fa-eye",tooltip:(0,v.default)("Show/Hide Scratchbook"),show_note:!0,visible:!1,onclick:function(e){t.frames.visible?t.frames.hide():t.frames.show()}}),this.frames.on("add 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a=n.dataset_ids,s=a.indexOf(e.get("id"));if(-1!==s&&s+i>=0&&s+it.top+t.height-1||e.top+e.height-1t[1]?1:0}),d.each(s,function(e){a._framePlace(e[0],n)}),this.top_max=0,d.each(this.frame_list,function(e){null!==e.grid_location&&(a.top_max=Math.max(a.top_max,e.grid_location.top+e.grid_location.height))}),this.top_max=e(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(e,t){e.grid_location=null;for(var i=this._toGrid(this._frameScreen(e)),n=!1,a=0;a
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");this.tiles_div.prepend(e("").html(l).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}r=("Squish"===this.mode?5:10)+"px",e(this.tiles_div).find(".sample").css({"font-size":r,"line-height":r}),e(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var se=function(e,t,i){ne.call(this,e,t,i),this.painter=C.default.ReadPainter,this.update_icons()};I(se.prototype,R.prototype,K.prototype,ne.prototype,{build_config_params:function(){return h.union(R.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:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var oe={CompositeTrack:Z,DrawableGroup:V,DiagonalHeatmapTrack:ie,FeatureTrack:ne,LineTrack:te,ReadTrack:se,VariantTrack:ae,VcfTrack:ae},re=function(e,t,i){if("copy"in e)return e.copy(i);var n=e.obj_type;return n||(n=e.track_type),new oe[n](t,i,e)};t.default={TracksterView:H,DrawableGroup:V,LineTrack:te,FeatureTrack:ne,DiagonalHeatmapTrack:ie,ReadTrack:se,VariantTrack:ae,CompositeTrack:Z,object_from_template:re}}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(5),d=s(l),c=i(10),u=s(c),h=i(17),f=s(h),p=i(55),_=s(p),m=i(25),g=s(m),v=e.View.extend({initialize:function(e){var t=this;this.modal=parent.Galaxy.modal||new f.default.View,this.form=new _.default(d.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(e,i){var a=i.model.attributes,s="",o={},l=a.job_id;l?s=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(s=Galaxy.root+"api/tools/"+a.id+"/build",o=n.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),a.version&&(o.tool_version=a.version),d.default.get({url:s,data:o,success:function(n){if(!n.display)return void(window.location=Galaxy.root);i.model.set(n),t._customize(i),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",n),e.resolve()},error:function(t,s){var o=t&&t.err_msg||"Uncaught error.";401==s?window.location=Galaxy.root+"user/login?"+n.param({redirect:Galaxy.root+"?tool_id="+a.id}):i.$el.is(":empty")?i.$el.prepend(new u.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:(0,r.default)("Tool request failed"),body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",t),e.reject()}})},postchange:function(e,t){var i={tool_id:t.model.get("id"),tool_version:t.model.get("version"),inputs:n.extend(!0,{},t.data.create())};t.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),d.default.request({type:"POST",url:Galaxy.root+"api/tools/"+t.model.get("id")+"/build",data:i,success:function(i){t.update(i),t.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",t),e.reject()}})}},e)),this.deferred=this.form.deferred,this.setElement(""),this.$el.append(this.form.$el)},_customize:function(e){var t=this,i=e.model.attributes,n=new u.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:(0,r.default)("Execute"),cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),e.portlet.disable(),t.submit(i,function(){n.unwait(),e.portlet.enable()})}});if(i.buttons={execute:n},i.job_id&&i.job_remap){if("job_produced_collection_elements"===i.job_remap)var a="Replace elements in collection ?",s="The previous run of this tool failed. Use this option to replace the failed element(s) in the dataset collectio that were produced during the previous tool run.";else var a="Resume dependencies from this job ?",s="The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.";i.inputs.push({label:a,name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:s})}var o={};Galaxy.user.attributes.preferences&&"extra_user_preferences"in Galaxy.user.attributes.preferences&&(o=JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences)),"true"===("use_cached_job|use_cached_job_checkbox"in o&&o["use_cached_job|use_cached_job_checkbox"])&&i.inputs.push({label:"BETA: Attempt to re-use jobs with identical parameters ?",help:"This may skip executing jobs that you have already run",name:"use_cached_job",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["No",!1],["Yes",!0]]})},submit:function(e,t){var i=this,s={tool_id:e.id,tool_version:e.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(s))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(t&&t());if(e.action!==Galaxy.root+"tool_runner/index"){var o=n("").attr({action:e.action,method:e.method,enctype:e.enctype});return a.each(s.inputs,function(e,t){o.append(n("").attr({name:t,value:e}))}),o.hide().appendTo("body").submit().remove(),void(t&&t())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",s),d.default.request({type:"POST",url:Galaxy.root+"api/tools",data:s,success:function(e){if(t&&t(),i.$el.children().hide(),i.$el.append(i._templateSuccess(e)),e.jobs&&e.jobs.length>0){i.$el.append(n("",{id:"webhook-view"}));new g.default.WebhookView({type:"tool",toolId:s.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(e){t&&t(),Galaxy.emit.debug("tool-form::submit","Submission failed.",e);var n=!1;if(e&&e.err_data){var a=i.form.data.matchResponse(e.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:(0,r.default)("Job submission failed"),body:i._templateError(s,e&&e.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(e){var t=this,i=e.inputs,n=-1,a=null;for(var s in i){var o=i[s],r=this.form.data.match(s),l=this.form.field_list[r],d=this.form.input_list[r];if(r&&d&&l){if(!d.optional&&null==o)return this.form.highlight(r),!1;if(l.validate){var c=function(){t.form.trigger("reset")},u=l.validate(c);if(!u.valid)return this.form.highlight(r,u.message),!1}if(o&&o.batch){var h=o.values.length,f=h>0&&o.values[0]&&o.values[0].src;if(f)if(null===a)a=f;else if(a!==f)return this.form.highlight(r,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===n)n=h;else if(n!==h)return this.form.highlight(r,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+h+" selection(s) while a previous field contains "+n+"."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(e){if(e.jobs&&e.jobs.length>0){var t=e.jobs.length,i=1==t?"1 job has":t+" jobs have",s=n("").addClass("donemessagelarge").append(n("").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(e.outputs,function(e){s.append(n("").addClass("messagerow").append(n("").text(e.hid+": "+e.name)))}),s.append(n("").append("").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),s}return this._templateError(e,"Invalid success response. No jobs found.")},_templateError:function(e,t){return n("").addClass("errormessagelarge").append(n("").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(t||""))).append(n("").text(JSON.stringify(e,null,4)))}});t.default={View:v}}).call(t,i(2),i(0),i(1))},,,function(e,t,i){"use strict";function n(e){i(88)}Object.defineProperty(t,"__esModule",{value:!0});var a=i(43),s=i.n(a);for(var o in a)"default"!==o&&function(e){i.d(t,e,function(){return a[e]})}(o);var r=i(136),l=i(23),d=n,c=Object(l.a)(s.a,r.a,r.b,!1,d,null,null);t.default=c.exports},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(6),l=o(r),d=i(3),c=(o(d),e.View.extend(l.default.LoggableMixin).extend({_logNamespace:"list",initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=n(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):n(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",a.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=n(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?s.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}})),u=c.extend(l.default.mixin(l.default.SelectableViewMixin,l.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){c.prototype.initialize.call(this,e),l.default.SelectableViewMixin.initialize.call(this,e),l.default.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=c.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return c.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=n(''),i=e.model.toJSON();return a.each(e.templates.warnings,function(a){t.append(n(a(i,e)))}),t},_renderTitleBar:function(){return n(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){return!e||"keydown"!==e.type||32!==e.keyCode&&13!==e.keyCode||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){return"ListItemView("+(this.model?""+this.model:"(no model)")+")"}}));u.prototype.templates=function(){return{el:l.default.wrapTemplate(['
','','
"]),warnings:{},titleBar:l.default.wrapTemplate(['','',"
",'','','',"','','
"],"element"),subtitle:l.default.wrapTemplate(['']),details:l.default.wrapTemplate([''])}}();var h=u.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,u.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return n();var e=u.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e);return new t(a.extend(i,{model:e}))},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});h.prototype.templates=function(){var e=l.default.wrapTemplate(['','<%- element.name %>',"
",'',"',"
"],"collection");return a.extend({},u.prototype.templates,{details:e})}(),t.default={ExpandableView:c,ListItemView:u,FoldoutListItemView:h}}).call(t,i(2),i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(6),o=a(s),r=i(3),l=a(r),d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",select_width:"100%",events:{},initialize:function(e){this.show_editor=!1,!1===e.usePrompt?this.label="":this.label='",this.workflow_mode=e.workflow_mode||!1,this.workflow_mode&&(this.events.click="showEditor",this.events.keydown="keydownHandler"),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.workflow_mode?this.$el.html(this._workflowTemplate()):this.$el.html(this._defaultTemplate()),this.$input().select2({placeholder:"Add tags",width:this.workflow_mode?this.width:this.select_width,tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_hashToName:function(e){return e.startsWith("#")?"name:"+e.slice(1):e},_nameToHash:function(e){return e.startsWith("name:")&&(e="#"+e.slice(5)),e},_defaultTemplate:function(){return[this.label,this._renderEditor()].join("")},_workflowTemplate:function(){return[this.show_editor?this._renderEditor():this._renderTags()].join(" ")},keydownHandler:function(e){switch(e.which){case 27:this.hideEditor()}},showEditor:function(){this.show_editor=!0,this.render()},hideEditor:function(){this.show_editor=!1,this.render()},_renderEditor:function(){return''},_renderTags:function(){var e=this.model.get("tags"),t=Galaxy.root+"static/images/fugue/tag--plus.png",i=[];return n.each(e,function(e){e=0==e.indexOf("name:")?e.slice(5):e;var t=''+e+"";i.push(t)}),0===i.length&&i.push("| '+this.grid_header(e)+' | \n\n | \n |
| \n | \n | \n |
'+e.info_text+"
"),t},grid_table:function(){return'\n '},grid_header:function(e){var t='';if(!e.embedded){var i="";e.title_id&&(i+=' id="'+e.title_id+'"'),t+=""+e.title+""}if(e.global_actions){t+='
"},header:function(e){var t="- ';var n=e.global_actions.length>=3;n&&(t+='
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- '+d.label+" "}}catch(e){s=!0,o=e}finally{try{!a&&l.return&&l.return()}finally{if(s)throw o}}n&&(t+="
');var a=!0,s=!1,o=void 0;try{for(var r,l=e.global_actions[Symbol.iterator]();!(a=(r=l.next()).done);a=!0){var d=r.value;t+='
"),t+="':p.attach_popup&&g?i+='
\n \n \n
':p.attach_popup?i+='":i+=g?''+v+"":"",i+="'+o.escape(e.message)+'
'},grid_filters:function(e){var t=e.default_filter_dict,i=e.filters,n="none";e.advanced_search&&(n="block");var a=!1,s=!0,o=!1,r=void 0;try{for(var l,d=e.columns[Symbol.iterator]();!(s=(l=d.next()).done);s=!0){var c=l.value;if("advanced"==c.filterable){var u=c.key,h=i[u],f=t[u];h&&f&&h!=f&&(n="block"),a=!0}}}catch(e){o=!0,r=e}finally{try{!s&&d.return&&d.return()}finally{if(o)throw r}}var p="block";"block"==n&&(p="none");var _='| ",a&&(_+='Advanced Search'),_+=" |
| Close Advanced Search |
','','","
"].join("")},_templateUsage:function(e){return['','
"].join("")},toString:function(){return"UserQuotaMeter("+this.model+")"}});t.default={UserQuotaMeter:f}}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(17),r=s(o),l=i(156),d=s(l),c=i(3),u=s(c),h={defaultName:e.template("Copy of '<%- name %>'"),title:e.template((0,u.default)("Copying history")+' "<%- name %>"'),submitLabel:(0,u.default)("Copy"),errorMessage:(0,u.default)("History could not be copied."),progressive:(0,u.default)("Copying history"),activeLabel:(0,u.default)("Copy only the active, non-deleted datasets"),allLabel:(0,u.default)("Copy all datasets including deleted ones"),anonWarning:(0,u.default)("As an anonymous user, unless you login or register, you will lose your current history ")+(0,u.default)("after copying this history. "),_template:e.template(["<% if( isAnon ){ %>",'',e.nice_total_disk_usage?(0,h.default)("Using ")+e.nice_total_disk_usage:"","
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","<% } %>",""].join("")),_showAjaxIndicator:function(){var e=''+this.progressive+"...
";this.modal.$(".modal-body").empty().append(e).css({"margin-top":"8px"})},dialog:function(t,i,s){function o(){var e=t.$("#copy-modal-title").val();if(!e)return void t.$(".invalid-title").show();var n="copy-all"===t.$('input[name="copy-what"]:checked').val();t.$("button").prop("disabled",!0),r._showAjaxIndicator(),i.copy(!0,e,n).done(function(e){l.resolve(e)}).fail(function(t,a,s){var o={name:e,copyAllDatasets:n};d.default.ajaxErrorModal(i,t,o,r.errorMessage),l.rejectWith(l,arguments)}).done(function(){_&&t.hide()})}s=s||{};var r=this,l=n.Deferred(),c=s.nameFn||this.defaultName,h=c({name:i.get("name")}),f=s.allDatasets?"copy-all":"copy-non-deleted",p=!!e.isUndefined(s.allowAll)||s.allowAll,_=!!e.isUndefined(s.autoClose)||s.autoClose;this.modal=t;var m=s.closing_callback;return t.show(e.extend(s,{title:this.title({name:i.get("name")}),body:a(r._template({name:h,isAnon:Galaxy.user.isAnonymous(),allowAll:p,copyWhat:f,activeLabel:this.activeLabel,allLabel:this.allLabel,anonWarning:this.anonWarning})),buttons:e.object([[(0,u.default)("Cancel"),function(){t.hide()}],[this.submitLabel,o]]),height:"auto",closing_events:!0,closing_callback:function(e){e&&l.reject({cancelled:!0}),m&&m(e)}})),t.$("#copy-modal-title").focus().select(),t.$("#copy-modal-title").on("keydown",function(e){13===e.keyCode&&(e.preventDefault(),o())}),l}},f=e.extend({},h,{defaultName:e.template("imported: <%- name %>"),title:e.template((0,u.default)("Importing history")+' "<%- name %>"'),submitLabel:(0,u.default)("Import"),errorMessage:(0,u.default)("History could not be imported."),progressive:(0,u.default)("Importing history"),activeLabel:(0,u.default)("Import only the active, non-deleted datasets"),allLabel:(0,u.default)("Import all datasets including deleted ones"),anonWarning:(0,u.default)("As an anonymous user, unless you login or register, you will lose your current history ")+(0,u.default)("after importing this history. ")}),p=function(e,t){t=t||{};var i=window.parent.Galaxy.modal||new r.default.View({});return t.useImport?f.dialog(i,e,t):h.dialog(i,e,t)};t.default=p}).call(t,i(1),i(0),i(0))},function(e,t,i){"use strict";(function(e){function n(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(57),o=a(s),r=i(175),l=a(r),d=i(5),c=a(d),u=i(6),h=a(u),f=i(3),p=a(f),_=i(1),m=n(_),g=i(2),v=n(g),w=v.Model.extend(h.default.LoggableMixin).extend(h.default.mixin(h.default.SearchableModelMixin,{_logNamespace:"history",UPDATE_DELAY:4e3,defaults:{model_class:"History",id:null,name:"Unnamed 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t+=this.contents.includeDeleted?e.deleted:0,t+=this.contents.includeHidden?e.hidden:0},nice_size:function(){var e=this.get("size");return e?c.default.bytesToString(e,!0,2):(0,p.default)("(empty)")},toJSON:function(){return m.extend(v.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(e){return"nice_size"===e?this.nice_size():v.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var e=this.get("non_ready_jobs");return e?e.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var t=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:e.param({keys:t.join(",")})})},refresh:function(e){var t=this;e=e||{};var i=this.lastUpdateTime;return this.contents.allFetched=!1,(0!==this.contents.currentPage?function(){return t.contents.fetchPage(t.contents.currentPage)}:function(){return t.contents.fetchUpdated(i)})().done(function(i,n,a){var s;try{s=new Date(a.getResponseHeader("Date"))}catch(e){console.error(e)}t.lastUpdateTime=s||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){var t=this;e=e||{};var i=this.UPDATE_DELAY;if(this.id){var n=function(){t.clearUpdateTimeout(),t.updateTimeoutId=setTimeout(function(){t.refresh(e)},i)};this.numOfUnfinishedShownContents()>0?n():this._fetchContentRelatedAttributes().done(function(e){t.numOfUnfinishedJobs()>0?n():t.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},stopPolling:function(){this.clearUpdateTimeout(),this.contents&&this.contents.stopPolling()},parse:function(e,t){var i=v.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},fetchWithContents:function(e,t){e=e||{};var i=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return i.contents.history=i,i.contents.setHistoryId(e.id),i.fetchContents(t)})},fetchContents:function(e){return e=e||{},this.lastUpdateTime=new Date,this.contents.fetchCurrentPage(e)},_delete:function(t){return this.get("deleted")?e.when():this.save({deleted:!0},t)},purge:function(t){return this.get("purged")?e.when():this.save({deleted:!0,purged:!0},t)},undelete:function(t){return this.get("deleted")?this.save({deleted:!1},t):e.when()},copy:function(t,i,n){if(t=void 0===t||t,!this.id)throw new Error("You must set the history ID before copying it.");var a={history_id:this.id};t&&(a.current=!0),i&&(a.name=i),n||(a.all_datasets=!1),a.view="dev-detailed";var s=this,o=e.post(this.urlRoot,a);return t?o.then(function(e){return new w(e).setAsCurrent().done(function(){s.trigger("copied",s,e)})}):o.done(function(e){s.trigger("copied",s,e)})},setAsCurrent:function(){var t=this,i=e.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return i.done(function(){t.trigger("set-as-current",t)}),i},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),y=l.default.InfinitelyScrollingCollection,b=y.extend(h.default.LoggableMixin).extend({_logNamespace:"history",model:w,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),this.urlRoot=Galaxy.root+"api/histories",y.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new w(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return m.extend(y.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=y.prototype._buildFetchFilters.call(this,e)||{},i={};return!0!==this.includeDeleted?(i.deleted=!1,i.purged=!1):i.deleted=null,m.defaults(t,i)},fetchFirst:function(t){var i=this,n=e.when();return this.currentHistoryId&&(n=y.prototype.fetchFirst.call(this,{silent:!0,limit:1,filters:{"encoded_id-in":this.currentHistoryId,deleted:null,purged:""}})),n.then(function(){return t=t||{},t.offset=0,i.fetchMore(t)})},comparators:m.extend(m.clone(y.prototype.comparators),{name:h.default.buildComparator("name",{ascending:!0}),"name-dsc":h.default.buildComparator("name",{ascending:!1}),size:h.default.buildComparator("size",{ascending:!1}),"size-asc":h.default.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,i=this.remove(this.get(this.currentHistoryId));return y.prototype.sort.call(this,m.defaults({silent:!0},e)),this.unshift(i,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(t,i,n,a){var s=this;return e.getJSON(Galaxy.root+"history/create_new_current").done(function(e){s.setCurrent(new w(e,[],n||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});t.default={History:w,HistoryCollection:b}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(196),s=n(a),o=i(197),r=n(o),l=i(6),d=n(l),c=i(3),u=(n(c),s.default.DatasetAssociation),h=r.default.HistoryContentMixin,f=u.extend(d.default.mixin(h,{defaults:e.extend({},u.prototype.defaults,h.defaults,{history_content_type:"dataset",model_class:"HistoryDatasetAssociation"})}));t.default={HistoryDatasetAssociation:f}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(67),r=s(o),l=i(58),d=s(l),c=i(6),u=s(c),h=i(3),f=s(h),p=r.default.FoldoutListItemView,_=r.default.ListItemView,m=p.extend({className:p.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(e){this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,p.prototype.initialize.call(this,e)},_setUpListeners:function(){p.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(t,i){e.has(t.changed,"deleted")?this.render():e.has(t.changed,"element_count")&&this.$("> .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var t=p.prototype._getFoldoutPanelOptions.call(this);return e.extend(t,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){return"DCListItemView("+(this.model?""+this.model:"(no model)")+")"}});m.prototype.templates=function(){var t=e.extend({},p.prototype.templates.warnings,{error:u.default.wrapTemplate(["<% if( model.error ){ %>",'',(0,f.default)("There was an error getting the data for this collection"),": <%- model.error %>","
","<% } %>"]),purged:u.default.wrapTemplate(["<% if( model.purged ){ %>",'',(0,f.default)("This collection has been deleted and removed from disk"),"
","<% } %>"]),deleted:u.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'',(0,f.default)("This collection has been deleted"),"
","<% } %>"])}),i=u.default.wrapTemplate(['','
"],"collection"),n=u.default.wrapTemplate(['','<%- collection.element_identifier || collection.name %>',"
",'',"','<% var countText = collection.element_count? ( collection.element_count + " " ) : ""; %>','<% if( collection.collection_type === "list" ){ %>',(0,f.default)("a list of <%- countText %>datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',(0,f.default)("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',(0,f.default)("a list of <%- countText %>dataset pairs"),'<% } else if( collection.collection_type === "list:list" ){ %>',(0,f.default)("a list of <%- countText %>dataset lists"),"<% } %>","
"],"collection");return e.extend({},p.prototype.templates,{warnings:t,titleBar:i,subtitle:n})}();var g=_.extend({className:_.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DCEListItemView.initialize:",e),_.prototype.initialize.call(this,e)},toString:function(){return"DCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});g.prototype.templates=function(){var t=u.default.wrapTemplate(['','
"],"element");return e.extend({},_.prototype.templates,{titleBar:t})}();var v=d.default.DatasetListItemView.extend({className:d.default.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DatasetDCEListItemView.initialize:",e),d.default.DatasetListItemView.prototype.initialize.call(this,e)},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):a.when()},toString:function(){return"DatasetDCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});v.prototype.templates=function(){var t=u.default.wrapTemplate(['','<%- element.element_identifier %>',"
",'',"','','
"],"element");return e.extend({},d.default.DatasetListItemView.prototype.templates,{titleBar:t})}();var w=m.extend({className:m.prototype.className+" dataset-collection-element",_swapNewRender:function(e){m.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){return"NestedDCDCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});t.default={DCListItemView:m,DCEListItemView:g,DatasetDCEListItemView:v,NestedDCDCEListItemView:w}}).call(t,i(1),i(0),i(0))},,,,,,,,,,function(e,t,i){"use strict";(function(e,n){function a(t,i,n){return Galaxy.modal.show({title:i,body:t,closing_events:!0,buttons:{Ok:function(){Galaxy.modal.hide()}}}),Galaxy.modal.$el.addClass("error-modal"),n&&(Galaxy.modal.$(".error-details").add(Galaxy.modal.$('button:contains("Details")')).remove(),e("").addClass("error-details").hide().appendTo(Galaxy.modal.$(".modal-content")).append([e("").text(p),e("").text(JSON.stringify(n,null," "))]),e('").appendTo(Galaxy.modal.$(".buttons")).click(function(){Galaxy.modal.$(".error-details").toggle()})),Galaxy.modal}function s(e,t,i){if(e){if(e=(0,u.default)(e),t=(0,u.default)(t)||(0,u.default)("Error:"),window.Galaxy&&Galaxy.modal)return a(e,t,i);alert(t+"\n\n"+e),console.log("error details:",JSON.stringify(i))}}function o(){return s((0,u.default)("You appear to be offline. Please check your connection and try again."),(0,u.default)("Offline?"))}function r(){return s((0,u.default)("Galaxy is currently unreachable. Please try again in a few minutes.")+" "+h,(0,u.default)("Cannot connect to Galaxy"))}function l(e,t,i,n,a){return n=n||f,n+=" "+h,a=a||(0,u.default)("An error occurred"),s(n,a,d(e,t,i))}function d(e,t,i){return{raven:n.result(window.Raven,"lastEventId"),userAgent:navigator.userAgent,onLine:navigator.onLine,version:n.result(Galaxy.config,"version_major"),xhr:n.omit(t,n.functions(t)),options:n.omit(i,"xhr"),url:n.result(Galaxy.lastAjax,"url"),data:n.result(Galaxy.lastAjax,"data"),model:n.result(e,"toJSON",""+e),user:n.omit(n.result(Galaxy.user,"toJSON"),"email")}}Object.defineProperty(t,"__esModule",{value:!0});var c=i(3),u=function(e){return e&&e.__esModule?e:{default:e}}(c),h=(0,u.default)("Please contact a Galaxy administrator if the problem persists."),f=(0,u.default)("An error occurred while updating information with the server."),p=(0,u.default)("The following information can assist the developers in finding the source of the error:");t.default={errorModal:s,offlineErrorModal:o,badGatewayErrorModal:r,ajaxErrorModal:l}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function a(t){e("#toggle-deleted").modeButton({initialMode:t.initialModeDeleted,modes:[{mode:"showing_deleted",html:(0,l.default)("Exclude deleted")},{mode:"not_showing_deleted",html:(0,l.default)("Include deleted")}]}),e("#toggle-hidden").modeButton({initialMode:t.initialModeHidden,modes:[{mode:"showing_hidden",html:(0,l.default)("Exclude hidden")},{mode:"not_showing_hidden",html:(0,l.default)("Include hidden")}]}),e("#switch").click(function(){var e=Galaxy.currHistoryPanel||window.top.Galaxy&&window.top.Galaxy.currHistoryPanel?window.top.Galaxy.currHistoryPanel:null;e?e.switchToHistory("${ history[ 'id' ] }"):window.location="${ switch_to_url }"}),t.hasMasthead&&e("#center").addClass("flex-vertical-container");var i=t.userIsOwner?T.default.HistoryViewEdit:O.HistoryView,n=new h.default.History(t.historyJSON);e("#import").click(function(){(0,$.default)(n,{useImport:!0,allDatasets:"showing_deleted"===e("#toggle-deleted").modeButton("getMode").mode}).done(function(){window===window.parent?window.location=Galaxy.root:Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.loadCurrentHistory()})});var a=new i({el:e("#history-"+t.historyJSON.id),className:i.prototype.className+" wide",$scrollContainer:t.hasMasthead?function(){return this.$el.parent()}:void 0,model:n,show_deleted:t.showDeletedJson,show_hidden:t.showHiddenJson,purgeAllowed:t.allow_user_dataset_purge});a.trigger("loading"),n.fetchContents({silent:!0}).fail(function(){alert("Galaxy history failed to load")}).done(function(){a.trigger("loading-done"),a.render()}),e("#toggle-deleted").on("click",function(){a.toggleShowDeleted()}),e("#toggle-hidden").on("click",function(){a.toggleShowHidden()})}Object.defineProperty(t,"__esModule",{value:!0}),t.historyEntry=a;var s=i(1),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=i(3),l=n(r),d=i(158),c=n(d),u=i(144),h=n(u),f=i(57),p=n(f),_=i(160),m=n(_),g=i(161),v=n(g),w=i(156),y=n(w),b=i(52),x=n(b),k=i(6),C=n(k),S=i(176),T=n(S),M=i(143),$=n(M);i(159),i(218);var P=c.default.ModelListPanel,O=P.extend({_logNamespace:"history",HDAViewClass:m.default.HDAListItemView,HDCAViewClass:v.default.HDCAListItemView,collectionClass:p.default.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:P.prototype.className+" history-panel",emptyMsg:(0,l.default)("This history is empty"),noneFoundMsg:(0,l.default)("No matching datasets found"),searchPlaceholder:(0,l.default)("search datasets"),initialize:function(e){P.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_createDefaultCollection:function(){return new this.collectionClass([],{history:this.model})},freeModel:function(){return P.prototype.freeModel.call(this),this.model&&this.model.stopPolling(),this},_setUpListeners:function(){P.prototype._setUpListeners.call(this),this.on({error:function(e,t,i,n,a){this.errorHandler(e,t,i,n,a)},"views:ready view:attached view:removed":function(e){this._renderSelectButton()},"view:attached":function(e){this.scrollTo(0)}})},loadHistory:function(e,t,i){var n=this;return i=o.extend(i||{silent:!0}),this.info("loadHistory:",e,t,i),this.setModel(new h.default.History({id:e})),i.silent=!0,this.trigger("loading"),this.model.fetchWithContents(t,i).always(function(){n.render(),n.trigger("loading-done")})},refreshContents:function(t){return this.model?this.model.refresh(t):e.when()},_setUpCollectionListeners:function(){return P.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"fetching-more":function(){this._toggleContentsLoadingIndicator(!0),this.$emptyMessage().hide()},"fetching-more-done":function(){this._toggleContentsLoadingIndicator(!1)}})},_showLoadingIndicator:function(t,i,n){var a=e('');this.$el.html(a.text(t).slideDown(o.isUndefined(i)?this.fxSpeed:i))},_hideLoadingIndicator:function(t){this.$(".loading-indicator").slideUp(o.isUndefined(t)?this.fxSpeed+200:t,function(){e(this).remove()})},_buildNewRender:function(){var e=P.prototype._buildNewRender.call(this);return this._renderSelectButton(e),e},_renderSelectButton:function(e){if(e=e||this.$el,!this.multiselectActions().length)return null;if(!this.views.length)return this.hideSelectors(),e.find(".controls .actions .show-selectors-btn").remove(),null;var t=e.find(".controls .actions .show-selectors-btn");return t.length?t:(0,x.default)({title:(0,l.default)("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o",tooltipConfig:{placement:"top"}}).prependTo(e.find(".controls .actions"))},_renderEmptyMessage:function(t){var i=this.$emptyMessage(t);return this.model.get("contents_active").active<=0?i.empty().append(this.emptyMsg).show():this.searchFor&&this.model.contents.haveSearchDetails()&&!this.views.length?i.empty().append(this.noneFoundMsg).show():(i.hide(),e())},$scrollContainer:function(e){return this.$list(e)},_toggleContentsLoadingIndicator:function(e){e?this.$list().html('','<%- element.element_identifier %>',"
","'):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(t){t=t||this.$el;var i=this.$list(t);e(".tooltip").remove(),i.empty(),this.views=[];var n=this._filterCollection();return n.length?(this._renderPagination(t),this.views=this._renderSomeItems(n,i)):t.find("> .controls .list-pagination").empty(),this._renderEmptyMessage(t).toggle(!n.length),this.trigger("views:ready",this.views),this.views},_renderPagination:function(e){var t=e.find("> .controls .list-pagination");return this.searchFor||!this.model.contents.shouldPaginate()?t.empty():(t.html(this.templates.pagination({current:this.model.contents.currentPage+1,last:this.model.contents.getLastPage()+1},this)),t.find("select.pages").tooltip(),t)},_renderSomeItems:function(e,t){var i=this,n=[];return t.append(e.map(function(e){var t=i._createItemView(e);return n.push(t),i._renderItemView$el(t)})),n},_filterItem:function(e){var t=this.model.contents;return(t.includeHidden||!e.hidden())&&(t.includeDeleted||!e.isDeletedOrPurged())&&P.prototype._filterItem.call(this,e)},_getItemViewClass:function(e){var t=e.get("history_content_type");switch(t){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+t)},_getItemViewOptions:function(e){var t=P.prototype._getItemViewOptions.call(this,e);return o.extend(t,{linkTarget:this.linkTarget,expanded:this.model.contents.storage.isExpanded(e.id),hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(e){var t=this;return P.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{expanded:function(e){t.model.contents.storage.addExpanded(e.model)},collapsed:function(e){t.model.contents.storage.removeExpanded(e.model)}})},collapseAll:function(){this.model.contents.storage.clearExpanded(),P.prototype.collapseAll.call(this)},getSelectedModels:function(){var e=P.prototype.getSelectedModels.call(this);return e.historyId=this.collection.historyId,e},events:o.extend(o.clone(P.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click > .controls .prev":"_clickPrevPage","click > .controls .next":"_clickNextPage","change > .controls .pages":"_changePageSelect","click .messages [class$=message]":"clearMessages"}),_clickPrevPage:function(e){this.model.stopPolling(),this.model.contents.fetchPrevPage()},_clickNextPage:function(e){this.model.stopPolling(),this.model.contents.fetchNextPage()},_changePageSelect:function(t){this.model.stopPolling();var i=e(t.currentTarget).val();this.model.contents.fetchPage(i)},toggleShowDeleted:function(e,t){e=void 0!==e?e:!this.model.contents.includeDeleted;var i=this.model.contents;return i.setIncludeDeleted(e,t),this.trigger("show-deleted",e),i.fetchCurrentPage({renderAll:!0}),e},toggleShowHidden:function(e,t,i){e=void 0!==e?e:!this.model.contents.includeHidden;var n=this.model.contents;return n.setIncludeHidden(e,i),this.trigger("show-hidden",e),n.fetchCurrentPage({renderAll:!0}),e},_firstSearch:function(e){var t=this;if(this.log("onFirstSearch",e),this.model.contents.haveSearchDetails())return void this.searchItems(e);this.$("> .controls .search-input").searchInput("toggle-loading"),this.searchFor=e,this.model.contents.progressivelyFetchDetails({silent:!0}).progress(function(e,i,n){t.renderItems(),t.trigger("search:loading-progress",i,n)}).always(function(){t.$el.find("> .controls .search-input").searchInput("toggle-loading")}).done(function(){t.searchItems(e,"force")})},clearSearch:function(e){var t=this;return this.searchFor?(this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.model.contents.fetchCurrentPage({silent:!0}).done(function(){t.renderItems()}),this):this},errorHandler:function(e,t,i){if(!t||0!==t.status||0!==t.readyState){if(this.error(e,t,i),o.isString(e)&&o.isString(t)){var n=e,a=t;return y.default.errorModal(n,a,i)}return t&&502===t.status?y.default.badGatewayErrorModal():y.default.ajaxErrorModal(e,t,i)}},clearMessages:function(t){return(o.isUndefined(t)?this.$messages().children('[class$="message"]'):e(t.currentTarget)).fadeOut(this.fxSpeed,function(){e(this).remove()}),this},scrollToHid:function(e){return this.scrollToItem(o.first(this.viewsWhereModel({hid:e})))},ordinalIndicator:function(e){var t=""+e;switch(t.charAt(t.length-1)){case"1":return t+"st";case"2":return t+"nd";case"3":return t+"rd";default:return t+"th"}},toString:function(){return"HistoryView("+(this.model?this.model.get("name"):"")+")"}});O.prototype.templates=function(){var e=function(){return'
\n \n
'},t=C.default.wrapTemplate(['','
"],"history"),i=C.default.wrapTemplate(['','",''],"pages");return o.extend(o.clone(P.prototype.templates),{el:e,controls:t,pagination:i})}(),t.default={HistoryView:O,historyEntry:a}}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(67),r=s(o),l=i(34),d=s(l),c=i(6),u=s(c),h=i(3),f=s(h);i(159);var p=e.View.extend(u.default.LoggableMixin).extend({_logNamespace:"list",viewClass:r.default.ListItemView,collectionClass:e.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:(0,f.default)("This list is empty"),noneFoundMsg:(0,f.default)("No matching items found"),searchPlaceholder:(0,f.default)("search"),initialize:function(e,t){e=e||{},e.logger&&(this.logger=e.logger),this.log(this+".initialize:",e),this.fxSpeed=n.has(e,"fxSpeed")?e.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=e.searchFor||"",this.selecting=void 0===e.selecting||e.selecting,this.selected=e.selected||[],this.lastSelected=null,this.dragItems=e.dragItems||!1,this.viewClass=e.viewClass||this.viewClass,this.views=[],this.collection=e.collection||this._createDefaultCollection(),this.filters=e.filters||[],this.$scrollContainer=e.$scrollContainer||this.$scrollContainer,this.title=e.title||"",this.subtitle=e.subtitle||"",this._setUpListeners()},_setUpListeners:function(){return this.off(),this.on({error:function(e,t,i,n,a){console.error(e,t,i,n,a)},loading:function(){this._showLoadingIndicator("loading...",40)},"loading-done":function(){this._hideLoadingIndicator(40)}}),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_createDefaultCollection:function(){return new this.collectionClass([])},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.stopListening(this.collection),this.listenTo(this.collection,{error:function(e,t,i,n,a){this.trigger("error",e,t,i,n,a)},update:function(e,t){var i=t.changes;return t.renderAll||i.added.length+i.removed.length>1?this.renderItems():1===i.added.length?this.addItemView(n.first(i.added),e,t):1===i.removed.length?this.removeItemView(n.first(i.removed),e,t):void 0}}),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on({"view:selected":function(e,t){if(t&&t.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);i&&this.selectRange(e,i)}else t&&t.altKey&&!this.selecting&&this.showSelectors();this.selected.push(e.model.id),this.lastSelected=e.model.id},"view:de-selected":function(e,t){this.selected=n.without(this.selected,e.model.id)}})},render:function(e){this.log(this+".render",e);var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var e=a(this.templates.el({},this));return this._renderControls(e),this._renderTitle(e),this._renderSubtitle(e),this._renderSearch(e),this.renderItems(e),e},_renderControls:function(e){this.debug(this+"(ListPanel)._renderControls");var t=a(this.templates.controls({},this));return e.find(".controls").replaceWith(t),t},_renderTitle:function(e){},_renderSubtitle:function(e){},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),a(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",this.className).append(e.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(e){return e=e||this.$el,this.$controls(e).find("[title]").tooltip(),this._renderMultiselectActionMenu(e),this},_renderMultiselectActionMenu:function(e){e=e||this.$el;var t=e.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return t.empty();var n=a(['','
",'','<%- history.name %>
',"<%- history.nice_size %>
','','',"<% if( history.deleted && history.purged ){ %>",'
",'','','',(0,l.default)("This history has been purged and deleted"),"
","<% } else if( history.deleted ){ %>",'',(0,l.default)("This history has been deleted"),"
","<% } else if( history.purged ){ %>",'',(0,l.default)("This history has been purged"),"
","<% } %>","<% if( history.message ){ %>",'messagesmall">',"<%= history.message.text %>","
","<% } %>","','',"
",'','
",'',"','",'","
",'',"
","','",'
"].join("")),s=i.map(function(e){var t=['- ',"
",'','','',"
"]),controls:u.default.wrapTemplate(['','
"])}}();var _=p.extend({modelCollectionKey:"contents",initialize:function(e){p.prototype.initialize.call(this,e),this.selecting=void 0!==e.selecting&&e.selecting,this.setModel(this.model,e)},setModel:function(e,t){if(t=t||{},this.debug(this+".setModel:",e,t),this.freeModel(),this.freeViews(),e){var i=this.model?this.model.get("id"):null;this.model=e,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.stopListening(this.collection),this.collection=this.model[this.modelCollectionKey]||t.collection||this._createDefaultCollection(),this._setUpCollectionListeners(),i&&e.get("id")!==i&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.listenTo(this.model,"error",function(){var e=Array.prototype.slice.call(arguments,0);e.unshift("error"),this.trigger.apply(this,e)},this),this.logger&&this.listenTo(this.model,"all",function(e){this.info(this+"(model)",e,arguments)}),this},_renderControls:function(e){this.debug(this+"(ModelListPanel)._renderControls");var t=this.model?this.model.toJSON():{},i=a(this.templates.controls(t,this));return e.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});_.prototype.templates=function(){var e=u.default.wrapTemplate(['','
",'<%- view.title %>
',"<%- view.subtitle %>
','','','','',"
",'','
","','",'","
",'',"
","','
"]);return n.extend(n.clone(p.prototype.templates),{controls:e})}(),t.default={ListPanel:p,ModelListPanel:_}}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";function n(e,t){function i(e){o(this).parent().children("input").val("").trigger("searchInput.clear").blur(),t.onclear()}function n(e,n){if(!n)return i();o(this).trigger("search.search",n),"function"==typeof t.onfirstsearch&&u?(u=!1,t.onfirstsearch(n)):t.onsearch(n)}function a(){return['"].join("")}var l=27,d=13,c=o(e),u=!0,h={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(e){},minSearchLen:0,escWillClear:!0,oninit:function(){}};return"string"===s.default.type(t)?("toggle-loading"===t&&function(){c.find(".search-loading").toggle(),c.find(".search-clear").toggle()}(),c):("object"===s.default.type(t)&&(t=s.default.extend(!0,{},h,t)),c.addClass("search-input").prepend([function(){return o(a()).focus(function(e){o(this).select()}).keyup(function(e){if(e.preventDefault(),e.stopPropagation(),e.which===l&&t.escWillClear)i.call(this,e);else{var a=o(this).val();(e.which===d||t.minSearchLen&&a.length>=t.minSearchLen)&&n.call(this,e,a)}}).val(t.initialVal)}(),function(){return o([''].join("")).tooltip({placement:"bottom"}).click(function(e){i.call(this,e)})}(),function(){return o([''].join("")).hide().tooltip({placement:"bottom"})}()]))}var a=i(0),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=s.default,r=window._l||function(e){return e};s.default.fn.extend({searchInput:function(e){return this.each(function(){return n(this,e)})}})},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(58),s=n(a),o=i(6),r=n(o),l=i(177),d=n(l),c=i(3),u=n(c),h=s.default.DatasetListItemView,f=h.extend({className:h.prototype.className+" history-content",initialize:function(e,t){h.prototype.initialize.call(this,e,t)},toString:function(){return"HDAListItemView("+(this.model?""+this.model:"(no model)")+")"}});f.prototype.templates=function(){var t=function(t){return'\n ','
",'<%- model.name %>
',"<%- view.subtitle %>
','','','','',"
",'','
","','",'","
",'',"
","\n \n
\n "},i=e.extend({},h.prototype.templates.warnings,{hidden:r.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'\n '+t.hid+'\n '+e.escape(t.name)+"\n
\n \n "+d.default.nametagTemplate(t)+"\n ',(0,u.default)("This dataset has been hidden"),"
","<% } %>"],"dataset")});return e.extend({},h.prototype.templates,{titleBar:t,warnings:i})}(),t.default={HDAListItemView:f}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(37),s=n(a),o=i(146),r=n(o),l=i(178),d=n(l),c=i(6),u=(n(c),i(177)),h=n(u),f=i(3),p=n(f),_=r.default.DCListItemView,m=_.extend({className:_.prototype.className+" history-content",_setUpListeners:function(){var e=this;_.prototype._setUpListeners.call(this);var t=function(t,i){e.render()};this.model.jobStatesSummary&&this.listenTo(this.model.jobStatesSummary,"change",t),this.listenTo(this.model,{"change:tags change:visible change:state":t})},_getFoldoutPanelClass:function(){return d.default.CollectionView},_swapNewRender:function(e){_.prototype._swapNewRender.call(this,e);var t,i=this.model.jobStatesSummary;t=i?i.new()?"loading":i.errored()?"error":i.terminal()?"ok":i.running()?"running":"queued":this.model.get("job_source_id")?"loading":this.model.get("populated_state")?s.default.OK:s.default.RUNNING,this.$el.addClass("state-"+t);var n=this.stateDescription();return this.$(".state-description").html(n),this.$el},stateDescription:function(){var e=this.model,t=(e.get("element_count"),e.get("job_source_type")),i=(this.model.get("collection_type"),d.default.collectionTypeDescription(e)),n=d.default.collectionDescription(e),a=e.jobStatesSummary;if(t&&"Job"!=t){if(a&&a.hasDetails()){var s=a.new(),o=s?null:a.jobCount();if(s)return'\n \n Creating jobs...\n
\n
';if(a.errored()){return"a "+i+" with "+a.numInError()+" / "+o+" jobs in error"}if(a.terminal())return n;var r=a.states().running||0,l=a.states().ok||0,c=l/(1*o),u=r/(1*o),h=1-c-u;return'\n \n '+(o&&o>1?o+" jobs":"a job")+" generating a "+i+'\n \n \n
\n
'}return'\n \n Loading job data for '+i+'...\n .controls .deleted-count").html(""+(0,A.default)("loading...")+"")},"fetching-hidden":function(e){this.$("> .controls .hidden-count").html(""+(0,A.default)("loading...")+"")},"fetching-deleted-done fetching-hidden-done":this._renderCounts}),this},_buildNewRender:function(){var e=D.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.user&&Galaxy.user.id&&Galaxy.user.id===this.model.get("user_id")&&(this._renderTags(e),this._renderAnnotation(e)),e):e},updateHistoryDiskSize:function(){this.$(".history-size").text(this.model.get("nice_size"))},renderItems:function(e){var t=D.prototype.renderItems.call(this,e);return this.searchFor?this._renderSearchFindings(e):this._renderCounts(e),t},_renderCounts:function(t){t=t instanceof e?t:this.$el;var i=this.templates.counts(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i)},_renderTags:function(e){var t=this;this.tagsEditor=new g.default.TagsEditor({model:this.model,el:e.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDATagEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDATagEditors(!1,t.fxSpeed)},$activator:(0,M.default)({title:(0,A.default)("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags",tooltipConfig:{placement:"top"}}).appendTo(e.find(".controls .actions"))})},_renderAnnotation:function(e){var t=this;this.annotationEditor=new w.default.AnnotationEditor({model:this.model,el:e.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDAAnnotationEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDAAnnotationEditors(!1,t.fxSpeed)},$activator:(0,M.default)({title:(0,A.default)("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment",tooltipConfig:{placement:"top"}}).appendTo(e.find(".controls .actions"))})},_setUpBehaviors:function(e){if(e=e||this.$el,D.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.model.get("user_id")){var t=this;e.find("> .controls .name").attr("title",(0,A.default)("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var i=t.model.get("name");e&&e!==i?(t.$el.find("> .controls .name").text(e),t.model.save({name:e}).fail(function(){t.$el.find("> .controls .name").text(t.model.previous("name"))})):t.$el.find("> .controls .name").text(i)}})}},multiselectActions:function(){var e=this,t=[{html:(0,A.default)("Hide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.hide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,A.default)("Unhide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.unhide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,A.default)("Delete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.delete;e.getSelectedModels().ajaxQueue(t)}},{html:(0,A.default)("Undelete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.undelete;e.getSelectedModels().ajaxQueue(t)}}];return e.purgeAllowed&&t.push({html:(0,A.default)("Permanently delete datasets"),func:function(){if(confirm((0,A.default)("This will permanently remove the data in your datasets. Are you sure?"))){var t=u.default.HistoryDatasetAssociation.prototype.purge,i=e.getSelectedModels(),n=i.filter(function(e){return"dataset"==e.get("history_content_type")});i.ajaxQueue(t,{},n)}}}),t=t.concat(e._collectionActions())},_collectionActions:function(){var e=this;return[{html:(0,A.default)("Build Dataset List"),func:function(){return e.buildCollection("list")}},{html:(0,A.default)("Build Dataset Pair"),func:function(){return e.buildCollection("paired")}},{html:(0,A.default)("Build List of Dataset Pairs"),func:function(){return e.buildCollection("list:paired")}},{html:(0,A.default)("Build Collection from Rules"),func:function(){return e.buildCollection("rules")}}]},buildCollection:function(e,t,i){var n,a=this,t=t||a.getSelectedModels(),i=i||!1;"list"==e?n=b.default.createListCollection:"paired"==e?n=k.default.createPairCollection:"list:paired"==e?n=S.default.createListOfPairsCollection:e.startsWith("rules")?n=b.default.createCollectionViaRules:console.warn("Unknown collectionType encountered "+e),n(t,i).done(function(){a.model.refresh()})},_getItemViewOptions:function(e){var t=D.prototype._getItemViewOptions.call(this,e);return n.extend(t,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),t},_handleItemDeletedChange:function(e){e.get("deleted")?this._handleItemDeletion(e):this._handleItemUndeletion(e),this._renderCounts()},_handleItemDeletion:function(e){var t=this.model.get("contents_active");t.deleted+=1,t.active-=1,this.model.contents.includeDeleted||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUndeletion:function(e){var t=this.model.get("contents_active");t.deleted-=1,this.model.contents.includeDeleted||(t.active-=1),this.model.set("contents_active",t)},_handleItemVisibleChange:function(e){e.hidden()?this._handleItemHidden(e):this._handleItemUnhidden(e),this._renderCounts()},_handleItemHidden:function(e){var t=this.model.get("contents_active");t.hidden+=1,t.active-=1,this.model.contents.includeHidden||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUnhidden:function(e){var t=this.model.get("contents_active");t.hidden-=1,this.model.contents.includeHidden||(t.active-=1),this.model.set("contents_active",t)},toggleHDATagEditors:function(e,t){n.each(this.views,function(i){i.tagsEditor&&i.tagsEditor.toggle(e,t)})},toggleHDAAnnotationEditors:function(e,t){n.each(this.views,function(i){i.annotationEditor&&i.annotationEditor.toggle(e,t)})},events:n.extend(n.clone(D.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(e){this.toggleShowDeleted()},"click .toggle-hidden-link":function(e){this.toggleShowHidden()}}),_renderSearchProgress:function(e,t){var i=e+t;return this.$("> .controls .subtitle").html(["",(0,A.default)("Searching "),i,"/",this.model.contentsShown(),""].join(""))},_renderSearchFindings:function(t){t=t instanceof e?t:this.$el;var i=this.templates.found(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i),this},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var e={dragenter:n.bind(this.dragenter,this),dragover:n.bind(this.dragover,this),dragleave:n.bind(this.dragleave,this),drop:n.bind(this.drop,this)},t=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),t]);for(var i in e)e.hasOwnProperty(i)&&t.on(i,e[i]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),a("").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),a("").addClass("history-drop-target-help").text((0,A.default)("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var e=this.$(".history-drop-target").get(0);for(var t in this._dropHandlers)this._dropHandlers.hasOwnProperty(t)&&e.off(t,this._dropHandlers[t]);return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(e){e.preventDefault(),e.stopPropagation()},dragleave:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(e){e.preventDefault();var t=this,i=e.originalEvent.dataTransfer,n=i.getData("text");i.dropEffect="move";try{n=JSON.parse(n)}catch(e){t.warn("error parsing JSON from drop:",n)}return t.trigger("droptarget:drop",e,n,t),!1},dataDropped:function(t){var i=this;return n.isObject(t)&&"HistoryDatasetAssociation"===t.model_class&&t.id?0!==i.contents.currentPage?i.contents.fetchPage(0).then(function(){return i.model.contents.copy(t.id)}):i.model.contents.copy(t.id):e.when()},toString:function(){return"HistoryViewEdit("+(this.model?this.model.get("name"):"")+")"}});z.prototype.templates=function(){var e=O.default.wrapTemplate(["<% var shown = Math.max( view.views.length, history.contents_active.active ) %>","<% if( shown ){ %>",'',"<%- shown %> ",(0,A.default)("shown"),"","<% } %>","<% if( history.contents_active.deleted ){ %>",'',"<% if( view.model.contents.includeDeleted ){ %>",'',(0,A.default)("hide deleted"),"","<% } else { %>","<%- history.contents_active.deleted %> ",'',(0,A.default)("deleted"),"","<% } %>","","<% } %>","<% if( history.contents_active.hidden ){ %>",'',"<% if( view.model.contents.includeHidden ){ %>",'',(0,A.default)("hide hidden"),"","<% } else { %>","<%- history.contents_active.hidden %> ",'',(0,A.default)("hidden"),"","<% } %>","","<% } %>"],"history"),t=O.default.wrapTemplate([(0,A.default)("Found")," <%- view.views.length %>, ","<% if( history.contents_active.deleted ){ %>","<% if( view.model.contents.includeDeleted ){ %>",'',(0,A.default)("hide deleted"),", ","<% } else { %>",'',(0,A.default)("show deleted"),", ","<% } %>","<% } %>","<% if( history.contents_active.hidden ){ %>","<% if( view.model.contents.includeHidden ){ %>",'',(0,A.default)("hide hidden"),"","<% } else { %>",'',(0,A.default)("show hidden"),"","<% } %>","<% } %>"],"history");return n.extend(n.clone(D.prototype.templates),{counts:e,found:t})}(),t.default={HistoryViewEdit:z}}).call(t,i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e){function i(t){return''+e.escape(t.slice(5))+""}function n(t){var n=e.filter(e.uniq(t.tags),function(e){return 0===e.indexOf("name:")}),a=e.sortBy(n).map(i);return'\n
","=c?r.push(e.createPair.call(this,{listA:n,indexA:s,listB:a,indexB:o.index})):s+=1,!n.length||!a.length)return r}return this.debug("paired:",JSON.stringify(r,null," ")),this.debug("autopair _strategy ---------------------------"),r}}function l(e,t){var i=e.toJSON();return b(i,{historyId:e.historyId,defaultHideSourceItems:t})}Object.defineProperty(t,"__esModule",{value:!0});var d=i(222),c=o(d),u=i(199),h=o(u),f=i(198),p=o(f),_=i(6),m=o(_),g=i(3),v=o(g);i(211);var w=e.View.extend(m.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"dataset paired",initialize:function(e){this.pair=e.pair||{}},template:n.template(['<%- pair.forward.name %>','','<%- pair.name %>',"",'<%- pair.reverse.name %>'].join("")),render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container").get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this},events:{dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(e){e.currentTarget.style.opacity="0.4",e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(e){e.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"PairView("+this.pair.name+")"}}),y=e.View.extend(m.default.LoggableMixin).extend(p.default.CollectionCreatorMixin).extend({_logNamespace:"collections",className:"list-of-pairs-collection-creator collection-creator flex-row-container",initialize:function(e){this.metric("PairedCollectionCreator.initialize",e),e=n.defaults(e,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:!0,strategy:"lcs",matchPercentage:.9,twoPassAutopairing:!0}),this.initialList=e.datasets,this.historyId=e.historyId,this.filters=this.commonFilters[e.filters]||this.commonFilters[this.DEFAULT_FILTERS],n.isArray(e.filters)&&(this.filters=e.filters),this.automaticallyPair=e.automaticallyPair,this.strategy=this.strategies[e.strategy]||this.strategies[this.DEFAULT_STRATEGY],n.isFunction(e.strategy)&&(this.strategy=e.strategy),this.matchPercentage=e.matchPercentage,this.twoPassAutopairing=e.twoPassAutopairing,this.removeExtensions=!0,this.oncancel=e.oncancel,this.oncreate=e.oncreate,this.autoscrollDist=e.autoscrollDist||24,this.unpairedPanelHidden=!1,this.pairedPanelHidden=!1,this.$dragging=null,this.blocking=!1,this._setUpCommonSettings(e),this._setUpBehaviors(),this._dataSetUp()},commonFilters:{illumina:["_1","_2"],Rs:["_R1","_R2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[],this.unpaired=[],this.selectedIds=[],this._sortInitialList(),this._ensureIds(),this.unpaired=this.initialList.slice(0),this.automaticallyPair&&(this.autoPair(),this.once("rendered:initial",function(){this.trigger("autopair")}))},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(e){return e.sort(function(e,t){return(0,h.default)(e.name,t.name)}),e},_ensureIds:function(){return this.initialList.forEach(function(e){e.hasOwnProperty("id")||(e.id=n.uniqueId())}),this.initialList},_splitByFilters:function(){function e(e,t){return t.test(e.name)}var t=this.filters.map(function(e){return new RegExp(e)}),i=[[],[]];return this.unpaired.forEach(function(n){t.forEach(function(t,a){e(n,t)&&i[a].push(n)})}),i},_addToUnpaired:function(e){var t=this;this.unpaired.splice(function i(n,a){if(n===a)return n;var s=Math.floor((a-n)/2)+n,o=(0,h.default)(e.name,t.unpaired[s].name);if(o<0)return i(n,s);if(o>0)return i(s+1,a);for(;t.unpaired[s]&&t.unpaired[s].name===e.name;)s++;return s}(0,this.unpaired.length),0,e)},autoPair:function(e){var t=this._splitByFilters(),i=[];return this.twoPassAutopairing&&(i=this.autopairSimple({listA:t[0],listB:t[1]}),t=this._splitByFilters()),e=e||this.strategy,t=this._splitByFilters(),i=i.concat(this[e].call(this,{listA:t[0],listB:t[1]}))},autopairSimple:r({scoreThreshold:function(){return.6},match:function(e){return e=e||{},e.matchTo===e.possible?{index:e.index,score:1}:e.bestMatch}}),autopairLevenshtein:r({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=(0,c.default)(e.matchTo,e.possible),i=1-t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),autopairLCS:r({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=this._naiveStartingAndEndingLCS(e.matchTo,e.possible).length,i=t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),_naiveStartingAndEndingLCS:function(e,t){for(var i="",n="",a=0,s=0;a=0&&s>=0&&e[a]===t[s];)n=[e[a],n].join(""),a-=1,s-=1;return i+n},_pair:function(e,t,i){i=i||{},this.debug("_pair:",e,t);var a=this._createPair(e,t,i.name);return this.paired.push(a),this.unpaired=n.without(this.unpaired,e,t),i.silent||this.trigger("pair:new",a),a},_createPair:function(e,t,i){if(!e||!t||e===t)throw new Error("Bad pairing: "+[JSON.stringify(e),JSON.stringify(t)]);return i=i||this._guessNameForPair(e,t),{forward:e,name:i,reverse:t}},_guessNameForPair:function(e,t,i){i=void 0!==i?i:this.removeExtensions;var n=e.name,a=t.name,s=this._naiveStartingAndEndingLCS(n.replace(new RegExp(this.filters[0]),""),a.replace(new RegExp(this.filters[1]),""));if(i){var o=s.lastIndexOf(".");if(o>0){var r=s.slice(o,s.length);s=s.replace(r,""),n=n.replace(r,""),a=a.replace(r,"")}}return s||n+" & "+a},_unpair:function(e,t){if(t=t||{},!e)throw new Error("Bad pair: "+JSON.stringify(e));return 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i=e.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(e){this.clear().set(this.defaults).set(e)}}),n=e.Collection.extend({model:i});t.default={Model:i,Collection:n}}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function n(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}Object.defineProperty(t,"__esModule",{value:!0});var a=i(1),s=n(a),o=i(2),r=n(o),l=i(6),d=function(e){return e&&e.__esModule?e:{default:e}}(l),c=r.Collection.extend({initialize:function(e,t){r.Collection.prototype.initialize.call(this,e,t),this.setOrder(t.order||this.order,{silent:!0})},_setUpListeners:function(){return this.on({"changed-order":this.sort})},fetch:function(e){return e=this._buildFetchOptions(e),Galaxy.debug("fetch options:",e),r.Collection.prototype.fetch.call(this,e)},_buildFetchOptions:function(e){e=s.clone(e)||{},e.traditional=!0,e.data=e.data||this._buildFetchData(e),Galaxy.debug("data:",e.data);var t=this._buildFetchFilters(e);return Galaxy.debug("filters:",t),s.isEmpty(t)||s.extend(e.data,this._fetchFiltersToAjaxData(t)),Galaxy.debug("data:",e.data),e},_buildFetchData:function(e){var t={};return this.order&&(t.order=this.order),s.defaults(s.pick(e,this._fetchParams),t)},_fetchParams:["order","limit","offset","view","keys"],_buildFetchFilters:function(e){return s.clone(e.filters||{})},_fetchFiltersToAjaxData:function(e){var t={q:[],qv:[]};return s.each(e,function(e,i){void 0!==e&&""!==e&&(!0===e&&(e="True"),!1===e&&(e="False"),null===e&&(e="None"),t.q.push(i),t.qv.push(e))}),t},reset:function(e,t){return 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this.getLastPage()+1},getPageLimitOffset:function(e){return e=this.constrainPageNum(e),{limit:this.limitPerPage,offset:e*this.limitPerPage}},constrainPageNum:function(e){return Math.max(0,Math.min(e,this.getLastPage()))},fetchPage:function(e,t){var i=this;return e=i.constrainPageNum(e),i.currentPage=e,t=s.defaults(t||{},i.getPageLimitOffset(e)),i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")})},fetchCurrentPage:function(e){return this.fetchPage(this.currentPage,e)},fetchPrevPage:function(e){return this.fetchPage(this.currentPage-1,e)},fetchNextPage:function(e){return this.fetchPage(this.currentPage+1,e)}}),h=c.extend({limitOnFirstFetch:null,limitPerFetch:100,initialize:function(e,t){c.prototype.initialize.call(this,e,t),this.limitOnFirstFetch=t.limitOnFirstFetch||this.limitOnFirstFetch,this.limitPerFetch=t.limitPerFetch||this.limitPerFetch,this.allFetched=!1,this.lastFetched=t.lastFetched||0},_buildFetchOptions:function(e){return e.remove=e.remove||!1,c.prototype._buildFetchOptions.call(this,e)},fetchFirst:function(e){return Galaxy.debug("ControlledFetchCollection.fetchFirst:",e),e=e?s.clone(e):{},this.allFetched=!1,this.lastFetched=0,this.fetchMore(s.defaults(e,{reset:!0,limit:this.limitOnFirstFetch}))},fetchMore:function(t){Galaxy.debug("ControlledFetchCollection.fetchMore:",t),t=s.clone(t||{});var i=this;if(Galaxy.debug("fetchMore, options.reset:",t.reset),!t.reset&&i.allFetched)return e.when();t.reset?t.offset=0:void 0===t.offset&&(t.offset=i.lastFetched);var n=t.limit=t.limit||i.limitPerFetch||null;return Galaxy.debug("fetchMore, limit:",n,"offset:",t.offset),i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")}).done(function(e){var t=s.isArray(e)?e.length:0;i.lastFetched+=t,Galaxy.debug("fetchMore, lastFetched:",i.lastFetched),(!n||t\n '+a.join("")+"\n
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\n '+(e.escape(t.name)||e.escape(t.element_identifier))+'
\n \n '+n+'\n
\n \n
\n \n \n \n \n \n
\n ',(0,h.default)("This dataset has been hidden"),'
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';t.name&&t.help?(a+="Tool help for "+t.name+"
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Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0===this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0===this.counter.running&&this.counter.announce>0,n=0===this.counter.running,a=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[n?"enable":"disable"](),this.btnFtp[n?"enable":"disable"](),this.btnCreate[n?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[a?"show":"hide"](),this.$(".upload-helper")[a?"hide":"show"]()},_eventAnnounce:function(e,t){this.counter.announce++;var i=new h.default.Model({id:e,file_name:t.name,file_size:t.size,file_mode:t.mode||"local",file_path:t.path,file_data:t});this.render(),this.collection.add(i)},_eventProgress:function(e,t){var i=this.collection.get(e);i.set({percentage:t,status:"running",info:""}),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"success"}),this.ui_button.model.set("percentage",this._uploadPercentage(100,i.get("file_size"))),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.success++,this.render(),Galaxy.currHistoryPanel.refreshContents()},_eventWarning:function(e,t){this.collection.get(e).set({status:"warning",info:t})},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this.render()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this.render()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this.render()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new m.default({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){return e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(0!==this.counter.announce&&0===this.counter.running){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this._uploadFtp(),this.uploadbox.start({id:Galaxy.user.id,chunk_upload_size:this.app.options.chunk_upload_size}),this.render()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),e(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){0===this.counter.running&&(this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this.render())},_changeExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},_changeGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_uploadFtp:function(){var t=this,i=[];this.collection.each(function(e){"queued"==e.get("status")&&"ftp"==e.get("file_mode")&&(t.uploadbox.remove(e.id),i.push(e))}),i.length>0&&e.uploadpost({data:this.app.toData(i),url:this.app.options.upload_path,success:function(e){l.each(i,function(e){t._eventSuccess(e.id)})},error:function(e){l.each(i,function(i){t._eventError(i.id,e)})}})},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_template:function(){return'\n
\n \n \n \n \n \n '+(0,d.default)("Search did not match any tools.")+'\n \n \n
\n \n \n '+(0,d.default)("Workflows")+'\n \n
\n \n \n
\n \n
'}})}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(5),d=s(l),c=i(174),u=(s(c),i(213)),h=s(u),f=i(64),p=s(f),_=i(189),m=s(_),g=i(39),v=s(g);t.default=e.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",warning:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this,s=this;this.app=e,this.list_extensions=e.list_extensions,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$settings=this.$(".upload-settings"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new p.default.View({title:(0,r.default)("Upload configuration"),container:this.$(".upload-settings"),placement:"bottom"});var o=this.app.select_genome.value(),l=this.app.select_extension.value();this.select_genome=new v.default.View({css:"upload-genome",data:s.app.list_genomes,container:this.$(".upload-genome"),value:o,onchange:function(e){s.model.set("genome",e)}}),this.select_extension=new v.default.View({css:"upload-extension",data:n.filter(this.list_extensions,function(e){return!e.composite_files}),container:this.$(".upload-extension"),value:l,onchange:function(e){s.model.set("extension",e)}}),this.model.set({genome:o,extension:l}),this.$symbol.on("click",function(){s._removeRow()}),this.$(".upload-extension-info").on("click",function(e){var t=i.upload_extension;t?t.extension_popup.visible?t.extension_popup.hide():(t.extension_popup.remove(),i._makeUploadExtensionsPopover(e)):i._makeUploadExtensionsPopover(e)}).on("mousedown",function(e){e.preventDefault()}),this.$settings.on("click",function(e){s._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.$text_content.on("change input",function(e){s.model.set({url_paste:a(e.target).val(),file_size:a(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){s._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){s._refreshStatus()}),this.listenTo(this.model,"change:info",function(){s._refreshInfo()}),this.listenTo(this.model,"change:genome",function(){s._refreshGenome()}),this.listenTo(this.model,"change:extension",function(){s._refreshExtension()}),this.listenTo(this.model,"change:file_size",function(){s._refreshFileSize()})},render:function(){this._refreshType(),this._refreshPercentage(),this._refreshStatus(),this._refreshInfo(),this._refreshGenome(),this._refreshExtension(),this._refreshFileSize()},remove:function(){this.select_genome.remove(),this.select_extension.remove(),e.View.prototype.remove.apply(this)},_refreshType:function(){var e=this.model.attributes;this.$title.html(n.escape(e.file_name)),this.$size.html(d.default.bytesToString(e.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==e.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==e.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==e.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("Warning: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),t?(this.select_genome.enable(),this.select_extension.enable()):(this.select_genome.disable(),this.select_extension.disable()),this.$info_progress.show(),this.$el.removeClass().addClass("upload-row"),"success"==e?(this.$el.addClass("table-success"),this.$percentage.html("100%")):"error"==e?(this.$el.addClass("table-danger"),this.$info_progress.hide()):"warning"==e&&(this.$el.addClass("table-warning"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(d.default.bytesToString(this.model.get("file_size")))},_removeRow:function(){-1!==["init","success","error"].indexOf(this.model.get("status"))&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new h.default(this).$el),this.settings.show())},_makeUploadExtensionsPopover:function(e){this.upload_extension=new m.default({$el:a(e.target),title:this.select_extension.text(),extension:this.select_extension.value(),list:this.list_extensions})},_template:function(e){return'\n \n
\n \n \n \n
\n
\n \n Drop files here\n
\n | Name | \nSize | \nType | \nGenome | \nSettings | \nStatus | \n\n |
|---|
\n Type (set all):\n \n \n Genome (set all):\n \n
\n \n You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
| Description | Name | Size | Settings | Status |
|---|
Composite Type: Genome/Build:
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
Drop files here
| Name | Size | Status |
|---|
Collection Type:File Type: Genome (set all):
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
\n
\n '}})}).call(t,i(2),i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(10),s=n(a),o=i(655),r=n(o),l=i(656),d=n(l),c=i(3),u=n(c),h=e.View.extend({initialize:function(t,i){var n=this;this.userIsAnonymous=Galaxy.user.isAnonymous(),this.allow_user_dataset_purge=i.config.allow_user_dataset_purge,this.root=i.root,this.historyView=new d.default.CurrentHistoryView({className:d.default.CurrentHistoryView.prototype.className+" middle",purgeAllowed:this.allow_user_dataset_purge,linkTarget:"galaxy_main"}),Galaxy.currHistoryPanel=this.historyView,Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),this.buttonRefresh=new s.default.ButtonLink({id:"history-refresh-button",title:(0,u.default)("Refresh history"),cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){n.historyView.loadCurrentHistory()}}),this.buttonOptions=new s.default.ButtonLink({id:"history-options-button",title:(0,u.default)("History options"),cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:this.root+"root/history_options"}),this.buttonViewMulti=new s.default.ButtonLink({id:"history-view-multi-button",title:(0,u.default)("View all histories"),cls:"panel-header-button",icon:"fa fa-columns",href:this.root+"history/view_multiple"}),this.model=new e.Model({cls:"history-right-panel",title:(0,u.default)("History"),buttons:[this.buttonRefresh,this.buttonOptions,this.buttonViewMulti]}),this.setElement(this._template()),this.historyView.setElement(this.$el),this.historyView.connectToQuotaMeter(Galaxy.quotaMeter),this.historyView.loadCurrentHistory(),Galaxy.listenTo(this.historyView,"history-size-change",function(){Galaxy.user.fetch({url:Galaxy.user.urlRoot()+"/"+(Galaxy.user.id||"current")})})},render:function(){this.optionsMenu=(0,r.default)(this.buttonOptions.$el,{anonymous:this.userIsAnonymous,purgeAllowed:this.allow_user_dataset_purge,root:this.root}),this.buttonViewMulti.$el[this.userIsAnonymous?"hide":"show"]()},_template:function(e){return[''].join("")},toString:function(){return"historyPanel"}});t.default=h}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function a(e,t,i){return o.clone(_).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target=n.target||"galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}Object.defineProperty(t,"__esModule",{value:!0});var s=i(1),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=i(3),l=n(r),d=i(41),c=n(d),u=i(143),h=n(u),f=i(25),p=n(f),_=[{html:(0,l.default)("History Lists"),header:!0},{html:(0,l.default)("Saved Histories"),href:"histories/list",target:"_top"},{html:(0,l.default)("Histories Shared with Me"),href:"histories/list_shared",target:"_top"},{html:(0,l.default)("Current History"),header:!0,anon:!0},{html:(0,l.default)("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:(0,l.default)("Copy History"),func:function(){(0,h.default)(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Share or Publish"),href:"history/sharing"},{html:(0,l.default)("Show Structure"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/show_structure")}},{html:(0,l.default)("Extract Workflow"),href:"workflow/build_from_current_history"},{html:(0,l.default)("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really delete the current history?"))&&Galaxy.currHistoryPanel.model._delete().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really delete the current history permanently? This cannot be undone."))&&Galaxy.currHistoryPanel.model.purge().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Dataset Actions"),header:!0,anon:!0},{html:(0,l.default)("Copy Datasets"),href:"dataset/copy_datasets"},{html:(0,l.default)("Dataset Security"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/permissions?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,l.default)("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:(0,l.default)("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:(0,l.default)("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really unhide all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really delete all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Purge Deleted Datasets"),confirm:(0,l.default)("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:(0,l.default)("Downloads"),header:!0},{html:(0,l.default)("Export Tool Citations"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/citations?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,l.default)("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:(0,l.default)("Other Actions"),header:!0},{html:(0,l.default)("Import from File"),href:"histories/import",target:"_top"}];p.default.load({type:"history-menu",async:!1,callback:function(t){var i=[];t.each(function(e){var t=e.toJSON();t.activate&&i.push({html:(0,l.default)(t.config.title),anon:!0})}),i.length>0&&(i.unshift({html:(0,l.default)("Webhooks"),header:!0}),e.merge(_,i))}});var m=function(e,t){t=t||{};var i=void 0===t.anonymous||t.anonymous,n=t.purgeAllowed||!1,s=a(i,n,Galaxy.root);return new c.default(e,s)};t.default=m}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(144),r=(s(o),i(176)),l=s(r),d=i(6),c=s(d),u=i(3),h=s(u),f=c.default.SessionStorageModel.extend({defaults:{tagsEditorShown:!1,annotationEditorShown:!1,scrollPosition:0},toString:function(){return"HistoryViewPrefs("+JSON.stringify(this.toJSON())+")"}});f.storageKey=function(){return"history-panel"};var p=l.default.HistoryViewEdit,_=p.extend({className:p.prototype.className+" current-history-panel",HDCAViewClass:p.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),emptyMsg:[(0,h.default)("This history is empty"),". ",(0,h.default)("You can "),'',(0,h.default)("load your own data"),"",(0,h.default)(" or "),'',(0,h.default)("get data from an external source"),""].join(""),initialize:function(t){t=t||{},this.preferences=new f(e.extend({id:f.storageKey()},e.pick(t,e.keys(f.prototype.defaults)))),p.prototype.initialize.call(this,t),this.panelStack=[],this.currentContentId=t.currentContentId||null},_setUpListeners:function(){p.prototype._setUpListeners.call(this);var e=this;this.on("new-model",function(){e.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(){return this.loadHistory(null,{url:Galaxy.root+"history/current_history_json"})},switchToHistory:function(e,t){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to switch histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(e,{url:Galaxy.root+"history/set_as_current?id="+e})},createNewHistory:function(e){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to create histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(null,{url:Galaxy.root+"history/create_new_current"})},setModel:function(e,t,i){return p.prototype.setModel.call(this,e,t,i),this.model&&this.model.id&&(this.log("checking for updates"),this.model.checkForUpdates()),this},_setUpModelListeners:function(){return p.prototype._setUpModelListeners.call(this),this.listenTo(this.model,{"change:nice_size change:size":function(){this.trigger("history-size-change",this,this.model,arguments)},"change:id":function(){this.once("loading-done",function(){this.model.checkForUpdates()})}})},_setUpCollectionListeners:function(){p.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,"state:ready",function(e,t,i){e.get("visible")||this.collection.storage.includeHidden()||this.removeItemView(e)})},_setUpBehaviors:function(t){t=t||this.$el;var i=this;return p.prototype._setUpBehaviors.call(i,t),this._debouncedScrollCaptureHandler||(this._debouncedScrollCaptureHandler=e.debounce(function(){i.$el.is(":visible")&&i.preferences.set("scrollPosition",n(this).scrollTop())},40)),i.$scrollContainer(t).off("scroll",this._debouncedScrollCaptureHandler).on("scroll",this._debouncedScrollCaptureHandler),i},_buildNewRender:function(){if(!this.model)return n();var e=p.prototype._buildNewRender.call(this);return e.find(".search").prependTo(e.find("> .controls")),this._renderQuotaMessage(e),e},_renderQuotaMessage:function(e){return e=e||this.$el,n(this.templates.quotaMsg({},this)).prependTo(e.find(".messages"))},_renderTags:function(e){var t=this;p.prototype._renderTags.call(t,e),t.preferences.get("tagsEditorShown")&&t.tagsEditor.toggle(!0),t.listenTo(t.tagsEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("tagsEditorShown",e.hidden)})},_renderAnnotation:function(e){var t=this;p.prototype._renderAnnotation.call(t,e),t.preferences.get("annotationEditorShown")&&t.annotationEditor.toggle(!0),t.listenTo(t.annotationEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("annotationEditorShown",e.hidden)})},_swapNewRender:function(t){p.prototype._swapNewRender.call(this,t);var i=this;return e.delay(function(){var e=i.preferences.get("scrollPosition");e&&i.scrollTo(e,0)},10),this},_attachItems:function(e){p.prototype._attachItems.call(this,e);var t=this;return t.currentContentId&&t._setCurrentContentById(t.currentContentId),this},addItemView:function(e,t,i){var n=p.prototype.addItemView.call(this,e,t,i);return n&&this.panelStack.length?this._collapseDrilldownPanel():n},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}})},setCurrentContent:function(e){this.$(".history-content.current-content").removeClass("current-content"),e?(e.$el.addClass("current-content"),this.currentContentId=e.model.id):this.currentContentId=null},_setCurrentContentById:function(e){var t=this.viewFromModelId(e)||null;this.setCurrentContent(t)},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$controls().add(this.$list()).hide(),e.parentName=this.model.get("name"),e.delegateEvents().render().$el.appendTo(this.$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.$controls().add(this.$list()).show()},events:e.extend(e.clone(p.prototype.events),{"click .uploader-link":function(e){Galaxy.upload.show(e)},"click .get-data-link":function(e){var t=n(".toolMenuContainer");t.parent().scrollTop(0),t.find('span:contains("Get Data")').click()}}),listenToGalaxy:function(t){this.listenTo(t,{"center-frame:load":function(t){var i=t.fullpath,n=null,a={display:/datasets\/([a-f0-9]+)\/display/,edit:/datasets\/([a-f0-9]+)\/edit/,report_error:/dataset\/errors\?id=([a-f0-9]+)/,rerun:/tool_runner\/rerun\?id=([a-f0-9]+)/,show_params:/datasets\/([a-f0-9]+)\/show_params/};e.find(a,function(t,a){return n=e.result(i.match(t),1)}),this._setCurrentContentById(n?"dataset-"+n:null)},"center-panel:load":function(e){this._setCurrentContentById()}})},connectToQuotaMeter:function(e){return e?(this.listenTo(e,"quota:over",this.showQuotaMessage),this.listenTo(e,"quota:under",this.hideQuotaMessage),this.on("rendered rendered:initial",function(){e&&e.isOverQuota()&&this.showQuotaMessage()}),this):this},clearMessages:function(t){var i=e.isUndefined(t)?this.$messages().children('[class$="message"]'):n(t.currentTarget);return i=i.not(".quota-message"),i.fadeOut(this.fxSpeed,function(){n(this).remove()}),this},showQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")&&e.slideDown(this.fxSpeed)},hideQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")||e.slideUp(this.fxSpeed)},unhideHidden:function(){var e=this;return confirm((0,h.default)("Really unhide all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{visible:!0}).done(function(){e.model.contents.includeHidden||e.renderItems()}):a.when()},deleteHidden:function(){var e=this;return confirm((0,h.default)("Really delete all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{deleted:!0,visible:!0}):a.when()},toString:function(){return"CurrentHistoryView("+(this.model?this.model.get("name"):"")+")"}});_.prototype.templates=function(){var t=c.default.wrapTemplate(['\n
\n \n Tabular source data to extract collection files and metadata from\n
\n\n \n
\n \n \x3c!--\n \n
\n '+(0,o.default)("Upload data as")+':
\n \n \n
\n '+(0,o.default)("Load tabular data from")+':
\n \n \n
\n \n \n \n \n '+(0,o.default)("Select dataset to load")+':
\n \n \n
\n --\x3e\n \n ',(0,h.default)("You are over your disk quota"),". ",(0,h.default)("Tool execution is on hold until your disk usage drops below your allocated quota"),".","
"],"history");return e.extend(e.clone(p.prototype.templates),{quotaMsg:t})}(),t.default={CurrentHistoryView:_}}).call(t,i(1),i(0),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(26),d=(s(l),i(10)),c=s(d),u=i(32),h=s(u),f=e.Model.extend({initialize:function(e){e=e||{},e.user_id=e.user_id||Galaxy.user.id,this.set({user_id:e.user_id,information:{title:(0,r.default)("Manage information"),description:"Edit your email, addresses and custom parameters or change your username.",url:"api/users/"+e.user_id+"/information/inputs",icon:"fa-user",redirect:"user"},password:{title:(0,r.default)("Change password"),description:(0,r.default)("Allows you to change your login credentials."),icon:"fa-unlock-alt",url:"api/users/"+e.user_id+"/password/inputs",submit_title:"Save password",redirect:"user"},communication:{title:(0,r.default)("Change communication settings"),description:(0,r.default)("Enable or disable the communication feature to chat with other users."),url:"api/users/"+e.user_id+"/communication/inputs",icon:"fa-comments-o",redirect:"user"},permissions:{title:(0,r.default)("Set dataset permissions for new histories"),description:"Grant others default access to newly created histories. Changes made here will only affect histories created after these settings have been stored.",url:"api/users/"+e.user_id+"/permissions/inputs",icon:"fa-users",submit_title:"Save permissions",redirect:"user"},api_key:{title:(0,r.default)("Manage API key"),description:(0,r.default)("Access your current API key or create a new one."),url:"api/users/"+e.user_id+"/api_key/inputs",icon:"fa-key",submit_title:"Create a new key",submit_icon:"fa-check"},toolbox_filters:{title:(0,r.default)("Manage Toolbox filters"),description:(0,r.default)("Customize your Toolbox by displaying or omitting sets of Tools."),url:"api/users/"+e.user_id+"/toolbox_filters/inputs",icon:"fa-filter",submit_title:"Save filters",redirect:"user"},openids:{title:(0,r.default)("Manage OpenIDs"),description:(0,r.default)("Associate OpenIDs with your account."),icon:"fa-openid",onclick:function(){window.location.href=Galaxy.root+"openids/list"}},custom_builds:{title:(0,r.default)("Manage custom builds"),description:(0,r.default)("Add or remove custom builds using history datasets."),icon:"fa-cubes",onclick:function(){window.location.href=Galaxy.root+"custom_builds"}},logout:{title:(0,r.default)("Sign out"),description:(0,r.default)("Click here to sign out of all sessions."),icon:"fa-sign-out",onclick:function(){Galaxy.modal.show({title:(0,r.default)("Sign out"),body:"Do you want to continue and sign out of all active sessions?",buttons:{Cancel:function(){Galaxy.modal.hide()},"Sign out":function(){window.location.href=Galaxy.root+"user/logout?session_csrf_token="+Galaxy.session_csrf_token}}})}}})}}),p=e.View.extend({title:(0,r.default)("User Preferences"),active_tab:"user",initialize:function(){this.model=new f,this.setElement(""),this.render()},render:function(){var e=this,t=Galaxy.config;n.getJSON(Galaxy.root+"api/users/"+Galaxy.user.id,function(i){e.$preferences=n("").addClass("ui-panel").append(n("").append("User preferences")).append(n("").append("You are logged in as "+a.escape(i.email)+".")).append(e.$table=n("'+e.description+"
You are using '+e.nice_total_disk_usage+" of disk space in this Galaxy instance. "+(Galaxy.config.enable_quotas?"Your disk quota is: "+e.quota+". ":"")+'Is your usage more than expected? See the documentation for tips on how to find all of the data in your account.
'}});t.default={View:p,Model:f}}).call(t,i(2),i(0),i(1))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),o=a(s),r=i(5),l=(a(r),i(10)),d=a(l),c=i(26),u=a(c),h=i(659),f=a(h),p=e.Collection.extend({comparator:function(e,t){return e=e.get("name"),t=t.get("name"),e>t?1:eLength Format
The length format is two-column, separated by whitespace, of the form:
chrom/contig length of chrom/contig
For example, the first few entries of mm9.len are as follows:
chr1 197195432\nchr2 181748087\nchr3 159599783\nchr4 155630120\nchr5 152537259
Trackster uses this information to populate the select box for chrom/contig, andto set the maximum basepair of the track browser. You may either upload a .len fileof this format (Len File option), or directly enter the information into the box (Len Entry option).
"},_templateFasta:function(){return"FASTA format
This is a multi-fasta file from your current history that provides the genomesequences for each chromosome/contig in your build.
Here is a snippet from an example multi-fasta file:
>chr1\nATTATATATAAGACCACAGAGAGAATATTTTGCCCGG...\n\n>chr2\nGGCGGCCGCGGCGATATAGAACTACTCATTATATATA...\n\n..."}});t.default={View:_}}).call(t,i(2),i(0))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var a=i(5),s=function(e){return e&&e.__esModule?e:{default:e}}(a),o=e.View.extend({initialize:function(e){this.options=s.default.merge(e,{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",selectable:!0,cls_tr:""}),this.setElement(this._template()),this.$thead=this.$("thead"),this.$tbody=this.$("tbody"),this.$tmessage=this.$("tmessage"),this.row=this._row(),this.row_count=0},events:{click:"_onclick",dblclick:"_ondblclick"},addHeader:function(e){this.row.append(n("
"}});t.default={View:o}}).call(t,i(2),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(24),r=s(o),l=i(34),d=s(l),c=e.View.extend({initialize:function(t){var i=this;d.default.markViewAsLoading(this),this.model=new e.Model(t),this.item=this.model.get("item"),this.title=this.model.get("plural"),t&&t.active_tab&&(this.active_tab=t.active_tab),n.ajax({url:Galaxy.root+this.item+"/"+this.model.get("action_id")+"?"+n.param(Galaxy.params),success:function(e){i.model.set(e),i.render()}})},render:function(){var e=new r.default(this.model.attributes);this.$el.empty().append(e.$el),this.$el.append(this._templateShared())},_templateShared:function(){var e=this,t=n("
"),i=this.model.attributes;if(i.shared_by_others&&i.shared_by_others.length>0){var s=n('
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'},_templateHeader:function(){return'"+this.model.get("plural")+" shared with you by others
| Title | Owner |
|---|
\n \n '+c.escape(this.model.get("name"))+'\n \n \n '+this._templateActions()+'\n
\n \n
\n You have no workflows.
'},_templateActionButtons:function(){return''},_templateWorkflowTable:function(){return'| Name | Tags | Owner | # of Steps | Published | Show in tools panel |
|---|
'+(0,v.default)("Your workflows")+"
'+c+"
");var u=d.hidden;u&&(a+=''+u+"
"),e(".delayed-value-datasets_by_state[data-id='"+t+"']").html(a),e(".delayed-value-disk_size[data-id='"+t+"']").html(i.nice_size)},e.ajax(a)}})).forEach(function(e){return t.add(e)}),t.start()},_showCopyDialog:function(e){var t=new f.default.History({id:e});t.fetch().fail(function(){alert("History could not be fetched. Please contact an administrator")}).done(function(){(0,_.default)(t,{}).done(function(){window.parent&&window.parent.Galaxy&&window.parent.Galaxy.currHistoryPanel&&window.parent.Galaxy.currHistoryPanel.loadCurrentHistory(),window.location.reload(!0)})})},add_operation:function(e,t,i){var n=this;"Copy"==t.label&&(t.onclick=function(e){n._showCopyDialog(e)}),u.default.prototype.add_operation.call(this,e,t,i)}}),b=w.View.extend({title:(0,s.default)("Histories"),initialize:function(t){var i=this;g.default.markViewAsLoading(this),"list_published"==t.action_id?this.active_tab="shared":"list"==t.action_id&&(this.active_tab="user"),this.model=new w.Model,d.default.get({url:Galaxy.root+"history/"+t.action_id+"?"+e.param(Galaxy.params),success:function(e){i.model.set(e),i.render()}})},render:function(){var e=new y(this.model.attributes);this.$el.empty().append(e.$el)}});t.default={View:b}}).call(t,i(0))},function(e,t,i){"use strict";function n(e){i(680)}Object.defineProperty(t,"__esModule",{value:!0});var a=i(403),s=i.n(a);for(var o in a)"default"!==o&&function(e){i.d(t,e,function(){return a[e]})}(o);var r=i(682),l=i(23),d=n,c=Object(l.a)(s.a,r.a,r.b,!1,d,null,null);t.default=c.exports},function(e,t,i){var n=i(681);"string"==typeof n&&(n=[[e.i,n,""]]),n.locals&&(e.exports=n.locals);var a=i(38).default;a("67f12bb6",n,!0,{})},function(e,t,i){t=e.exports=i(27)(void 0),t.push([e.i,".ui-show{display:block;margin-top:0}.ui-bold{font-weight:700;margin-bottom:5px}.ui-float-left{float:left;margin-top:10px}",""])},function(e,t,i){"use strict";i.d(t,"a",function(){return n}),i.d(t,"b",function(){return a});var n=function(){var e=this,t=e.$createElement,i=e._self._c||t;return i("div",{staticClass:"ui-thumbnails"},[e.error?i("div",{staticClass:"ui-message ui-show alert alert-danger"},[e._v("\n "+e._s(e.error)+"\n ")]):i("div",{staticClass:"ui-thumbnails-grid"},[i("input",{directives:[{name:"model",rawName:"v-model",value:e.search,expression:"search"}],staticClass:"search-query parent-width",attrs:{name:"query",placeholder:"search visualizations",autocomplete:"off",type:"text"},domProps:{value:e.search},on:{input:function(t){t.target.composing||(e.search=t.target.value)}}}),e._v(" "),e._l(e.plugins,function(t){return i("div",[e.match(t)?i("table",[i("tr",{staticClass:"ui-thumbnails-item",on:{click:function(i){e.select(t)}}},[i("td",[t.logo?i("img",{staticClass:"ui-thumbnails-image",attrs:{src:t.logo}}):i("div",{staticClass:"ui-thumbnails-icon fa fa-eye"})]),e._v(" "),i("td",[i("div",{staticClass:"ui-thumbnails-description-title ui-form-info"},[e._v("\n "+e._s(t.html)+"\n ")]),e._v(" "),i("div",{staticClass:"ui-thumbnails-description-text ui-form-info"},[e._v("\n "+e._s(t.description)+"\n ")])])]),e._v(" "),e.fixed?e._e():i("tr",[i("td"),e._v(" "),t.name==e.name?i("td",[e.hdas&&e.hdas.length>0?i("div",[i("div",{staticClass:"ui-form-info ui-bold"},[e._v("Select a dataset to visualize:")]),e._v(" "),i("div",{staticClass:"ui-select"},[i("select",{directives:[{name:"model",rawName:"v-model",value:e.selected,expression:"selected"}],staticClass:"select",on:{change:function(t){var i=Array.prototype.filter.call(t.target.options,function(e){return e.selected}).map(function(e){return"_value"in e?e._value:e.value});e.selected=t.target.multiple?i:i[0]}}},e._l(e.hdas,function(t){return i("option",{domProps:{value:t.id}},[e._v(e._s(t.name))])})),e._v(" "),i("div",{staticClass:"icon-dropdown fa fa-caret-down"})]),e._v(" "),i("button",{staticClass:"ui-button-default ui-float-left btn btn-primary",attrs:{type:"button"},on:{click:function(i){e.create(t)}}},[i("i",{staticClass:"icon fa fa-check ui-margin-right"}),e._v(" "),i("span",{staticClass:"title"},[e._v("Create Visualization")])])]):i("div",{staticClass:"ui-message ui-show alert alert-danger"},[e._v("\n There is no suitable dataset in your current history which can be visualized with this plugin.\n ")])]):e._e()])]):e._e()])})],2)])},a=[]},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(5),d=s(l),c=i(10),u=s(c),h=i(26),f=s(h),p=e.View.extend({initialize:function(){this.setElement(""),this.model=new e.Model({dataset_id:Galaxy.params.dataset_id}),this.active_tab="user",this.render()},render:function(){var e=this,t=Galaxy.root+"api/datasets/"+this.model.get("dataset_id");d.default.get({url:t,success:function(t){var i=Galaxy.root+"api/jobs/"+t.creating_job+"?full=True";d.default.get({url:i,success:function(i){e.render_error_page(t,i)},error:function(t){var i={status:"error",message:"Error occured while loading the job.",persistent:!0,cls:"errormessage"};e.display_message(i,e.$(".response-message"))}})},error:function(t){var i={status:"error",message:"Error occured while loading the dataset.",persistent:!0,cls:"errormessage"};e.display_message(i,e.$(".response-message"))}})},render_error_page:function(e,t){this.$el.empty().append("\n "+this._templateHeader()+"\n Dataset Error
\nAn error occured while running the tool "+t.tool_id+'.
\nTool execution generated the following messages:
\n'+n.escape(t.stderr)+"\n
Report This Error
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o=y.extend(y.clone(e),{view:"summary",keys:t,limit:n,offset:a,reset:0===a,remove:!1});y.defer(function(){s.fetch.call(s,o).fail(i.reject).done(function(o){i.notify(o,n,a),o.length!==n?(s.allFetched=!0,i.resolve(o,n,a)):s._recursivelyFetch(e,t,i,n,a+n)})})},progressivelyFetchDetails:function(t){t=t||{};var i=e.Deferred();return this._recursivelyFetch(t,l.default.HistoryDatasetAssociation.prototype.searchAttributes.join(","),i,t.limitPerCall||this.limitPerProgressiveFetch),i},isCopyable:function(e){var t=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return y.isObject(e)&&e.id&&y.contains(t,e.model_class)},copy:function(t){var i,n,a;y.isString(t)?(i=t,a="hda",n="dataset"):(i=t.id,a={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",n="hdca"===a?"dataset_collection":"dataset");var s=this,o=e.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:i,source:a,type:n})}).done(function(e){s.add([e],{parse:!0})}).fail(function(e,t,r){s.trigger("error",s,o,{},"Error copying contents",{type:n,id:i,source:a})});return o},createHDCA:function(e,t,i,n,a){return this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:e}).save(a)},haveSearchDetails:function(){return this.allFetched&&this.all(function(e){return y.has(e.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=x.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});t.default={HistoryContents:S}}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(67),l=o(r),d=i(37),c=o(d),u=i(52),h=o(u),f=i(6),p=o(f),_=i(3),m=o(_),g=l.default.ListItemView,v=g.extend({_logNamespace:"dataset",className:g.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),g.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var t=this;return t.listenTo(t.model,{change:function(i){t.model.changedAttributes().state&&t.model.inReadyState()&&t.expanded&&!t.model.hasDetails()?t.model.fetch({silent:!0}).done(function(){t.render()}):e.has(i.changed,"tags")&&1===e.keys(i.changed).length?t.$(".nametags").html(t._renderNametags()):t.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):n.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){a.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return g.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===c.default.NOT_VIEWABLE||e===c.default.DISCARDED||!this.model.get("accessible"))return null;var t={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))t.disabled=!0,t.title=(0,m.default)("Cannot display datasets removed from disk");else if(e===c.default.UPLOAD)t.disabled=!0,t.title=(0,m.default)("This dataset must finish uploading before it can be viewed");else if(e===c.default.NEW)t.disabled=!0,t.title=(0,m.default)("This dataset is not yet viewable");else{t.title=(0,m.default)("View data"),t.href=this.model.urls.display;var i=this;t.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(i.model.get("id")),e.preventDefault())}}return t.faIcon="fa-eye",(0,h.default)(t)},_renderDetails:function(){if(this.model.get("state")===c.default.NOT_VIEWABLE)return s(this.templates.noAccess(this.model.toJSON(),this));var e=g.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var t=this,i=s(''),n=t.model.toJSON();return e.each(t.templates.detailMessages,function(e){i.append(s(e(n,t)))}),i},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case c.default.NOT_VIEWABLE:return[];case c.default.OK:case c.default.FAILED_METADATA:case c.default.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return(0,h.default)({title:(0,m.default)("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle",onclick:function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:(0,m.default)("Dataset details"),url:this.href}),e.preventDefault(),e.stopPropagation())}})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:e.isEmpty(this.model.get("meta_files"))?s('\n \n \n '):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return s('\n ").addClass("bookmark").appendTo(s),r=e("").addClass("position").appendTo(o);e("").text(t).appendTo(r).click(function(){return a.view.go_to(t),!1});var l=e("").text(i).appendTo(o);if(n){var d=e("").addClass("delete-icon-container").prependTo(o).click(function(){return o.slideUp("fast"),o.remove(),a.view.has_changes=!0,!1});e("").addClass("icon-button delete").appendTo(d),l.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return this.view.has_changes=!0,o}},{key:"create_visualization",value:function(t,i,n,a,s){var o=this;return this.view=new m.default.TracksterView(h.extend(t,{header:!1})),this.view.editor=!0,e.when(this.view.load_chroms_deferred).then(function(e){var t=null;if(i){var r=i.chrom,l=i.start,d=i.end;t=i.overview,r&&void 0!==l&&d?o.view.change_chrom(r,l,d):o.view.change_chrom(e[0].chrom)}else o.view.change_chrom(e[0].chrom);if(n)for(var c=0;c"),e("#right-border").click(function(){t.ui.view.resize_window()}),window.force_right_panel("hide"),window.galaxy_config.app.id?this.view_existing():x.default.get("dataset_id")?this.choose_existing_or_new():this.view_new()}},{key:"choose_existing_or_new",value:function(){var e=this,t=x.default.get("dbkey"),i={},n={dbkey:t,dataset_id:x.default.get("dataset_id"),hda_ldda:x.default.get("hda_ldda"),gene_region:x.default.get("gene_region")};t&&(i["f-dbkey"]=t),Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:"r)return e(this).insertAfter(s),f.remove_drawable(h),void f.container.add_drawable(h)}for(s=null,l=0;l=o&&i.offsetY<=r)return i.offsetY-o0?l-1:l))}).bind("dragstart",function(){e(this).addClass("dragging")}).bind("dragend",function(){e(this).removeClass("dragging")})}function r(e,t){t||(t=0);var i=Math.pow(10,t);return Math.round(e*i)/i}function l(t){var i=e.Deferred();return e.ajax({type:"HEAD",url:t,beforeSend:function(e){e.setRequestHeader("Range","bytes=0-10")},success:function(e,t,n){i.resolve(206===n.status)}}),i}Object.defineProperty(t,"__esModule",{value:!0});var d=i(3),c=a(d),u=i(1),h=n(u),f=i(2),p=n(f),_=i(15),m=a(_),g=i(81),v=a(g),w=i(18),y=a(w),b=i(82),x=a(b),k=i(83),C=a(k),S=i(84),T=a(S),M=i(14),$=a(M),P=i(54),O=a(P),E=i(33),A=a(E),D=i(137),z=a(D);i(19);var I=h.extend,j={},L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G=["Histogram","Line","Filled","Intensity"],R=function e(t,i,n){if(e.id_counter||(e.id_counter=0),this.id=e.id_counter++,this.view=t,this.container=i,this.drag_handle_class=n.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=A.default.ConfigSettingCollection.from_models_and_saved_values(this.build_config_params(),n.prefs),this.config.get_value("name")||this.config.set_value("name",n.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,!1!==n.header){var a=new v.default.TrackHeaderView({model:this,id:this.id});this.header_div=a.$el,this.container_div.append(this.header_div);var s=a.icons_div;this.action_icons=a.action_icons,this.container_div.hover(function(){s.show()},function(){s.hide()})}};R.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(e){e.config.get_value("content_visible")?(e.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),e.hide_contents(),e.config.set_value("content_visible",!1)):(e.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),e.config.set_value("content_visible",!0),e.show_contents())}},{name:"settings_icon",title:(0,c.default)("Edit settings"),css_class:"gear",on_click_fn:function(e){new A.default.ConfigSettingCollectionView({collection:e.config}).render_in_modal("Configure Track")}},{name:"remove_icon",title:(0,c.default)("Remove"),css_class:"remove-icon",on_click_fn:function(t){e(".tooltip").remove(),t.remove()}}],I(R.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],build_config_params:function(){return this.config_params},config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return!(!this.enabled||!this.config.get_value("content_visible"))},request_draw:function(){},_draw:function(e){},to_dict:function(){},set_name:function(e){this.old_name=this.config.get_value("name"),this.config.set_value("name",e)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var t=this.view;this.container_div.hide(0,function(){e(this).remove(),t.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var N=function(e,t,i){R.call(this,e,t,i),this.obj_type=i.obj_type,this.drawables=[]};I(N.prototype,R.prototype,{unpack_drawables:function(e){this.drawables=[];for(var t,i=0;i").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),s(this.container_div,this),s(this.content_div,this),o(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new T.default.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after(e("")),this.saved_filters_managers=[],"drawables"in n&&this.unpack_drawables(n.drawables),"filters"in n){var a=this.filters_manager;this.filters_manager=new T.default.FiltersManager(this,n.filters),a.parent_div.replaceWith(this.filters_manager.parent_div),n.filters.visible&&this.setup_multitrack_filtering()}};I(V.prototype,R.prototype,N.prototype,{action_icons_def:[R.prototype.action_icons_def[0],R.prototype.action_icons_def[1],{name:"composite_icon",title:(0,c.default)("Show composite track"),css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_composite_track()}},{name:"filters_icon",title:(0,c.default)("Filters"),css_class:"ui-slider-050",on_click_fn:function(e){e.filters_manager.visible()?(e.filters_manager.clear_filters(),e._restore_filter_managers()):(e.setup_multitrack_filtering(),e.request_draw({clear_tile_cache:!0})),e.filters_manager.toggle()}},R.prototype.action_icons_def[2]],build_container_div:function(){var t=e("").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(t),t},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var t=this.drawables.length;if(0===t)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===t)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof Z),this.action_icons.filters_icon.hide();else{var i,n,a,s=this.drawables[0].get_type(),o=0;for(i=0;i1&&o===this.drawables.length){var r,l={};for(a=this.drawables[0],n=0;n0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var e=0;e0){this.saved_filters_managers=[];for(var e=0;e").addClass("top-container").appendTo(t),this.browser_content_div=e("").addClass("content").appendTo(t),this.bottom_container=e("").addClass("bottom-container").appendTo(t),this.top_labeltrack=e("").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=e("").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,s(this.viewport_container,i),this.intro_div=e("").addClass("intro").appendTo(this.viewport_container),e("").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){m.default.select_datasets({dbkey:i.dbkey},function(e){h.each(e,function(e){i.add_drawable(re(e,i,i))})})}),this.nav_container=e("").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=e("").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=e("").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=e("").addClass("overview-viewport").appendTo(this.overview),this.overview_close=e("").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=e("").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=e("").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=e("").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=e("").addClass("nav-controls").appendTo(this.nav),this.chrom_select=e("").attr({name:"chrom"}).addClass("chrom-nav").append("").appendTo(this.nav_controls);var n=function(t){"focusout"!==t.type&&13!==(t.keyCode||t.which)&&27!==(t.keyCode||t.which)||(27!==(t.keyCode||t.which)&&i.go_to(e(this).val()),e(this).hide(),e(this).val(""),i.location_span.show(),i.chrom_select.show()),t.stopPropagation()};this.nav_input=e("").addClass("nav-input").hide().bind("keyup focusout",n).appendTo(this.nav_controls),this.location_span=e("").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){i.location_span.hide(),i.chrom_select.hide(),i.nav_input.val(i.chrom+":"+i.low+"-"+i.high),i.nav_input.css("display","inline-block"),i.nav_input.select(),i.nav_input.focus(),i.nav_input.autocomplete({source:function(t,n){var a=[],s=e.map(i.get_tracks(ne),function(e){return e.data_manager.search_features(t.term).success(function(e){a=a.concat(e)})});e.when.apply(e,s).done(function(){n(e.map(a,function(e){return{label:e[0],value:e[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=e("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=e("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){i.zoom_out()}).appendTo(this.nav_controls),this.zi_link=e("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){i.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){i.change_chrom(i.chrom_select.val())}),this.browser_content_div.click(function(t){e(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(e){i.zoom_in(e.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(e,t){this.current_x=t.offsetX}).bind("drag",function(e,t){var n=t.offsetX-this.current_x;this.current_x=t.offsetX;var a=Math.round(n/i.viewport_container.width()*(i.max_high-i.max_low));i.move_delta(-a)}),this.overview_close.click(function(){i.reset_overview()}),this.viewport_container.bind("draginit",function(e,t){if(e.clientX>i.viewport_container.width()-16)return!1}).bind("dragstart",function(e,t){t.original_low=i.low,t.current_height=e.clientY,t.current_x=t.offsetX}).bind("drag",function(t,n){var a=e(this),s=n.offsetX-n.current_x,o=a.scrollTop()-(t.clientY-n.current_height);a.scrollTop(o),n.current_height=t.clientY,n.current_x=n.offsetX;var r=Math.round(s/i.viewport_container.width()*(i.high-i.low));i.move_delta(r)}),this.top_labeltrack.bind("dragstart",function(t,n){return e("").addClass("zoom-area").css("height",i.browser_content_div.height()+i.top_labeltrack.height()+1).appendTo(e(this))}).bind("drag",function(t,n){e(n.proxy).css({left:Math.min(t.pageX,n.startX)-i.container.offset().left,width:Math.abs(t.pageX-n.startX)});var a=Math.min(t.pageX,n.startX)-i.container.offset().left,s=Math.max(t.pageX,n.startX)-i.container.offset().left,o=i.high-i.low,r=i.viewport_container.width();i.update_location(Math.round(a/r*o)+i.low,Math.round(s/r*o)+i.low)}).bind("dragend",function(t,n){var a=Math.min(t.pageX,n.startX),s=Math.max(t.pageX,n.startX),o=i.high-i.low,r=i.viewport_container.width(),l=i.low;i.low=Math.round(a/r*o)+l,i.high=Math.round(s/r*o)+l,e(n.proxy).remove(),i.request_redraw()}),this.add_label_track(new Q(this,{content_div:this.top_labeltrack})),e(window).bind("resize",function(){this.resize_timer&&window.clearTimeout(this.resize_timer),this.resize_timer=window.setTimeout(function(){i.resize_window()},500)}),e(document).bind("redraw",function(){i.redraw()}),this.reset(),e(window).trigger("resize")},get_base_color:function(e){return this.config.get_value(e.toLowerCase()+"_color")||this.config.get_value("n_color")}});I(H.prototype,N.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(e,t,i,n){var a=this;this.timer&&window.clearTimeout(this.timer),n?this.timer=window.setTimeout(function(){a.trigger("navigate",e+":"+t+"-"+i)},500):this.trigger("navigate",e+":"+t+"-"+i)},update_location:function(e,t){this.location_span.text(y.default.commatize(e)+" - "+y.default.commatize(t)),this.nav_input.val(this.chrom+":"+y.default.commatize(e)+"-"+y.default.commatize(t));var i=this.chrom_select.val();""!==i&&this.trigger_navigate(i,this.low,this.high,!0)},load_chroms:function(t){var i=this;t.num=100;var n=e.Deferred();return e.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:t,dataType:"json",success:function(t){if(0!==t.chrom_info.length){if(t.reference){var a=new ee(i);i.add_label_track(a),i.reference_track=a}i.chrom_data=t.chrom_info,i.chrom_select.html(""),i.chrom_select.append(e(''));for(var 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d=i[1],c=i[2],u=i[3],h=i[4],f=Math.floor(Math.max(0,(d-a-.5)*o)),p=Math.ceil(Math.min(l,Math.max(0,(c-a-.5)*o))),_=f,m=p,g=("Dense"===t?0:0+n)*r+this.get_top_padding(l),v=null,w=null,y=h&&"+"!==h&&"."!==h?this.prefs.reverse_strand_color:this.prefs.block_color,b=this.prefs.label_color;if(e.globalAlpha=this.alpha_scaler.gen_val(i),"Dense"===t&&(n=1),"no_detail"===t)e.fillStyle=y,e.fillRect(f,g+5,p-f,1);else{var x=i[5],k=i[6],C=i[7],S=!0;x&&k&&(v=Math.floor(Math.max(0,(x-a)*o)),w=Math.ceil(Math.min(l,Math.max(0,(k-a)*o))));var T,M;if("Squish"===t?(T=1,M=3,S=!1):(T=5,M=9),C){var $,P;"Squish"===t||"Dense"===t?($=g+Math.floor(1.5)+1,P=1):h?($=g,P=M):($+=2.5,P=1),this.draw_background_connector&&("Squish"===t||"Dense"===t?e.fillStyle="#ccc":h?"+"===h?e.fillStyle=e.canvas.manager.get_pattern("right_strand"):"-"===h&&(e.fillStyle=e.canvas.manager.get_pattern("left_strand")):e.fillStyle="#ccc",e.fillRect(f,$,p-f,P));for(var O=0,E=C.length;Oj)){if(e.fillStyle=y,e.fillRect(I,g+(M-T)/2+1,j-I,T),void 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0!==h&&i>C){switch(e.fillStyle="yellow",e.fillRect(J-k,n-9,w-v,9),E[E.length]={type:"triangle",data:[B,n+4,5]},e.fillStyle="#ccc",o([V,V+N],y)){case _:Y=Y.slice(a-V);break;case m:Y=Y.slice(0,V-s);break;case g:break;case p:Y=Y.slice(a-V,V-s)}for(var W=0,X=Y.length;WC&&E.push({type:"text",data:[Y.length,B,n+9]})}x+=N}else b=function(e,t,i){return-1!=="M=NXD".indexOf(t)&&(e+=i),e}(b,R,N),x=function(e,t,i){return-1!=="IX".indexOf(t)&&(e+=i),e}(x,R,N)}e.fillStyle="yellow";for(var Q,Z,ee,te=0;te=a&&i[4][0]<=s&&i[4][2]?this.draw_read(e,t,o,_,a,s,i[4][0],i[4][2],i[4][3],i[4][4]):g=!1,i[5][1]>=a&&i[5][0]<=s&&i[5][2]?this.draw_read(e,t,o,_,a,s,i[5][0],i[5][2],i[5][3],i[5][4]):g=!1;var v=Math.ceil(Math.min(d,Math.max(-.5*o,(i[4][1]-a-.5)*o))),w=Math.floor(Math.max(-.5*o,(i[5][0]-a-.5)*o));if(g&&w>v){e.fillStyle="#ccc";var y=_+1+(m-1)/2;l(e,v,y,w,y)}}else this.draw_read(e,t,o,_,a,s,c,i[4],i[5],i[6]);return"Pack"===t&&c>=a&&"."!==h&&(e.fillStyle=this.prefs.label_color,0===a&&f-e.measureText(h).width<0?(e.textAlign="left",e.fillText(h,p+2,_+9,this.max_label_length)):(e.textAlign="right",e.fillText(h,f-2,_+9,this.max_label_length))),[0,0]}}]),t}(C),M=function(e){function t(e,i,a,o,r,l,d){s(this,t);var c=n(this,(t.__proto__||Object.getPrototypeOf(t)).call(this,e,i,a,o,r,l,d));return c.longest_feature_length=c.calculate_longest_feature_length(),c.draw_background_connector=!1,c.draw_individual_connectors=!0,c}return a(t,e),c(t,[{key:"calculate_longest_feature_length",value:function(){for(var e=0,t=0,i=this.data.length;t0&&(e.beginPath(),e.arc(o,s,n-o,Math.PI,0),e.stroke())}}]),t}(S),$=function(){function e(t,i){s(this,e),Array.isArray(t)?this.rgb=t:6==t.length?this.rgb=t.match(/.{2}/g).map(function(e){return parseInt(e,16)}):7==t.length?this.rgb=t.substring(1,7).match(/.{2}/g).map(function(e){return 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e(t,i,n,a){s(this,e),this.start_color=new $(t),this.end_color=new $(i),this.start_value=n,this.end_value=a,this.value_range=a-n}return c(e,[{key:"map_value",value:function(e){return e=Math.max(e,this.start_value),e=Math.min(e,this.end_value),e=(e-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-e).toCSS()}}]),e}(),O=function(){function e(t,i,n,a,o){s(this,e),this.positive_ramp=new P(i,n,0,o),this.negative_ramp=new P(i,t,0,-a),this.start_value=a,this.end_value=o}return c(e,[{key:"map_value",value:function(e){return e=Math.max(e,this.start_value),e=Math.min(e,this.end_value),e>=0?this.positive_ramp.map_value(e):this.negative_ramp.map_value(-e)}}]),e}(),E=function(e){function t(e,i,a,o,r){s(this,t);var l,d,c=n(this,(t.__proto__||Object.getPrototypeOf(t)).call(this,e,i,a,o,r));if(void 0===c.prefs.min_value){var u=1/0;for(l=0,d=c.data.length;l=t.canvas.manager.char_width_px,this.delete_details_thickness=.2}return c(e,[{key:"draw_deletion",value:function(e,t,i){this.ctx.fillStyle="black";var n=(this.draw_details?this.delete_details_thickness:1)*this.row_height;t+=.5*(this.row_height-n),this.ctx.fillRect(e,t,i*this.px_per_base,n)}}]),e}(),D=function(e){function t(e,i,a,o,r,l){s(this,t);var d=n(this,(t.__proto__||Object.getPrototypeOf(t)).call(this,e,i,a,o,r));return d.base_color_fn=l,d.divider_height=1,d}return a(t,e),c(t,[{key:"get_row_height",value:function(){var e=this.mode;return"Dense"===e?10:"Squish"===e?5:10}},{key:"get_required_height",value:function(e){var t=this.prefs.summary_height;return e>1&&this.prefs.show_sample_data&&(t+=this.divider_height+e*this.get_row_height()),t}},{key:"draw",value:function(e,t,i,n){e.save();var a,s,o,r,l,d,c,u,f,p,_,m=function(e,t){var i=e.length,n=t.length,a=0,s=1,o=null;return"-"===t?(o="deletion",s=e.length):0===e.indexOf(t)&&i>n?(o="deletion",s=i-n,a=n):0===t.indexOf(e)&&ithis.view_end)){if(b)for(e.fillStyle="#999999",e.globalAlpha=1,_=0;_").addClass("display-controls").appendTo(i.parent_div);this.transparency_icon=d("Use filter for data transparency","layer-transparent",function(){i.manager.alpha_filter!==i?(i.manager.alpha_filter=i,i.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),i.transparency_icon.addClass("active").show()):(i.manager.alpha_filter=null,i.transparency_icon.removeClass("active")),i.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(r).hide(),this.height_icon=d("Use filter for data 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i=t.values;this.values_span.text(i[0]+"-"+i[1]),this.low=i[0],this.high=i[1];var n=this;setTimeout(function(){i[0]===n.low&&i[1]===n.high&&n.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(e){return e.length>this.index},_keep_val:function(e){return isNaN(e)||e>=this.low&&e<=this.high},keep:function(e){if(!this.applies_to(e))return!0;var t=e[this.index];if(t instanceof Array){for(var i=!0,n=0;nthis.max&&(this.max=Math.ceil(a),t=!0)}return t},update_ui_elt:function(){this.mint)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var 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n([]);this.getFirstAdjacentById(a,t,i,n)},d.prototype.getFirstAdjacentById=function(e,t,i,n){var a=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(s){a.cirHeader=s;var o=new Int32Array(a.cirHeader);a.cirBlockSize=o[1],a.getFirstAdjacentById(e,t,i,n)});var s=null,o=-1,l=-1,d=0,c=(Date.now(),function(e,t){d+=e.length;for(var i,n=4+32*a.cirBlockSize,s=0;s0&&(0!=e||t>0)?a.getFirstAdjacentById(0,0,i,n):i<0&&(e!=a.bwg.maxID||t<1e9)?a.getFirstAdjacentById(a.bwg.maxID,1e9,i,n):n([]);a.fetchFeatures(function(n,a,s,o){return i<0&&(n0&&(n>e||a>t)},[s],function(e){for(var t=null,a=-1,s=-1,o=0;oa||c>s)||i>0&&(l0&&(b>e||b==e&&x>=t))&&(/_random/.exec(a.bwg.idsToChroms[w])||(null==s||i<0&&(b>o||b==o&&x>l)||i>0&&(w=e||i>0&&(b>e||b==e&&x>=t)&&w<=e)&&(S<0||x>T)&&(S=k,T=i<0?x:y,i<0?b:w),d+=24}S>=0&&c([S],u+1)}};c([a.cirTreeOffset+48],1)},l.prototype.readWigData=function(e,t,i){var n,a=i-t;if(a<=25e3||0===this.zoomLevels.length)n=this.getUnzoomedView();else for(var s=0;s=this.zoomLevels.length-1)){var o;return o=e<0?this.getUnzoomedView():this.getZoomedView(e),o.readWigDataById(t,i,n,a)}if(this.topLevelReductionCache){for(var r=[],l=this.topLevelReductionCache,d=0;d0?0:3e8;e.fromRef&&(r=t);for(var d=0;d0){if(c>n)if(e.zoom<0){if(u.min>r)return a(u)}else u.max>r&&l.push({chr:e.chr,chrOrd:e.chrOrd,zoom:e.zoom-2,min:u.min,max:u.max,fromRef:e.fromRef})}else if(c>n)if(e.zoom<0){if(u.maxi.field-3)return s[i.field-3]==e},[{offset:v,size:w}],t)}f+=u}return t([])}for(var y=null,p=0;pn._max&&(n._max=e._max):(i.push(n),n=e)}),i.push(n),this._ranges=i}function i(e,i){return e instanceof t||(e instanceof Array||(e=[e]),e=new t(e)),i&&e.insertRange(i),e}function n(i,n){for(var a=i.ranges(),s=n.ranges(),o=a.length,r=s.length,l=0,d=0,c=[];l=u&&c.push(new e(u,h)),i.max()>n.max()?++d:++l}return 0==c.length?null:1==c.length?c[0]:new t(c)}function a(e){for(var t=0,i=e.ranges(),n=0;nt.min()?1:e.max()e.max()?1:0}function o(e,t){return e._mint._min?1:e._maxe._max?1:0}return e.prototype.min=function(){return this._min},e.prototype.max=function(){return this._max},e.prototype.contains=function(e){return e>=this._min&&e<=this._max},e.prototype.isContiguous=function(){return!0},e.prototype.ranges=function(){return[this]},e.prototype._pushRanges=function(e){e.push(this)},e.prototype.toString=function(){return"["+this._min+"-"+this._max+"]"},t.prototype.min=function(){return this._ranges[0].min()},t.prototype.max=function(){return this._ranges[this._ranges.length-1].max()},t.prototype.lower_bound=function(e){var t=this.ranges();if(e>this.max())return t.length;if(et[a]._max)i=a+1;else{if(!(ee._max&&(e._max=i[n]._max),this._ranges.splice(t,n-t+1,e)},t.prototype.isContiguous=function(){return this._ranges.length>1},t.prototype.ranges=function(){return this._ranges},t.prototype._pushRanges=function(e){for(var t=0;t0&&(e+=","),e+=this._ranges[t].toString();return e},{Range:e,union:i,intersection:n,coverage:a,rangeOver:s,_rangeOrder:o}}.apply(t,n))&&(e.exports=a)},function(e,t,i){var n,a;n=[],void 0!==(a=function(){function e(){}function t(){this.was=[0]}function i(e,t,i){this.hufts=new Int32Array(3*u),this.window=new Uint8Array(i),this.end=i,this.checkfn=t,this.mode=g,this.reset(e,null),this.left=0,this.table=0,this.index=0,this.blens=null,this.bb=new Int32Array(1),this.tb=new Int32Array(1),this.codes=new n,this.last=0,this.bitk=0,this.bitb=0,this.read=0,this.write=0,this.check=0,this.inftree=new a}function n(){}function a(){}function s(e,t,i,n,a){return e[0]=v,t[0]=w,i[0]=y,n[0]=b,f}function o(e,t,i,n,a){if(0!=a){if(!e)throw"Undef src";if(!i)throw"Undef dest";0==t&&a==e.length?l(e,i,n):P?l(e.subarray(t,t+a),i,n):1==e.BYTES_PER_ELEMENT&&a>100?l(new Uint8Array(e.buffer,e.byteOffset+t,a),i,n):r(e,t,i,n,a)}}function r(e,t,i,n,a){for(var s=0;s15?(this.inflateEnd(e),-2):(this.wbits=t,e.istate.blocks=new i(e,0!=e.istate.nowrap?null:this,1<>4)>e.istate.wbits){e.istate.mode=13,e.msg="invalid window size",e.istate.marker=5;break}e.istate.mode=1;case 1:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,n=255&e.next_in[e.next_in_index++],((e.istate.method<<8)+n)%31!=0){e.istate.mode=13,e.msg="incorrect header check",e.istate.marker=5;break}if(0==(32&n)){e.istate.mode=7;break}e.istate.mode=2;case 2:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need=(255&e.next_in[e.next_in_index++])<<24&4278190080,e.istate.mode=3;case 3:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<16&16711680,e.istate.mode=4;case 4:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<8&65280,e.istate.mode=5;case 5:return 0==e.avail_in?i:(i=t,e.avail_in--,e.total_in++,e.istate.need+=255&e.next_in[e.next_in_index++],e.adler=e.istate.need,e.istate.mode=6,2);case 6:return e.istate.mode=13,e.msg="need dictionary",e.istate.marker=0,-2;case 7:if(-3==(i=e.istate.blocks.proc(e,i))){e.istate.mode=13,e.istate.marker=0;break}if(i==f&&(i=t),i!=p)return i;if(i=t,e.istate.blocks.reset(e,e.istate.was),0!=e.istate.nowrap){e.istate.mode=12;break}e.istate.mode=8;case 8:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need=(255&e.next_in[e.next_in_index++])<<24&4278190080,e.istate.mode=9;case 9:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<16&16711680,e.istate.mode=10;case 10:if(0==e.avail_in)return i;i=t,e.avail_in--,e.total_in++,e.istate.need+=(255&e.next_in[e.next_in_index++])<<8&65280,e.istate.mode=11;case 11:if(0==e.avail_in)return i;if(i=t,e.avail_in--,e.total_in++,e.istate.need+=255&e.next_in[e.next_in_index++],e.istate.was[0]!=e.istate.need){e.istate.mode=13,e.msg="incorrect data check",e.istate.marker=5;break}e.istate.mode=12;case 12:return p;case 13:return-3;default:return-2}},t.prototype.inflateSetDictionary=function(e,t,i){var n=0,a=i;return null==e||null==e.istate||6!=e.istate.mode?-2:e._adler.adler32(1,t,0,i)!=e.adler?-3:(e.adler=e._adler.adler32(0,null,0,0),a>=1<>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var u=new Int32Array(1),h=new Int32Array(1),_=[],v=[];s(u,h,_,v,e),this.codes.init(u[0],h[0],_[0],0,v[0],0,e),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,e.msg="invalid block type",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<>>16&65535)!=(65535&n))return this.mode=13,e.msg="invalid stored block lengths",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:g;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,write=d,this.inflate_flush(e,t);if(0==c&&(d==end&&0!=read&&(d=0,c=dl&&(i=l),i>c&&(i=c),o(e.next_in,r,this.window,d,i),r+=i,l-=i,d+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:g;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<29||(i>>5&31)>29)return this.mode=9,e.msg="too many length or distance symbols",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);t=f,l--,n|=(255&e.next_in[r++])<>>=3,a-=3}for(;this.index<19;)this.blens[M[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,e))!=f)return t=i,-3==t&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,write=d,this.inflate_flush(e,t);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var w,y,b;for(i=this.bb[0];a>>=i,a-=i,this.blens[this.index++]=b;else{for(w=18==b?7:b-14,y=18==b?11:3;a>>=i,a-=i,y+=n&m[w],n>>>=w,a-=w,w=this.index,i=this.table,w+y>258+(31&i)+(i>>5&31)||16==b&&w<1)return this.blens=null,this.mode=9,e.msg="invalid bit length repeat",t=-3,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);b=16==b?this.blens[w-1]:0;do{this.blens[w++]=b}while(0!=--y);this.index=w}}this.tb[0]=-1;var u=new Int32Array(1),h=new Int32Array(1),_=new Int32Array(1),v=new Int32Array(1);if(u[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,u,h,_,v,this.hufts,e))!=f)return-3==i&&(this.blens=null,this.mode=13),t=i,this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,this.inflate_flush(e,t);this.codes.init(u[0],h[0],this.hufts,_[0],this.hufts,v[0],e),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,e.avail_in=l,e.total_in+=r-e.next_in_index,e.next_in_index=r,this.write=d,(t=this.codes.proc(this,e,t))!=p)return this.inflate_flush(e,t);if(t=f,this.codes.free(e),r=e.next_in_index,l=e.avail_in,n=this.bitb,a=this.bitk,d=this.write,c=de.avail_out&&(i=e.avail_out),0!=i&&t==_&&(t=f),e.avail_out-=i,e.total_out+=i,null!=this.checkfn&&(e.adler=this.check=e._adler.adler32(this.check,this.window,a,i)),o(this.window,a,e.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>e.avail_out&&(i=e.avail_out),0!=i&&t==_&&(t=f),e.avail_out-=i,e.total_out+=i,null!=this.checkfn&&(e.adler=this.check=e._adler.adler32(this.check,this.window,a,i)),o(this.window,a,e.next_out,n,i),n+=i,a+=i),e.next_out_index=n,this.read=a,t};n.prototype.init=function(e,t,i,n,a,s,o){this.mode=0,this.lbits=e,this.dbits=t,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=s,this.tree=null},n.prototype.proc=function(e,t,i){var n,a,s,o,r,l,d,c=0,u=0,h=0;for(h=t.next_in_index,o=t.avail_in,c=e.bitb,u=e.bitk,r=e.write,l=r=258&&o>=10&&(e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,e,t),h=t.next_in_index,o=t.avail_in,c=e.bitb,u=e.bitk,r=e.write,l=r>>=this.tree[a+1],u-=this.tree[a+1],0==(s=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&s)){this.get=15&s,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&s)){this.need=s,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&s)){this.mode=7;break}return this.mode=9,t.msg="invalid literal/length code",i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 2:for(n=this.get;u>=n,u-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;u>=this.tree[a+1],u-=this.tree[a+1],0!=(16&(s=this.tree[a]))){this.get=15&s,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&s)){this.need=s,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,t.msg="invalid distance code",i=-3,e.bitb=c,e.bitk=u,t.avail_in=o,t.total_in+=h-t.next_in_index,t.next_in_index=h,e.write=r,e.inflate_flush(t,i);case 4:for(n=this.get;u>=n,u-=n,this.mode=5;case 5:for(d=r-this.dist;d<0;)d+=e.end;for(;0!=this.len;){if(0==l&&(r==e.end&&0!=e.read&&(r=0,l=r7&&(u-=8,o++,h--),e.write=r,i=e.inflate_flush(t,i),r=e.write,l=r>=c[M+1],g-=c[M+1],0!=(16&h)){for(h&=15,C=c[M+2]+(_&m[h]),_>>=h,g-=h;g<15;)w--,_|=(255&l.next_in[v++])<
\n Dataset:"+t.config.get_value("name")+'
\n Region(s):\n \n ',n=function(){Galaxy.modal.hide(),e(window).unbind("keypress.check_enter_esc")},a=function(){var i,n=e('select[name="regions"] option:selected').val(),a=new m.default.GenomeRegion({chrom:(void 0).view.chrom,start:(void 0).view.low,end:(void 0).view.high}),s=h.map(e(".bookmark"),function(t){return new m.default.GenomeRegion({from_str:e(t).children(".position").text()})});i="cur"===n?[a]:"bookmarks"===n?s:[a].concat(s),Galaxy.modal.hide(),window.top.location.href=Galaxy.root+"visualization/sweepster?"+e.param({dataset_id:t.dataset.id,hda_ldda:t.dataset.get("hda_ldda"),regions:JSON.stringify(new p.Collection(i).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:i,buttons:{No:n,Yes:a}})}},R.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&R.prototype.can_draw.call(this)},build_container_div:function(){return e("").addClass("track").attr("id","track_"+this.id)},set_dataset:function(e){this.dataset=e,this.data_manager.set("dataset",e)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var t=this,i=!1,n=!1,a=e("
");e(t.container_div).hover(function(){t.config.get_value("content_visible")&&(i=!0,a.show())},function(){i=!1,n||a.hide()}),a.hide().bind("dragstart",function(i,a){n=!0,a.original_height=e(t.content_div).height()}).bind("drag",function(i,n){var a=Math.min(Math.max(n.original_height+n.deltaY,t.min_height_px),t.max_height_px);e(t.tiles_div).css("height",a),t.visible_height_px=t.max_height_px===a?0:a,t.on_resize()}).bind("dragend",function(e,s){t.tile_cache.clear(),n=!1,i||a.hide(),t.config.set_value("height",t.visible_height_px),t.changed()}).appendTo(t.container_div)},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(){return this instanceof Q?"LabelTrack":this instanceof ee?"ReferenceTrack":this instanceof te?"LineTrack":this instanceof se?"ReadTrack":this instanceof ae?"VariantTrack":this instanceof Z?"CompositeTrack":this instanceof ne?"FeatureTrack":""},show_message:function(t){return this.tiles_div.remove(),e("").addClass("message").html(t).appendTo(this.content_div)},init:function(t){var i=this;if(i.enabled=!1,i.tile_cache.clear(),i.data_manager.clear(),i.content_div.children().remove(),i.container_div.removeClass("nodata error pending"),i.tiles_div=e("").addClass("tiles").appendTo(i.content_div),i.dataset.id){var n=e.Deferred(),a={hda_ldda:i.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:i.view.chrom,retry:t};return e.getJSON(this.dataset.url(),a,function(t){if(t&&"error"!==t&&"error"!==t.kind)"no converter"===t?(i.container_div.addClass("error"),i.show_message(L)):"no data"===t||void 0!==t.data&&(null===t.data||0===t.data.length)?(i.container_div.addClass("nodata"),i.show_message("No data for this chrom/contig.")):"pending"===t?(i.container_div.addClass("pending"),i.show_message("Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background."),window.setTimeout(function(){i.init()},i.data_query_wait)):"data"!==t&&"data"!==t.status||(t.valid_chroms&&(i.valid_chroms=t.valid_chroms,i.update_icons()),i.tiles_div.text("Ready for display"),i.view.chrom?(i.tiles_div.text(""),i.tiles_div.css("height",i.visible_height_px+"px"),i.enabled=!0,e.when.apply(e,i.predraw_init()).done(function(){n.resolve(),i.container_div.removeClass("nodata error pending"),i.request_draw()})):n.resolve());else{i.container_div.addClass("error");var a=i.show_message("Cannot display dataset due to an error. ");t.message&&(a.append(e("").text("View error").click(function(){Galaxy.modal.show({title:(0,c.default)("Trackster Error"),body:"").text(d).make_text_editable({num_cols:12,on_finish:function(t){e(".tooltip").remove(),this.config.set_value(o,r(t,1)),i()},help_text:"Set "+s+" value"}).addClass("yaxislabel "+a).css("color",this.config.get_value("label_color")),this.container_div.prepend(l))},postdraw_actions:function(e,t,i,n){var a=this;h.filter(e,function(e){return e instanceof J}).length>0?(this.max_height_px=0,h.each(e,function(e){e instanceof J||(e.html_elt.remove(),a.draw_helper(e.region,i,{force:!0,mode:"Coverage"}))}),this._add_yaxis_label("max")):(this.container_div.find(".yaxislabel").remove(),h.find(e,function(e){return e.has_icons})&&h.each(e,function(e){e.has_icons||e.html_elt.css("padding-top",20)}))},get_mode:function(e){return this.mode},update_auto_mode:function(e){},_get_drawables:function(){return[this]},draw_helper:function(t,i,n){var a=this;n||(n={});var s=n.force,o=n.mode||this.mode,r=1/i,l=this._get_drawables(),d=this._gen_tile_cache_key(i,t),c=s?void 0:this.tile_cache.get_elt(d);if(c)return function(e){return e&&"track"in e}(c)&&this.show_tile(c,i),c;if(!1===n.data_fetch)return null;var u=function(){var e=h.find(G,function(e){return e===o})?"Coverage":o,i=h.map(l,function(i){return i.data_manager.get_data(t,e,r,a.data_url_extra_params)});return a.view.reference_track&&i.push(a.view.reference_track.data_manager.get_data(t,o,r,a.view.reference_track.data_url_extra_params)),i},f=e.Deferred();return this.tile_cache.set_elt(d,f),e.when.apply(e,u()).then(function(){var s,o=u(),r=o;if(h.find(o,function(e){return y.default.is_deferred(e)}))return a.tile_cache.set_elt(d,void 0),void e.when(a.draw_helper(t,i,n)).then(function(e){f.resolve(e)});a.view.reference_track&&(s=a.view.reference_track.data_manager.subset_entry(o.pop(),t));var c=[],p=[];h.each(l,function(e,t){var n=r[t];"Auto"===e.mode&&(e.mode=e.get_mode(n),e.update_auto_mode(e.mode)),c.push(e.mode),p.push(e.get_canvas_height(n,e.mode,i,w))});var _,m=a.view.canvas_manager.new_canvas(),g=t.get("start"),v=t.get("end"),w=Math.ceil((v-g)*i)+a.left_offset,b=h.max(p);m.width=w,m.height=n.height||b;var x=m.getContext("2d");x.translate(a.left_offset,0),l.length>1&&(x.globalAlpha=.5,x.globalCompositeOperation="source-over"),h.each(l,function(e,n){_=e.draw_tile(r[n],x,c[n],t,i,s)}),void 0!==_&&(a.tile_cache.set_elt(d,_),a.show_tile(_,i)),f.resolve(_)}),f},get_canvas_height:function(e,t,i,n){return this.visible_height_px},_draw_line_track_tile:function(e,t,i,n,a){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",h.max(h.map(e.data,function(e){return e[1]}))||0);var s=t.canvas;return new C.default.LinePainter(e.data,n.get("start"),n.get("end"),this.config.to_key_value_dict(),i).draw(t,s.width,s.height,a),new J(this,n,a,s,e.data)},draw_tile:function(e,t,i,n,a,s){},show_tile:function(e,t){var i=e.html_elt;e.predisplay_actions();var n=Math.round((e.low-(this.is_overview?this.view.max_low:this.view.low))*t);this.left_offset&&(n-=this.left_offset),i.css("left",n),i.hasClass("remove")?i.removeClass("remove"):this.tiles_div.append(i),i.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,i.height()-2),i.parent().children().css("height",this.max_height_px+"px");var a=this.max_height_px;0!==this.visible_height_px&&(a=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",a+"px")},tool_region_and_parameters_str:function(e){var t=this;return" - region=["+(void 0!==e?e.toString():"all")+"], parameters=["+h.values(t.tool.get_inputs_dict()).join(", ")+"]"},data_and_mode_compatible:function(e,t){return"Auto"===t||("Coverage"===t?"bigwig"===e.dataset_type:"bigwig"!==e.dataset_type&&"no_detail"!==e.extra_info)},can_subset:function(e){return!e.message&&"no_detail"!==e.extra_info&&("bigwig"!==e.dataset_type||e.data[1][0]-e.data[0][0]==1)},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var Q=function(e,t){X.call(this,e,t,{resize:!1,header:!1}),this.container_div.addClass("label-track")};I(Q.prototype,X.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(t){for(var i=this.view,n=i.high-i.low,a=Math.floor(Math.pow(10,Math.floor(Math.log(n)/Math.log(10)))),s=Math.floor(i.low/a)*a,o=this.view.container.width(),r=e("").addClass("label-container");s").addClass("pos-label").text(y.default.commatize(s)).css({left:l})),s+=a}this.content_div.children(":first").remove(),this.content_div.append(r)}});var Z=function(e,t,i){if(K.call(this,e,t,i),this.drawables=[],"drawables"in i){for(var n,a=0;athis.left_offset&&(this.left_offset=n.left_offset);this.enabled=!0}h.each(this.drawables,function(e){(e instanceof ne||e instanceof se)&&e.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};I(Z.prototype,K.prototype,{display_modes:G,build_config_params:function(){return h.union(R.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}])},action_icons_def:[{name:"composite_icon",title:(0,c.default)("Show individual tracks"),css_class:"layers-stack",on_click_fn:function(t){e(".tooltip").remove(),t.show_group()}}].concat(K.prototype.action_icons_def),to_dict:N.prototype.to_dict,add_drawable:N.prototype.add_drawable,unpack_drawables:N.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var e=this.visible_height_px;h.each(this.drawables,function(t){t.visible_height_px=e}),X.prototype.on_resize.call(this)},change_mode:function(e){K.prototype.change_mode.call(this,e);for(var t=0;ts&&(s=o)}for(a=0;athis.view.canvas_manager.char_width_px?(this.tiles_div.show(),n=!0,s=K.prototype.draw_helper.call(this,e,t,i)):(n=!1,this.tiles_div.hide()),a!==n&&this.view.resize_viewport(),s},can_subset:function(e){return!0},draw_tile:function(e,t,i,n,a){var s=this.data_manager.subset_entry(e,n),o=s.data,r=t.canvas;t.font=t.canvas.manager.default_font,t.textAlign="center";for(var l=0,d=o.length;l12e3?"Squish":"Pack"},get_canvas_height:function(e,t,i,n){if("Coverage"===t||"bigwig"===e.dataset_type)return this.summary_draw_height;var a=this.incremental_slots(i,e.data,t),s=new this.painter(null,null,null,this.config.to_key_value_dict(),t);return Math.max(this.min_height_px,s.get_required_height(a,n))},draw_tile:function(e,t,i,n,a,s,o){var r=this,l=t.canvas,d=n.get("start"),c=n.get("end"),u=this.left_offset;if("bigwig"===e.dataset_type)return this._draw_line_track_tile(e,t,i,n,a);var h=[],f=this.slotters[a].slots,p=!0;if(e.data)for(var _=this.filters_manager.filters,m=0,g=e.data.length;m1){var r;if(0===this.container_div.find(".yaxislabel.variant").length&&(r=this.config.get_value("summary_height")/2,this.tiles_div.prepend(e("").text("Summary").addClass("yaxislabel variant top").css({"font-size":r+"px",top:(this.config.get_value("summary_height")-r)/2+"px"})),this.config.get_value("show_sample_data"))){var l=o.join("
");this.tiles_div.prepend(e("").html(l).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}r=("Squish"===this.mode?5:10)+"px",e(this.tiles_div).find(".sample").css({"font-size":r,"line-height":r}),e(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var se=function(e,t,i){ne.call(this,e,t,i),this.painter=C.default.ReadPainter,this.update_icons()};I(se.prototype,R.prototype,K.prototype,ne.prototype,{build_config_params:function(){return h.union(R.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:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}])},config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var oe={CompositeTrack:Z,DrawableGroup:V,DiagonalHeatmapTrack:ie,FeatureTrack:ne,LineTrack:te,ReadTrack:se,VariantTrack:ae,VcfTrack:ae},re=function(e,t,i){if("copy"in e)return e.copy(i);var n=e.obj_type;return n||(n=e.track_type),new oe[n](t,i,e)};t.default={TracksterView:H,DrawableGroup:V,LineTrack:te,FeatureTrack:ne,DiagonalHeatmapTrack:ie,ReadTrack:se,VariantTrack:ae,CompositeTrack:Z,object_from_template:re}}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(5),d=s(l),c=i(10),u=s(c),h=i(17),f=s(h),p=i(55),_=s(p),m=i(25),g=s(m),v=e.View.extend({initialize:function(e){var t=this;this.modal=parent.Galaxy.modal||new f.default.View,this.form=new _.default(d.default.merge({listen_to_history:!0,always_refresh:!1,buildmodel:function(e,i){var a=i.model.attributes,s="",o={},l=a.job_id;l?s=Galaxy.root+"api/jobs/"+l+"/build_for_rerun":(s=Galaxy.root+"api/tools/"+a.id+"/build",o=n.extend({},Galaxy.params),o.tool_id&&delete o.tool_id),a.version&&(o.tool_version=a.version),d.default.get({url:s,data:o,success:function(n){if(!n.display)return void(window.location=Galaxy.root);i.model.set(n),t._customize(i),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",n),e.resolve()},error:function(t,s){var o=t&&t.err_msg||"Uncaught error.";401==s?window.location=Galaxy.root+"user/login?"+n.param({redirect:Galaxy.root+"?tool_id="+a.id}):i.$el.is(":empty")?i.$el.prepend(new u.default.Message({message:o,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:(0,r.default)("Tool request failed"),body:o,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",t),e.reject()}})},postchange:function(e,t){var i={tool_id:t.model.get("id"),tool_version:t.model.get("version"),inputs:n.extend(!0,{},t.data.create())};t.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",i),d.default.request({type:"POST",url:Galaxy.root+"api/tools/"+t.model.get("id")+"/build",data:i,success:function(i){t.update(i),t.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",i),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",t),e.reject()}})}},e)),this.deferred=this.form.deferred,this.setElement(""),this.$el.append(this.form.$el)},_customize:function(e){var t=this,i=e.model.attributes,n=new u.default.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:(0,r.default)("Execute"),cls:"btn btn-primary ui-clear-float",wait_cls:"btn btn-info ui-clear-float",onclick:function(){n.wait(),e.portlet.disable(),t.submit(i,function(){n.unwait(),e.portlet.enable()})}});if(i.buttons={execute:n},i.job_id&&i.job_remap){if("job_produced_collection_elements"===i.job_remap)var a="Replace elements in collection ?",s="The previous run of this tool failed. Use this option to replace the failed element(s) in the dataset collectio that were produced during the previous tool run.";else var a="Resume dependencies from this job ?",s="The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.";i.inputs.push({label:a,name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:s})}var o={};Galaxy.user.attributes.preferences&&"extra_user_preferences"in Galaxy.user.attributes.preferences&&(o=JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences)),"true"===("use_cached_job|use_cached_job_checkbox"in o&&o["use_cached_job|use_cached_job_checkbox"])&&i.inputs.push({label:"BETA: Attempt to re-use jobs with identical parameters ?",help:"This may skip executing jobs that you have already run",name:"use_cached_job",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["No",!1],["Yes",!0]]})},submit:function(e,t){var i=this,s={tool_id:e.id,tool_version:e.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(s))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(t&&t());if(e.action!==Galaxy.root+"tool_runner/index"){var o=n("").attr({action:e.action,method:e.method,enctype:e.enctype});return a.each(s.inputs,function(e,t){o.append(n("").attr({name:t,value:e}))}),o.hide().appendTo("body").submit().remove(),void(t&&t())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",s),d.default.request({type:"POST",url:Galaxy.root+"api/tools",data:s,success:function(e){if(t&&t(),i.$el.children().hide(),i.$el.append(i._templateSuccess(e)),e.jobs&&e.jobs.length>0){i.$el.append(n("",{id:"webhook-view"}));new g.default.WebhookView({type:"tool",toolId:s.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(e){t&&t(),Galaxy.emit.debug("tool-form::submit","Submission failed.",e);var n=!1;if(e&&e.err_data){var a=i.form.data.matchResponse(e.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:(0,r.default)("Job submission failed"),body:i._templateError(s,e&&e.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(e){var t=this,i=e.inputs,n=-1,a=null;for(var s in i){var o=i[s],r=this.form.data.match(s),l=this.form.field_list[r],d=this.form.input_list[r];if(r&&d&&l){if(!d.optional&&null==o)return this.form.highlight(r),!1;if(l.validate){var c=function(){t.form.trigger("reset")},u=l.validate(c);if(!u.valid)return this.form.highlight(r,u.message),!1}if(o&&o.batch){var h=o.values.length,f=h>0&&o.values[0]&&o.values[0].src;if(f)if(null===a)a=f;else if(a!==f)return this.form.highlight(r,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===n)n=h;else if(n!==h)return this.form.highlight(r,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+h+" selection(s) while a previous field contains "+n+"."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(e){if(e.jobs&&e.jobs.length>0){var t=e.jobs.length,i=1==t?"1 job has":t+" jobs have",s=n("").addClass("donemessagelarge").append(n("").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(e.outputs,function(e){s.append(n("").addClass("messagerow").append(n("").text(e.hid+": "+e.name)))}),s.append(n("").append("").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),s}return this._templateError(e,"Invalid success response. No jobs found.")},_templateError:function(e,t){return n("").addClass("errormessagelarge").append(n("").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(t||""))).append(n("").text(JSON.stringify(e,null,4)))}});t.default={View:v}}).call(t,i(2),i(0),i(1))},,,function(e,t,i){"use strict";function n(e){i(88)}Object.defineProperty(t,"__esModule",{value:!0});var a=i(43),s=i.n(a);for(var o in a)"default"!==o&&function(e){i.d(t,e,function(){return a[e]})}(o);var r=i(136),l=i(23),d=n,c=Object(l.a)(s.a,r.a,r.b,!1,d,null,null);t.default=c.exports},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(6),l=o(r),d=i(3),c=(o(d),e.View.extend(l.default.LoggableMixin).extend({_logNamespace:"list",initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=n(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):n(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",a.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=n(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?s.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}})),u=c.extend(l.default.mixin(l.default.SelectableViewMixin,l.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){c.prototype.initialize.call(this,e),l.default.SelectableViewMixin.initialize.call(this,e),l.default.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=c.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return c.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=n(''),i=e.model.toJSON();return a.each(e.templates.warnings,function(a){t.append(n(a(i,e)))}),t},_renderTitleBar:function(){return n(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){return!e||"keydown"!==e.type||32!==e.keyCode&&13!==e.keyCode||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){return"ListItemView("+(this.model?""+this.model:"(no model)")+")"}}));u.prototype.templates=function(){return{el:l.default.wrapTemplate([''),i.join(" ")},tagsToCSV:function(){var e=this,t=this.model.get("tags");return!n.isArray(t)||n.isEmpty(t)?"":t.map(function(t){return n.escape(e._nameToHash(t))}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){var e=this;return n.map(Galaxy.user.get("tags_used"),e._nameToHash)},_setUpBehaviors:function(){var e=this;this.$input().on("change",function(t){t.val=n.map(t.val,e._hashToName),e.model.save({tags:t.val}),t.added&&e._addNewTagToTagsUsed(""+t.added.text)})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");n.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",""+this.model,")"].join("")}});t.default={TagsEditor:d}}).call(t,i(2),i(1))},,function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function a(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}function s(e,t){return this._init(e||{},t||{})}Object.defineProperty(t,"__esModule",{value:!0});var o=i(1),r=a(o),l=i(2),d=a(l),c=i(6),u=n(c),h=i(60),f=n(h),p=i(72),_=n(p),m=i(71),g=n(m),v=i(3),w=n(v);(0,g.default)(s,"GalaxyApp");var y="galaxy:debug:namespaces",b=!1;try{b="true"==localStorage.getItem("galaxy:debug")}catch(e){console.log((0,w.default)("localStorage not available for debug flag retrieval"))}s.prototype._init=function(e,t){var i=this;return r.extend(i,d.Events),b&&(i.logger=console,console.debug("debugging galaxy:","options:",e,"bootstrapped:",t)),i._processOptions(e),i.root=e.root||"/",i.params=e.params||{},i.session_csrf_token=e.session_csrf_token||null,i._initConfig(e.config||{}),i._patchGalaxy(window.Galaxy),i._initLogger(i.options.loggerOptions||{}),i.debug("GalaxyApp.options: ",i.options),i.debug("GalaxyApp.config: ",i.config),i.debug("GalaxyApp.logger: ",i.logger),i._initLocale(),i.debug("GalaxyApp.localize: ",i.localize),i.config=e.config||{},i.debug("GalaxyApp.config: ",i.config),i._initUser(e.user||{}),i.debug("GalaxyApp.user: ",i.user),i._initUserLocale(),i.debug("currentLocale: 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t.debug("_initUser:",e),t.user=new f.default.User(e),t.user.logger=t.logger,t},s.prototype._setUpListeners=function(){var t=this;return t.lastAjax={},e(document).bind("ajaxSend",function(e,i,n){var a=n.data;try{a=JSON.parse(a)}catch(e){}t.lastAjax={url:location.href.slice(0,-1)+n.url,data:a}}),t},s.prototype.debugging=function(e){var t=this;try{if(void 0===e)return"true"===localStorage.getItem("galaxy:debug");if(e)return localStorage.setItem("galaxy:debug",!0),!0;localStorage.removeItem("galaxy:debug"),t.debuggingNamespaces(null)}catch(e){console.log((0,w.default)("localStorage not available for debug flag retrieval"))}return!1},s.prototype.debuggingNamespaces=function(e){var t=this;try{if(void 0===e){var i=localStorage.getItem(y);return"string"==typeof i?i.split(","):[]}null===e?localStorage.removeItem(y):localStorage.setItem(y,e);var n=t.debuggingNamespaces();return t.logger&&(t.logger.options.consoleNamespaceWhitelist=n),n}catch(e){console.log((0,w.default)("localStorage not 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e(".tooltip").remove(),this.$el.removeClass().addClass(this.model.get("disabled")&&"disabled").addClass(this.model.get("active")&&"active").addClass(this.model.get("menu")&&"dropdown").attr("id",this.model.id).css({visibility:this.model.get("visible")&&"visible"||"hidden"}),this.model.set("url",this._formatUrl(this.model.get("url"))),this.$note.html(this.model.get("note")||"").removeClass().addClass("nav-note").addClass(this.model.get("note_cls")).css({display:this.model.get("show_note")&&"block"||"none"}),this.$link.html(this.model.get("title")||"").removeClass().addClass("nav-link").addClass(this.model.get("cls")).addClass(this.model.get("icon")&&"nav-icon fa 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t=l.defaults(t||{},{title:"",url:"",target:"_parent",noscratchbook:!1}),t.url=this._formatUrl(t.url),e("").addClass("dropdown-item").attr("href",t.url).attr("target",t.target).html(t.title).on("click",function(e){e.preventDefault(),i.model.set("show_menu",!1),t.onclick?t.onclick():Galaxy.frame.add(t)})},buildLink:function(t,i){return e("").append(e("").attr("href",Galaxy.root+i).html(t)).html()},_toggleClick:function(t){var i=this,n=this.model;t.preventDefault(),e(".tooltip").hide(),n.trigger("dispatch",function(e){n.id!==e.id&&e.get("menu")&&e.set("show_menu",!1)}),n.get("disabled")?(this.$link.popover&&this.$link.popover("dispose"),this.$link.popover({html:!0,placement:"bottom",content:"Please "+this.buildLink("login","user/login?use_panels=True")+" or "+this.buildLink("register","user/create?use_panels=True")+" to use this 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i=window.Galaxy.config.communication_server_host,n=window.Galaxy.config.communication_server_port,a=l.escape(window.Galaxy.user.attributes.username),s=l.escape(window.Galaxy.config.persistent_communication_rooms),o="?username="+a+"&persistent_communication_rooms="+s,r=i+":"+n+o,d=null,c=null,u='';return e(".chat-modal").length>0&&e(".chat-modal").remove(),f.modal=new h.default.View({body:u,height:350,width:600,closing_events:!0,title_separator:!1,cls:"ui-modal chat-modal"}),f.modal.show(),d=e(".chat-modal .modal-header"),c=e(".chat-modal .modal-body"),d.addClass("modal-header-body"),c.addClass("modal-header-body"),d.find("h4").remove(),d.removeAttr("min-height padding border"),d.append(''),e(".close-modal").click(function(t){e(".chat-modal").css("display","none")}),e(".expand-compress-modal").click(function(t){e(".expand-compress-modal").hasClass("fa-expand")?(e(".chat-modal .modal-dialog").width("1000px"),e(".chat-modal 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s=i(9),o=a(s),r=i(1),l=a(r),d=i(77),c=n(d),u=i(14),h=n(u),f=i(15),p=n(f),_=i(61),m=n(_),g=i(3),v=n(g);t.default=o.View.extend({initialize:function(e){var t=this;e=e||{},this.frames=new c.default.View({visible:!1}),this.setElement(this.frames.$el),this.buttonActive=e.collection.add({id:"enable-scratchbook",icon:"fa-th",tooltip:(0,v.default)("Enable/Disable Scratchbook"),onclick:function(){t.active=!t.active,t.buttonActive.set({toggle:t.active,show_note:t.active,note_cls:t.active&&"fa fa-check"}),t.active||t.frames.hide()},onbeforeunload:function(){if(t.frames.length()>0)return"You opened "+t.frames.length()+" frame(s) which will be lost."}}),this.buttonLoad=e.collection.add({id:"show-scratchbook",icon:"fa-eye",tooltip:(0,v.default)("Show/Hide Scratchbook"),show_note:!0,visible:!1,onclick:function(e){t.frames.visible?t.frames.hide():t.frames.show()}}),this.frames.on("add 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a=n.dataset_ids,s=a.indexOf(e.get("id"));if(-1!==s&&s+i>=0&&s+it.top+t.height-1||e.top+e.height-1t[1]?1:0}),d.each(s,function(e){a._framePlace(e[0],n)}),this.top_max=0,d.each(this.frame_list,function(e){null!==e.grid_location&&(a.top_max=Math.max(a.top_max,e.grid_location.top+e.grid_location.height))}),this.top_max=e(window).height()-this.top_max*this.options.cell-2*this.options.margin,this.top_max=Math.min(this.top_max,this.options.top_min),this.render()},_framePlace:function(e,t){e.grid_location=null;for(var i=this._toGrid(this._frameScreen(e)),n=!1,a=0;a
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Use this option to replace the failed element(s) in the dataset collectio that were produced during the previous tool run.";else var a="Resume dependencies from this job ?",s="The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.";i.inputs.push({label:a,name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:s})}var o={};Galaxy.user.attributes.preferences&&"extra_user_preferences"in Galaxy.user.attributes.preferences&&(o=JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences)),"true"===("use_cached_job|use_cached_job_checkbox"in o&&o["use_cached_job|use_cached_job_checkbox"])&&i.inputs.push({label:"BETA: Attempt to re-use jobs with identical parameters ?",help:"This may skip executing jobs that you have already run",name:"use_cached_job",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["No",!1],["Yes",!0]]})},submit:function(e,t){var i=this,s={tool_id:e.id,tool_version:e.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!i.validate(s))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(t&&t());if(e.action!==Galaxy.root+"tool_runner/index"){var o=n("").attr({action:e.action,method:e.method,enctype:e.enctype});return a.each(s.inputs,function(e,t){o.append(n("").attr({name:t,value:e}))}),o.hide().appendTo("body").submit().remove(),void(t&&t())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",s),d.default.request({type:"POST",url:Galaxy.root+"api/tools",data:s,success:function(e){if(t&&t(),i.$el.children().hide(),i.$el.append(i._templateSuccess(e)),e.jobs&&e.jobs.length>0){i.$el.append(n("",{id:"webhook-view"}));new g.default.WebhookView({type:"tool",toolId:s.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(e){t&&t(),Galaxy.emit.debug("tool-form::submit","Submission failed.",e);var n=!1;if(e&&e.err_data){var a=i.form.data.matchResponse(e.err_data);for(var o in a){i.form.highlight(o,a[o]),n=!0;break}}n||i.modal.show({title:(0,r.default)("Job submission failed"),body:i._templateError(s,e&&e.err_msg),buttons:{Close:function(){i.modal.hide()}}})}})},validate:function(e){var t=this,i=e.inputs,n=-1,a=null;for(var s in i){var o=i[s],r=this.form.data.match(s),l=this.form.field_list[r],d=this.form.input_list[r];if(r&&d&&l){if(!d.optional&&null==o)return this.form.highlight(r),!1;if(l.validate){var c=function(){t.form.trigger("reset")},u=l.validate(c);if(!u.valid)return this.form.highlight(r,u.message),!1}if(o&&o.batch){var h=o.values.length,f=h>0&&o.values[0]&&o.values[0].src;if(f)if(null===a)a=f;else if(a!==f)return this.form.highlight(r,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===n)n=h;else if(n!==h)return this.form.highlight(r,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+h+" selection(s) while a previous field contains "+n+"."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(e){if(e.jobs&&e.jobs.length>0){var t=e.jobs.length,i=1==t?"1 job has":t+" jobs have",s=n("").addClass("donemessagelarge").append(n("").text(i+" been successfully added to the queue - resulting in the following datasets:"));return a.each(e.outputs,function(e){s.append(n("").addClass("messagerow").append(n("").text(e.hid+": "+e.name)))}),s.append(n("").append("").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),s}return this._templateError(e,"Invalid success response. No jobs found.")},_templateError:function(e,t){return n("").addClass("errormessagelarge").append(n("").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(t||""))).append(n("").text(JSON.stringify(e,null,4)))}});t.default={View:v}}).call(t,i(2),i(0),i(1))},,,function(e,t,i){"use strict";function n(e){i(88)}Object.defineProperty(t,"__esModule",{value:!0});var a=i(43),s=i.n(a);for(var o in a)"default"!==o&&function(e){i.d(t,e,function(){return a[e]})}(o);var r=i(136),l=i(23),d=n,c=Object(l.a)(s.a,r.a,r.b,!1,d,null,null);t.default=c.exports},function(e,t,i){"use strict";(function(e,n,a,s){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(6),l=o(r),d=i(3),c=(o(d),e.View.extend(l.default.LoggableMixin).extend({_logNamespace:"list",initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=n(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):n(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",a.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=n(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?s.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}})),u=c.extend(l.default.mixin(l.default.SelectableViewMixin,l.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){c.prototype.initialize.call(this,e),l.default.SelectableViewMixin.initialize.call(this,e),l.default.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=c.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return c.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=n(''),i=e.model.toJSON();return a.each(e.templates.warnings,function(a){t.append(n(a(i,e)))}),t},_renderTitleBar:function(){return n(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){return!e||"keydown"!==e.type||32!==e.keyCode&&13!==e.keyCode||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){return"ListItemView("+(this.model?""+this.model:"(no model)")+")"}}));u.prototype.templates=function(){return{el:l.default.wrapTemplate(['
','','
"]),warnings:{},titleBar:l.default.wrapTemplate(['','',"
",'','','',"','','
"],"element"),subtitle:l.default.wrapTemplate(['']),details:l.default.wrapTemplate([''])}}();var h=u.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,u.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return n();var e=u.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e);return new t(a.extend(i,{model:e}))},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});h.prototype.templates=function(){var e=l.default.wrapTemplate(['','<%- element.name %>',"
",'',"',"
"],"collection");return a.extend({},u.prototype.templates,{details:e})}(),t.default={ExpandableView:c,ListItemView:u,FoldoutListItemView:h}}).call(t,i(2),i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(6),o=a(s),r=i(3),l=a(r),d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",select_width:"100%",events:{},initialize:function(e){this.show_editor=!1,!1===e.usePrompt?this.label="":this.label='",this.workflow_mode=e.workflow_mode||!1,this.workflow_mode&&(this.events.click="showEditor",this.events.keydown="keydownHandler"),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.workflow_mode?this.$el.html(this._workflowTemplate()):this.$el.html(this._defaultTemplate()),this.$input().select2({placeholder:"Add tags",width:this.workflow_mode?this.width:this.select_width,tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_hashToName:function(e){return e.startsWith("#")?"name:"+e.slice(1):e},_nameToHash:function(e){return e.startsWith("name:")&&(e="#"+e.slice(5)),e},_defaultTemplate:function(){return[this.label,this._renderEditor()].join("")},_workflowTemplate:function(){return[this.show_editor?this._renderEditor():this._renderTags()].join(" ")},keydownHandler:function(e){switch(e.which){case 27:this.hideEditor()}},showEditor:function(){this.show_editor=!0,this.render()},hideEditor:function(){this.show_editor=!1,this.render()},_renderEditor:function(){return''},_renderTags:function(){var e=this.model.get("tags"),t=Galaxy.root+"static/images/fugue/tag--plus.png",i=[];return n.each(e,function(e){e=0==e.indexOf("name:")?e.slice(5):e;var t=''+e+"";i.push(t)}),0===i.length&&i.push("| '+this.grid_header(e)+' | \n\n | \n |
| \n | \n | \n |
'+e.info_text+"
"),t},grid_table:function(){return'\n '},grid_header:function(e){var t='';if(!e.embedded){var i="";e.title_id&&(i+=' id="'+e.title_id+'"'),t+=""+e.title+""}if(e.global_actions){t+='
"},header:function(e){var t="- ';var n=e.global_actions.length>=3;n&&(t+='
- Actions
- '+d.label+" "}}catch(e){s=!0,o=e}finally{try{!a&&l.return&&l.return()}finally{if(s)throw o}}n&&(t+="
');var a=!0,s=!1,o=void 0;try{for(var r,l=e.global_actions[Symbol.iterator]();!(a=(r=l.next()).done);a=!0){var d=r.value;t+='
"),t+="':p.attach_popup&&g?i+='
\n \n \n
':p.attach_popup?i+='":i+=g?''+v+"":"",i+="'+o.escape(e.message)+'
'},grid_filters:function(e){var t=e.default_filter_dict,i=e.filters,n="none";e.advanced_search&&(n="block");var a=!1,s=!0,o=!1,r=void 0;try{for(var l,d=e.columns[Symbol.iterator]();!(s=(l=d.next()).done);s=!0){var c=l.value;if("advanced"==c.filterable){var u=c.key,h=i[u],f=t[u];h&&f&&h!=f&&(n="block"),a=!0}}}catch(e){o=!0,r=e}finally{try{!s&&d.return&&d.return()}finally{if(o)throw r}}var p="block";"block"==n&&(p="none");var _='| ",a&&(_+='Advanced Search'),_+=" |
| Close Advanced Search |