From 600112256970c1024b3ba4e6fa57cd61f9fe199d Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 13 Oct 2016 22:45:16 -0400 Subject: [PATCH 1/3] remove the communication server check from non-galaxy calls --- templates/user/index.mako | 3 --- 1 file changed, 3 deletions(-) diff --git a/templates/user/index.mako b/templates/user/index.mako index 9922659d0d9..7acad136793 100644 --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -22,9 +22,6 @@ %else:
  • ${_('Manage your information')}
  • ${_('Change your password')}
    • - %if trans.app.config.enable_communication_server: -
  • ${_('Change your communication settings')}
    • - %endif
  • ${_('Manage your API keys')}
  • ${_('Manage your email alerts')}
  • ${_('Logout')} ${_('of all user sessions')}
    • From 096a7bf94d799f905013f7052c1bdf87062a45a7 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 20 Oct 2016 20:46:47 -0400 Subject: [PATCH 2/3] fix the incorrect handling of root when prefix is in play --- .../mvc/library/library-dataset-view.js | 4 +-- .../mvc/library/library-folderrow-view.js | 2 +- .../mvc/library/library-foldertoolbar-view.js | 4 +-- .../mvc/library/library-dataset-view.js.map | 2 +- .../mvc/library/library-folderrow-view.js.map | 2 +- .../library/library-foldertoolbar-view.js.map | 2 +- static/scripts/bundled/analysis.bundled.js | 23 +++++++------ .../scripts/bundled/analysis.bundled.js.map | 2 +- static/scripts/bundled/libs.bundled.js | 32 +++++++++---------- static/scripts/bundled/libs.bundled.js.map | 2 +- .../mvc/library/library-dataset-view.js | 2 +- .../mvc/library/library-folderrow-view.js | 2 +- .../mvc/library/library-foldertoolbar-view.js | 2 +- 13 files changed, 40 insertions(+), 41 deletions(-) diff --git a/client/galaxy/scripts/mvc/library/library-dataset-view.js b/client/galaxy/scripts/mvc/library/library-dataset-view.js index e7f51f1a499..dfa7dab4e7e 100644 --- a/client/galaxy/scripts/mvc/library/library-dataset-view.js +++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js @@ -186,7 +186,7 @@ var LibraryDatasetView = Backbone.View.extend({ this.histories.fetch({ success: function (histories){ if (histories.length === 0){ - mod_toastr.warning('You have to create history first. Click this to do so.', '', {onclick: function() {window.location='/';}}); + mod_toastr.warning('You have to create history first. Click this to do so.', '', {onclick: function() {window.location=Galaxy.root;}}); } else { callback(self); } @@ -233,7 +233,7 @@ var LibraryDatasetView = Backbone.View.extend({ historyItem.save({ content : this.id, source : 'library' }, { success : function(){ Galaxy.modal.hide(); - mod_toastr.success('Dataset imported. Click this to start analyzing it.', '', {onclick: function() {window.location='/';}}); + mod_toastr.success('Dataset imported. Click this to start analyzing it.', '', {onclick: function() {window.location=Galaxy.root;}}); }, error : function(model, response){ if (typeof response.responseJSON !== "undefined"){ diff --git a/client/galaxy/scripts/mvc/library/library-folderrow-view.js b/client/galaxy/scripts/mvc/library/library-folderrow-view.js index 67f450ba308..ebb2d5e2822 100644 --- a/client/galaxy/scripts/mvc/library/library-folderrow-view.js +++ b/client/galaxy/scripts/mvc/library/library-folderrow-view.js @@ -112,7 +112,7 @@ var FolderRowView = Backbone.View.extend({ Galaxy.libraries.folderListView.collection.sortByNameAsc(); mod_toastr.success('Dataset undeleted. Click this to see it.', '', {onclick: function() { var folder_id = that.model.get('folder_id'); - window.location='#folders/' + folder_id + '/datasets/' + that.id; + window.location = Galaxy.root + 'library/list#folders/' + folder_id + '/datasets/' + that.id; }}); }, error : function(model, response){ diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js index 5a34894251f..411bad9fcf5 100644 --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -764,11 +764,11 @@ var FolderToolbarView = Backbone.View.extend({ var popped_item = history_item_set.pop(); if ( typeof popped_item == "undefined" ) { if ( this.options.chain_call_control.failed_number === 0 ){ - mod_toastr.success( 'Selected datasets imported into history. Click this to start analyzing it.', '', { onclick: function() { window.location='/' } } ); + mod_toastr.success( 'Selected datasets imported into history. Click this to start analyzing it.', '', { onclick: function() { window.location=Galaxy.root } } ); } else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){ mod_toastr.error( 'There was an error and no datasets were imported into history.' ); } else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){ - mod_toastr.warning( 'Some of the datasets could not be imported into history. Click this to see what was imported.', '', { onclick: function() { window.location='/' } } ); + mod_toastr.warning( 'Some of the datasets could not be imported into history. Click this to see what was imported.', '', { onclick: function() { window.location=Galaxy.root } } ); } Galaxy.modal.hide(); return true; diff --git a/static/maps/mvc/library/library-dataset-view.js.map b/static/maps/mvc/library/library-dataset-view.js.map index 308e5254b56..cecbc1ce870 100644 --- a/static/maps/mvc/library/library-dataset-view.js.map +++ b/static/maps/mvc/library/library-dataset-view.js.map @@ -1 +1 @@ -{"version":3,"file":"library-dataset-view.js","sources":["../../../src/mvc/library/library-dataset-view.js"],"names":["define","mod_toastr","mod_library_model","mod_utils","mod_select","LibraryDatasetView","Backbone","View","extend","el","model","options","events","click .toolbtn_modify_dataset","click .toolbtn_cancel_modifications","click .toolbtn-download-dataset","click .toolbtn-import-dataset","click .toolbtn-share-dataset","click .btn-copy-link-to-clipboard","click .btn-make-private","click .btn-remove-restrictions","click .toolbtn_save_permissions","click 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    "))),this.listenTo(this.model,"change",this.render,this),this.render()},value:function(t){return void 0!==t&&this.model.set("value",t),this.model.get("value")},render:function(){return this.$el.attr("id",this.model.id),this.$hidden.val(this.model.get("value")),this.model.get("info")?this.$info.show().html(this.model.get("info")):this.$info.hide(),this}});return{Button:l.ButtonDefault,ButtonIcon:l.ButtonIcon,ButtonCheck:l.ButtonCheck,ButtonMenu:l.ButtonMenu,ButtonLink:l.ButtonLink,Input:h,Label:c,Message:d,Modal:r,RadioButton:n.RadioButton,Checkbox:n.Checkbox,Radio:n.Radio,Select:e,Hidden:u,Slider:i,Drilldown:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1))},,function(t,e,i){var n,s;(function(a,o,l){n=[i(4),i(7)],s=function(t,e){var i=a.View.extend({visible:!1,initialize:function(i){var n=this;this.model=i&&i.model||new a.Model({id:t.uid(),cls:"ui-portlet",title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,collapsible:!1,collapsible_button:!1,collapsed:!1}).set(i),this.setElement(this._template()),this.$body=this.$(".portlet-body"),this.$title_text=this.$(".portlet-title-text"),this.$title_icon=this.$(".portlet-title-icon"),this.$header=this.$(".portlet-header"),this.$content=this.$(".portlet-content"),this.$footer=this.$(".portlet-footer"),this.$backdrop=this.$(".portlet-backdrop"),this.$buttons=this.$(".portlet-buttons"),this.$operations=this.$(".portlet-operations"),this.model.get("body")&&this.append(this.model.get("body")),this.collapsible_button=new e.ButtonIcon({icon:"fa-eye",tooltip:"Collapse/Expand",cls:"ui-button-icon-plain",onclick:function(){n[n.collapsed?"expand":"collapse"]()}}),this.render()},render:function(){var t=this,e=this.model.attributes;return this.$el.removeClass().addClass(e.cls).attr("id",e.id),this.$header[e.title?"show":"hide"](),this.$title_text.html(e.title),o.each([this.$content,this.$body],function(t){t[e.nopadding?"addClass":"removeClass"]("no-padding")}),e.icon?this.$title_icon.removeClass().addClass("portlet-title-icon fa").addClass(e.icon).show():this.$title_icon.hide(),this.$title_text[e.collapsible?"addClass":"removeClass"]("no-highlight collapsible").off(),e.collapsible&&(this.$title_text.on("click",function(){t[t.collapsed?"expand":"collapse"]()}),e.collapsed?this.collapse():this.expand()),e.buttons?(this.$buttons.empty().show(),l.each(this.model.get("buttons"),function(e,i){i.$el.prop("id",e),t.$buttons.append(i.$el)})):this.$buttons.hide(),this.$operations.empty,e.collapsible_button&&this.$operations.append(this.collapsible_button.$el),e.operations&&l.each(e.operations,function(e,i){i.$el.prop("id",e),t.$operations.append(i.$el)}),this},append:function(t){this.$body.append(t)},empty:function(){this.$body.empty()},header:function(){return this.$header},body:function(){return this.$body},footer:function(){return this.$footer},show:function(){this.visible=!0,this.$el.fadeIn("fast")},hide:function(){this.visible=!1,this.$el.fadeOut("fast")},enableButton:function(t){this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(t){this.$buttons.find("#"+t).prop("disabled",!0)},hideOperation:function(t){this.$operations.find("#"+t).hide()},showOperation:function(t){this.$operations.find("#"+t).show()},setOperation:function(t,e){this.$operations.find("#"+t).off("click").on("click",e)},title:function(t){return t&&this.$title_text.html(t),this.$title_text.html()},collapse:function(){this.collapsed=!0,this.$content.height("0%"),this.$body.hide(),this.$footer.hide(),this.collapsible_button.setIcon("fa-eye-slash")},expand:function(){this.collapsed=!1,this.$content.height("100%"),this.$body.fadeIn("fast"),this.$footer.fadeIn("fast"),this.collapsible_button.setIcon("fa-eye")},disable:function(){this.$backdrop.show()},enable:function(){this.$backdrop.hide()},_template:function(){return l("
    ").append(l("
    ").addClass("portlet-header").append(l("
    ").addClass("portlet-operations")).append(l("
    ").addClass("portlet-title").append(l("").addClass("portlet-title-icon")).append(l("").addClass("portlet-title-text")))).append(l("
    ").addClass("portlet-content").append(l("
    ").addClass("portlet-body")).append(l("
    ").addClass("portlet-buttons"))).append(l("
    ").addClass("portlet-footer")).append(l("
    ").addClass("portlet-backdrop"))}});return{View:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(2),i(1))},function(t,e,i){var n,s;n=[],s=function(){"use strict";var t={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};return t.READY_STATES=[t.OK,t.EMPTY,t.PAUSED,t.FAILED_METADATA,t.NOT_VIEWABLE,t.DISCARDED,t.ERROR],t.NOT_READY_STATES=[t.UPLOAD,t.QUEUED,t.RUNNING,t.SETTING_METADATA,t.NEW],t}.apply(e,n),!(void 0!==s&&(t.exports=s))},,function(t,e,i){var n,s;(function(a,o,l){n=[i(8),i(24),i(15)],s=function(t,e,i){var n=a.Model.extend({}),s=a.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.get("metadata")||this._set_metadata(),this.on("change",this._set_metadata,this)},_set_metadata:function(){var t=new n;o.each(o.keys(this.attributes),function(e){if(0===e.indexOf("metadata_")){var i=e.split("metadata_")[1];t.set(i,this.attributes[e]),delete this.attributes[e]}},this),this.set("metadata",t,{silent:!0})},get_metadata:function(t){return this.attributes.metadata.get(t)},urlRoot:Galaxy.root+"api/datasets"}),r=s.extend({defaults:o.extend({},s.prototype.defaults,{chunk_url:null,first_data_chunk:null,offset:0,at_eof:!1}),initialize:function(t){s.prototype.initialize.call(this),this.attributes.first_data_chunk&&(this.attributes.offset=this.attributes.first_data_chunk.offset),this.attributes.chunk_url=Galaxy.root+"dataset/display?dataset_id="+this.id,this.attributes.url_viz=Galaxy.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof)return null;var t=this,e=l.Deferred();return l.getJSON(this.attributes.chunk_url,{offset:t.attributes.offset}).success(function(i){var n;""!==i.ck_data?(n=i,t.attributes.offset=i.offset):(t.attributes.at_eof=!0,n=null),e.resolve(n)}),e}}),c=a.Collection.extend({model:s}),d=a.View.extend({initialize:function(t){this.row_count=0,this.loading_chunk=!1,new p({model:t.model,$el:this.$el})},expand_to_container:function(){this.$el.height()").attr("id","loading_indicator"),this.$el.append(this.loading_indicator);var t=l("").attr({id:"content_table",cellpadding:0});this.$el.append(t);var e=this.model.get_metadata("column_names"),i=l("").appendTo(t),n=l("").appendTo(i);if(e)n.append("");else for(var s=1;s<=this.model.get_metadata("columns");s++)n.append("");var a=this,o=this.model.get("first_data_chunk");o?this._renderChunk(o):l.when(a.model.get_next_chunk()).then(function(t){a._renderChunk(t)}),this.scroll_elt.scroll(function(){a.attempt_to_fetch()})},scrolled_to_bottom:function(){return!1},_renderCell:function(t,e,i){var n=l("");e.append(t),this.row.append(e)},appendHeader:function(){this.$thead.append(this.row),this.row=o("")},add:function(t,e,i){var n=o("");e&&n.css("width",e),i&&n.css("text-align",i),n.append(t),this.row.append(n)},append:function(t,e){this._commit(t,e,!1)},prepend:function(t,e){this._commit(t,e,!0)},get:function(t){return this.$el.find("#"+t)},del:function(t){var e=this.$tbody.find("#"+t);e.length>0&&(e.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(t){this.before=this.$tbody.find(".current").attr("id"),void 0!==t&&(this.$tbody.find("tr").removeClass("current"),t&&this.$tbody.find("#"+t).addClass("current"));var e=this.$tbody.find(".current").attr("id");return void 0===e?null:(e!=this.before&&this.options.onchange&&this.options.onchange(t),e)},size:function(){return this.$tbody.find("tr").length},_commit:function(t,e,i){this.del(t),this.row.attr("id",t),i?this.$tbody.prepend(this.row):this.$tbody.append(this.row),e&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return o('')},_onclick:function(t){var e=this.value(),i=o(t.target).closest("tr").attr("id");""!=i&&i&&e!=i&&(this.options.onconfirm?this.options.onconfirm(i):this.value(i))},_ondblclick:function(t){var e=this.value();e&&this.options.ondblclick&&this.options.ondblclick(e)},_refresh:function(){0==this.row_count?this.$tmessage.show():this.$tmessage.hide()},_template:function(t){return'
    "+e.join("")+""+s+"").text(t),s=this.model.get_metadata("column_types");return void 0!==i?n.attr("colspan",i).addClass("stringalign"):s&&e"),n=this.model.get_metadata("columns");return this.row_count%2!==0&&i.addClass("dark_row"),e.length===n?o.each(e,function(t,e){i.append(this._renderCell(t,e))},this):e.length>n?(o.each(e.slice(0,n-1),function(t,e){i.append(this._renderCell(t,e))},this),i.append(this._renderCell(e.slice(n-1).join("\t"),n-1))):n>5&&e.length===n-1?(o.each(e,function(t,e){i.append(this._renderCell(t,e))},this),i.append(l(""))):i.append(this._renderCell(t,0,n)),this.row_count++,i},_renderChunk:function(t){var e=this.$el.find("table");o.each(t.ck_data.split("\n"),function(t,i){""!==t&&e.append(this._renderRow(t))},this)}}),h=d.extend({initialize:function(t){d.prototype.initialize.call(this,t),scroll_elt=o.find(this.$el.parents(),function(t){return"auto"===l(t).css("overflow")}),scroll_elt||(scroll_elt=window),this.scroll_elt=l(scroll_elt)},scrolled_to_bottom:function(){return this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0}}),u=d.extend({initialize:function(t){d.prototype.initialize.call(this,t),this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:t.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}}),p=a.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(t){function e(t,e){for(var i=0;i").attr("type","button").append(this.$icon=o("")).append(this.$title=o("")).append(this.$progress=o("
    ").append(this.$progress_bar=o("
    ")))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var t=this,e=this.model.attributes;this.$el.removeClass().addClass("ui-button-default").addClass(e.disabled&&"disabled").attr("id",e.id).attr("disabled",e.disabled).css("float",e.floating).off("click").on("click",function(){o(".tooltip").hide(),e.onclick&&!t.disabled&&e.onclick()}).tooltip({title:e.tooltip,placement:"bottom"}),this.$progress.addClass("progress").css("display",e.percentage!==-1?"block":"none"),this.$progress_bar.addClass("progress-bar").css({width:e.percentage+"%"}),this.$icon.removeClass().addClass("icon fa"),this.$title.removeClass().addClass("title"),e.wait?(this.$el.addClass(e.wait_cls).prop("disabled",!0),this.$icon.addClass("fa-spinner fa-spin ui-margin-right"),this.$title.html(e.wait_text)):(this.$el.addClass(e.cls),this.$icon.addClass(e.icon),this.$title.html(e.title),e.icon&&e.title&&this.$icon.addClass("ui-margin-right"))},show:function(){this.$el.show()},hide:function(){this.$el.hide()},disable:function(){this.model.set("disabled",!0)},enable:function(){this.model.set("disabled",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},setIcon:function(t){this.model.set("icon",t)}}),i=e.extend({initialize:function(e){this.model=e&&e.model||new a.Model({id:t.uid(),title:"",icon:"",cls:""}).set(e),this.setElement(o("").append(this.$icon=o(""))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var t=this.model.attributes;this.$el.removeClass().addClass(t.cls).attr({id:t.id,href:t.href||"javascript:void(0)",title:t.title,target:t.target||"_top",disabled:t.disabled}).off("click").on("click",function(){t.onclick&&!t.disabled&&t.onclick()}),this.$icon.removeClass().addClass(t.icon)}}),n=a.View.extend({initialize:function(e){this.model=e&&e.model||new a.Model({id:t.uid(),title:"Select/Unselect all",icons:["fa-square-o","fa-minus-square-o","fa-check-square-o"],value:0,onchange:function(){}}).set(e),this.setElement(o("
    ").append(this.$icon=o("")).append(this.$title=o(""))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(t){var e=this,t=this.model.attributes;this.$el.addClass("ui-button-check").off("click").on("click",function(){e.model.set("value",0===e.model.get("value")&&2||0),t.onclick&&t.onclick()}),this.$title.html(t.title),this.$icon.removeClass().addClass("icon fa ui-margin-right").addClass(t.icons[t.value])},value:function(t,e){return void 0!==t&&(e&&0!==t&&(t=t!==e&&1||2),this.model.set("value",t),this.model.get("onchange")(this.model.get("value"))),this.model.get("value")}}),s=e.extend({initialize:function(e){this.model=e&&e.model||new a.Model({id:t.uid(),title:"",floating:"right",icon:"",cls:"ui-button-icon",disabled:!1}).set(e),this.setElement(o("
    ").append(this.$button=o("
    ").append(this.$icon=o("")).append(this.$title=o("")))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(t){var t=this.model.attributes;this.$el.removeClass().addClass(t.cls).addClass(t.disabled&&"disabled").attr("disabled",t.disabled).attr("id",t.id).css("float",t.floating).off("click").on("click",function(){o(".tooltip").hide(),!t.disabled&&t.onclick&&t.onclick()}),this.$button.addClass("button").tooltip({title:t.tooltip,placement:"bottom"}),this.$icon.removeClass().addClass("icon fa").addClass(t.icon),this.$title.addClass("title").html(t.title),t.icon&&t.title&&this.$icon.addClass("ui-margin-right")}}),l=e.extend({$menu:null,initialize:function(t){this.model=t&&t.model||new a.Model({id:"",title:"",floating:"right",pull:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""}).set(t),this.setElement(o("
    ").append(this.$root=o("
    ").append(this.$icon=o("")).append(this.$title=o("")))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var t=this.model.attributes;this.$el.removeClass().addClass("dropdown").addClass(t.cls).attr("id",t.id).css({"float":t.floating,display:t.visible?"block":"none"}),this.$root.addClass("root button dropdown-toggle").attr("data-toggle","dropdown").tooltip({title:t.tooltip,placement:"bottom"}).off("click").on("click",function(e){o(".tooltip").hide(),e.preventDefault(),t.onclick&&t.onclick()}),this.$icon.removeClass().addClass("icon fa").addClass(t.icon),this.$title.removeClass().addClass("title").html(t.title),t.icon&&t.title&&this.$icon.addClass("ui-margin-right")},addMenu:function(e){var e=t.merge(e,{title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"});this.$menu||(this.$menu=o("
    '+t.content+"
    "}});return{View:e}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1))},function(t,e,i){var n,s;(function(i,a,o){n=[],s=function(){var t=i.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:!0,id:null,href:null,target:null,enabled:!0,visible:!0,tooltip_config:{}}}),e=i.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"},this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var t=this.template(this.model.toJSON());return t.tooltip(this.model.get("tooltip_config")),this.$el.replaceWith(t),this.setElement(t),this},events:{click:"click"},click:function(t){return!a.isFunction(this.model.get("on_click"))||(this.model.get("on_click")(t),!1)},template:function(t){var e='title="'+t.title+'" class="icon-button';return t.is_menu_button&&(e+=" menu-button"),e+=" "+t.icon_class,t.enabled||(e+="_disabled"),e+='"',t.id&&(e+=' id="'+t.id+'"'),e+=' href="'+t.href+'"',t.target&&(e+=' target="'+t.target+'"'),t.visible||(e+=' style="display: none;"'),e=t.enabled?"":"",o(e)}}),n=i.Collection.extend({model:t}),s=i.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var t=this;return this.collection.each(function(e){var i=o("").attr("href","javascript:void(0)").attr("title",e.attributes.title).addClass("icon-button menu-button").addClass(e.attributes.icon_class).appendTo(t.$el).click(e.attributes.on_click);e.attributes.tooltip_config&&i.tooltip(e.attributes.tooltip_config);var n=e.get("options");n&&make_popupmenu(i,n)}),this}}),l=function(e,i){i||(i={});var o=new n(a.map(e,function(e){return new t(a.extend(e,i))}));return new s({collection:o})};return{IconButton:t,IconButtonView:e,IconButtonCollection:n,IconButtonMenuView:s,create_icon_buttons_menu:l}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(2),i(1))},function(t,e,i){var n,s,a;!function(o){s=[i(1)],n=o,a="function"==typeof n?n.apply(e,s):n,!(void 0!==a&&(t.exports=a))}(function(t){"use_strict";var e=t;e.fn.make_text_editable=function(t){var i="num_cols"in t?t.num_cols:30,n="num_rows"in t?t.num_rows:4,s="use_textarea"in t&&t.use_textarea,a="on_finish"in t?t.on_finish:null,o="help_text"in t?t.help_text:null,l=e(this);return l.addClass("editable-text").click(function(o){if(!(e(this).children(":input").length>0)){l.removeClass("editable-text");var r,c,d=function(t){l.find(":input").remove(),""!==t?l.text(t):l.html("
    "),l.addClass("editable-text"),a&&a(t)},h="cur_text"in t?t.cur_text:l.text();s?(r=e("',"
    ","
    "].join("")}});return{CitationView:n,CitationListView:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(a,o,l){n=[i(42),i(32),i(6),i(5)],s=function(t,e,i,n){"use strict";var s=t.FoldoutListItemView,r=t.ListItemView,c=s.extend({className:s.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(t){this.linkTarget=t.linkTarget||"_blank",this.hasUser=t.hasUser,s.prototype.initialize.call(this,t)},_setUpListeners:function(){s.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(t,e){a.has(t.changed,"deleted")?this.render():a.has(t.changed,"element_count")&&this.$("> .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return o(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var t=s.prototype._getFoldoutPanelOptions.call(this);return a.extend(t,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){var t=this.model?this.model+"":"(no model)";return"DCListItemView("+t+")"}});c.prototype.templates=function(){var t=a.extend({},s.prototype.templates.warnings,{error:i.wrapTemplate(["<% if( model.error ){ %>",'
    ',n("There was an error getting the data for this collection"),": <%- model.error %>","
    ","<% } %>"]),purged:i.wrapTemplate(["<% if( model.purged ){ %>",'
    ',n("This collection has been deleted and removed from disk"),"
    ","<% } %>"]),deleted:i.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
    ',n("This collection has been deleted"),"
    ","<% } %>"])}),e=i.wrapTemplate(['
    ','
    ','<%- collection.element_identifier || collection.name %>',"
    ",'
    ',"
    "],"collection"),o=i.wrapTemplate(['
    ','<% var countText = collection.element_count? ( collection.element_count + " " ) : ""; %>','<% if( collection.collection_type === "list" ){ %>',n("a list of <%- countText %>datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',n("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',n("a list of <%- countText %>dataset pairs"),'<% } else if( collection.collection_type === "list:list" ){ %>',n("a list of <%- countText %>dataset lists"),"<% } %>","
    "],"collection");return a.extend({},s.prototype.templates,{warnings:t,titleBar:e,subtitle:o})}();var d=r.extend({className:r.prototype.className+" dataset-collection-element",initialize:function(t){t.logger&&(this.logger=this.model.logger=t.logger),this.log("DCEListItemView.initialize:",t),r.prototype.initialize.call(this,t)},toString:function(){var t=this.model?this.model+"":"(no model)";return"DCEListItemView("+t+")"}});d.prototype.templates=function(){var t=i.wrapTemplate(['
    ','
    ','<%- element.element_identifier %>',"
    ",'
    ',"
    "],"element");return a.extend({},r.prototype.templates,{titleBar:t})}();var h=e.DatasetListItemView.extend({className:e.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(t){t.logger&&(this.logger=this.model.logger=t.logger),this.log("DatasetDCEListItemView.initialize:",t),e.DatasetListItemView.prototype.initialize.call(this,t)},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):l.when()},toString:function(){var t=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+t+")"}});h.prototype.templates=function(){var t=i.wrapTemplate(['
    ','','
    ','<%- element.element_identifier %>',"
    ","
    "],"element");return a.extend({},e.DatasetListItemView.prototype.templates,{titleBar:t})}();var u=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(t){c.prototype._swapNewRender.call(this,t);var e=this.model.get("state")||"ok";return this.$el.addClass("state-"+e),this.$el},toString:function(){var t=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+t+")"}});return{DCListItemView:c,DCEListItemView:d,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(1))},function(t,e,i){var n,s;(function(a,o,l){n=[i(70),i(6),i(5)],s=function(t,e,i){"use strict";var n="collections",s={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(t){return a.extend(t,t.object,{element_id:t.id}),delete 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    "],"dataset"),o[e.NOT_VIEWABLE]=n.wrapTemplate(["
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    "],"dataset"),o[e.DISCARDED]=n.wrapTemplate(["
    ",s("The job creating this dataset was cancelled before completion"),"
    "],"dataset"),o[e.QUEUED]=n.wrapTemplate(["
    ",s("This job is waiting to run"),"
    "],"dataset"),o[e.RUNNING]=n.wrapTemplate(["
    ",s("This job is currently running"),"
    "],"dataset"),o[e.UPLOAD]=n.wrapTemplate(["
    ",s("This dataset is currently uploading"),"
    "],"dataset"),o[e.SETTING_METADATA]=n.wrapTemplate(["
    ",s("Metadata is being auto-detected"),"
    "],"dataset"),o[e.PAUSED]=n.wrapTemplate(["
    ",s('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
    "],"dataset"),o[e.ERROR]=n.wrapTemplate(["<% if( !dataset.purged ){ %>","
    <%- dataset.misc_blurb %>
    ","<% } %>",'',s("An error occurred with this dataset"),":",'
    <%- dataset.misc_info %>
    '],"dataset"),o[e.EMPTY]=n.wrapTemplate(["
    ",s("No data"),": <%- dataset.misc_blurb %>
    "],"dataset"),o.unknown=n.wrapTemplate(['
    Error: unknown dataset state: "<%- dataset.state %>"
    '],"dataset");var l={resubmitted:n.wrapTemplate(["<% if( model.resubmitted ){ %>",'
    ',s("The job creating this dataset has been resubmitted"),"
    ","<% } %>"])},c=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'
    ','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
    ","<% }); %>"],"apps");return r.extend({},d.prototype.templates,{warnings:t,details:i,noAccess:a,summaries:o,detailMessages:l,displayApplications:c})}(),{DatasetListItemView:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(3),i(1),i(2))},function(t,e,i){var n,s;(function(a,o,l){n=[i(4)],s=function(t){var e=a.Model.extend({initialize:function(t){this.app=t},checksum:function(){var t="",e=this;return this.app.section.$el.find(".section-row").each(function(){var i=o(this).attr("id"),n=e.app.field_list[i];n&&(t+=i+":"+JSON.stringify(n.value&&n.value())+":"+n.collapsed+";")}),t},set:function(t){for(var e in t.attributes){var i=this.match(e);i&&this.app.field_list[i].value(t.get(e))}},create:function(){function t(t,e,i){n.flat_dict[t]=e,a[t]=i,n.app.element_list[e]&&n.app.element_list[e].$el.attr("tour_id",t)}function e(s,a){for(var o in a){var l=a[o];if(l.input){var r=l.input,c=s;switch(""!=s&&(c+="|"),c+=r.name,r.type){case"repeat":var d="section-",h=[],u=null;for(var p in l){var g=p.indexOf(d);g!=-1&&(g+=d.length,h.push(parseInt(p.substr(g))),u||(u=p.substr(0,g)))}h.sort(function(t,e){return t-e});var o=0;for(var f in h)e(c+"_"+o++,l[u+h[f]]);break;case"conditional":var m=n.app.field_list[r.id].value();t(c+"|"+r.test_param.name,r.id,m);var v=i(r,m);v!=-1&&e(c,a[r.id+"-section-"+v]);break;case"section":e(!r.flat&&c||"",l);break;default:var _=n.app.field_list[r.id];if(_&&_.value){var m=_.value();if((void 0===r.ignore||r.ignore!=m)&&(_.collapsed&&r.collapsible_value&&(m=r.collapsible_value),t(c,r.id,m),r.payload))for(var y in r.payload)t(y,r.id,r.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$el,s);var a={};return this.flat_dict={},e("",s),a},match:function(t){return this.flat_dict&&this.flat_dict[t]},matchCase:function(t,e){return i(t,e)},matchModel:function(t,e){var i=this;n(t.inputs,function(t,n){i.flat_dict[n]&&e(t,i.flat_dict[n])})},matchResponse:function(t){function e(t,s){if("string"==typeof s){var a=n.flat_dict[t];a&&(i[a]=s)}else for(var o in s){var l=o;if(""!==t){var r="|";s instanceof Array&&(r="_"),l=t+r+l}e(l,s[o])}}var i={},n=this;return e("",t),i},_iterate:function(t,e){var i=this,n=o(t).children();n.each(function(){var t=this,n=o(t).attr("id");if(o(t).hasClass("section-row")){var s=i.app.input_list[n];e[n]=s&&{input:s}||{},i._iterate(t,e[n])}else i._iterate(t,e)})}}),i=function(t,e){"boolean"==t.test_param.type&&(e="true"==e?t.test_param.truevalue||"true":t.test_param.falsevalue||"false");for(var i in t.cases)if(t.cases[i].value==e)return i;return-1},n=function(t,e,s,a){a=o.extend(!0,{},a),l.each(t,function(t){t&&t.type&&t.name&&(a[t.name]=t)});for(var r in t){var c=t[r],d=s?s+"|"+c.name:c.name;switch(c.type){case"repeat":l.each(c.cache,function(t,i){n(t,e,d+"_"+i,a)});break;case"conditional":if(c.test_param){e(c.test_param,d+"|"+c.test_param.name,a);var h=i(c,c.test_param.value);h!=-1?n(c.cases[h].inputs,e,d,a):Galaxy.emit.debug("form-data::visitInputs() - Invalid case for "+d+".")}else Galaxy.emit.debug("form-data::visitInputs() - Conditional test parameter missing for "+d+".");break;case"section":n(c.inputs,e,d,a);break;default:e(c,d,a)}}};return{Manager:e,visitInputs:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(2))},function(t,e,i){var n,s;(function(i,a,o){n=[],s=function(){return i.View.extend({initialize:function(t,e){this.app=t,this.app_options=t.options||{},this.field=e&&e.field||new i.View,this.model=e&&e.model||new i.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up"}).set(e),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var s=this;this.$collapsible.on("click",function(){s.field.collapsed=!s.field.collapsed,t.trigger&&t.trigger("change"),s.render()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){this.model.set("error_text",null)},render:function(){a(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&t.indexOf("("+e+")")==-1&&(t+=" ("+e+")"),this.$info.html(t),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(o.escape(this.model.get("text_value")));var i=this.model.get("error_text");if(this.$error[i?"show":"hide"](),this.$el[i?"addClass":"removeClass"]("ui-error"),this.$error_text.html(i),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.fadeIn("fast"),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var n=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+n)).attr("data-original-title",this.model.get("text_"+n)).tooltip({placement:"bottom"})}},_template:function(){return a("
    ").addClass("ui-form-element").append(a("
    ").addClass("ui-form-error ui-error").append(a("").addClass("fa fa-arrow-down")).append(a("").addClass("ui-form-error-text"))).append(a("
    ").addClass("ui-form-title").append(a("
    ").addClass("ui-form-collapsible").append(a("").addClass("ui-form-collapsible-icon")).append(a("").addClass("ui-form-collapsible-text"))).append(a("").addClass("ui-form-title-text"))).append(a("
    ").addClass("ui-form-field").append(a("").addClass("ui-form-info")).append(a("
    ").addClass("ui-form-backdrop"))).append(a("
    ").addClass("ui-form-preview"))}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(2))},function(t,e,i){var n,s;(function(a,o,l){n=[i(4),i(7),i(49),i(51),i(50),i(47)],s=function(t,e,i,n,s,r){return a.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp"},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){return new i.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var i=t.data;i||(i=[],o.each(t.options,function(t){i.push({label:t[0],value:t[1]})}));var n=e.Select;switch(t.display){case"checkboxes":n=e.Checkbox;break;case"radio":n=e.Radio;break;case"radiobutton":n=e.RadioButton}return new n.View({id:"field-"+t.id,data:i,error_text:t.error_text||"No options available",multiple:t.multiple,optional:t.optional,onchange:t.onchange})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new e.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(i){if(i.options&&i.data)if(i.area=i.multiple,t.isEmpty(i.value))i.value=null;else if(l.isArray(i.value)){var n="";for(var s in i.value){if(n+=String(i.value[s]),!i.multiple)break;n+="\n"}i.value=n}return new e.Input({id:"field-"+i.id,area:i.area,placeholder:i.placeholder,onchange:i.onchange})},_fieldSlider:function(t){return new e.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new e.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new e.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new r({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new n.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new s.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(2),i(1))},function(t,e,i){var n,s;(function(a,o,l){n=[i(4),i(14),i(9),i(7)],s=function(t,e,i,n){var s=a.View.extend({initialize:function(i){this.options=t.merge(i,{title:"Section",empty_text:"Not available.",max:null,min:null}),this.setElement("
    "),this.button_new=new n.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title_new,tooltip:"Add new "+this.options.title_new+" block",floating:"clear",onclick:function(){i.onnew&&i.onnew()}}),this.table=new e.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append(o("
    ").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate repeat block id.");this.n++;var e=new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){t.ondel&&t.ondel()}}),s=new i.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:e}});s.append(t.$el),s.$el.addClass("section-row"),this.list[t.id]=s,this.table.add(s.$el),this.table.append("row_"+t.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.n--;var e=this.table.get("row_"+t);e.remove(),delete this.list[t],this.button_new.enable(),this._refresh()},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),l.each(this.list,function(t){t.hideOperation("button_delete")}),l.isEmpty(this.list)&&this.$el.append(o("
    ").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),this.n>this.options.min?i.showOperation("button_delete"):i.hideOperation("button_delete")}}});return{View:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(2))},function(t,e,i){var n,s;(function(a,o,l,r){n=[i(4),i(14),i(7),i(9),i(36),i(34),i(35)],s=function(t,e,i,n,s,c,d){var h=a.View.extend({initialize:function(t,i){this.app=t,this.inputs=i.inputs,i.cls="ui-table-plain",i.cls_tr="section-row",this.table=new e.View(i),this.parameters=new d,this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var t in this.inputs)this.add(this.inputs[t])},add:function(e){var i=o.extend(!0,{},e);i.id=e.id=t.uid(),this.app.input_list[i.id]=i;var n=i.type;switch(n){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.options.sustain_conditionals&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.model&&i.model.set("onchange",function(i){var n=e.app.data.matchCase(t,i);for(var s in t.cases){var a=t.cases[s],o=t.id+"-section-"+s,l=e.table.get(o),r=!1;for(var c in a.inputs)if(!a.inputs[c].hidden){r=!0;break}s==n&&r?l.fadeIn("fast"):l.hide()}e.app.trigger("change")});for(var n in t.cases){var s=t.id+"-section-"+n,a=new h(this.app,{inputs:t.cases[n].inputs});a.$el.addClass("ui-table-section"),this.table.add(a.$el),this.table.append(s)}i.trigger("change")},_addRepeat:function(t){function e(e){var s=t.id+"-section-"+n++,o=new h(i.app,{inputs:e});a.add({id:s,$el:o.$el,ondel:function(){a.del(s),i.app.trigger("change")}})}for(var i=this,n=0,a=new s.View({title:t.title||"Repeat",title_new:t.title||"",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),o=l.size(t.cache),r=0;r").addClass("ui-form-info").html(t.help)),this.app.on("expand",function(t){e.$("#"+t).length>0&&e.expand()}),this.table.add(e.$el),this.table.append(t.id)},_addRow:function(t){var e=this,i=t.id;t.onchange=function(){e.app.trigger("change",i)};var n=this.parameters.create(t);this.app.field_list[i]=n;var s=new c(this.app,{name:t.name,label:t.label||t.name,value:t.value,text_value:t.text_value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,color:t.color,style:t.style,backdrop:t.backdrop,field:n});return this.app.element_list[i]=s,this.table.add(s.$el),this.table.append(i),t.hidden&&this.table.get(i).hide(),n}});return{View:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(2),i(1))},function(t,e,i){var n,s;(function(a,o,l){n=[i(4),i(9),i(7),i(37),i(33)],s=function(t,e,i,n,s){return a.View.extend({initialize:function(e){this.options=t.merge(e,{initial_errors:!1,cls:"ui-portlet-limited",icon:null,always_refresh:!0}),this.setElement("
    "),this.render()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[i];if(n&&n.options&&!o.isEqual(n.options,t.options)){n.options=t.options;var s=e.field_list[i];if(s.update){var a=[];if(["data","data_collection","drill_down"].indexOf(n.type)!=-1)a=n.options;else for(var l in t.options){var r=t.options[l];r.length>2&&a.push({label:r[0],value:r[1]})}s.update(a),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+i)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.portlet.expand(),this.trigger("expand",t),!i)){var s=this.$el.parents().filter(function(){return["auto","scroll"].indexOf(l(this).css("overflow"))!=-1}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-120},500)}},errors:function(t){if(this.trigger("reset"),t&&t.errors){var e=this.data.matchResponse(t.errors);for(var i in this.element_list){this.element_list[i];e[i]&&this.highlight(i,e[i],!0)}}},setOnChange:function(t){this.options.onchange=t},render:function(){var t=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var e=this.data.checksum();return this.on("change",function(i){var n=t.input_list[i];if(!n||n.refresh_on_change||t.options.always_refresh){var s=t.data.checksum();s!=e&&(e=s,t.options.onchange&&t.options.onchange())}}),this.on("reset",function(){for(var t in this.element_list)this.element_list[t].reset()}),this},_renderForm:function(){this.message=new i.Message,this.section=new n.View(this,{inputs:this.options.inputs}),l(".tooltip").remove(),this.portlet=new e.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(2),i(1))},function(t,e,i){var n,s;(function(a){n=[i(30),i(40),i(5)],s=function(t,e,i){"use strict";function n(t){return function(e,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),t.call(this,e,i)}}var s=e.HistoryContentMixin,o=t.ListDatasetCollection,l=t.PairDatasetCollection,r=t.ListPairedDatasetCollection,c=t.ListOfListsDatasetCollection,d=o.extend(s).extend({defaults:a.extend(a.clone(o.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){o.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(o.prototype.save),toString:function(){return["HistoryListDatasetCollection(",this.get("name"),")"].join("")}}),h=l.extend(s).extend({defaults:a.extend(a.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){l.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(l.prototype.save),toString:function(){return["HistoryPairDatasetCollection(",this.get("name"),")"].join("")}}),u=r.extend(s).extend({defaults:a.extend(a.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){r.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(r.prototype.save),toString:function(){return["HistoryListPairedDatasetCollection(",this.get("name"),")"].join("")}}),p=c.extend(s).extend({defaults:a.extend(a.clone(c.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){c.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(c.prototype.save),toString:function(){return["HistoryListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:d,HistoryPairDatasetCollection:h,HistoryListPairedDatasetCollection:u,HistoryListOfListsDatasetCollection:p}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(a,o){n=[i(10),i(6),i(5)],s=function(t,e,i){"use strict";var n="history",s=function(t,e){return[t,e].join("-")},l={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",constructor:function(t,e){t.type_id=s(t.history_content_type,t.id),this.debug("HistoryContentMixin.constructor:",t.type_id),a.Model.apply(this,arguments)},_typeIdStr:function(){return s(this.get("history_content_type"),this.get("id"))},initialize:function(t,e){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",this._typeIdStr())},isNew:function(){return!this.get("id")},hidden:function(){return!this.get("visible")},isVisible:function(t,e){var i=!0;return t||!this.get("deleted")&&!this.get("purged")||(i=!1),e||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var t=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return t},hide:function(t){return this.get("visible")?this.save({visible:!1},t):o.when()},unhide:function(t){return this.get("visible")?o.when():this.save({visible:!0},t)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HistoryContent("+t+")"}},r=a.Model.extend(e.LoggableMixin).extend(l).extend({_logNamespace:n});return{typeIdStr:s,HistoryContentMixin:l,HistoryContent:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1))},function(t,e,i){var n,s;(function(a,o,l){n=[i(40),i(72),i(39),i(10),i(6),i(5)],s=function(t,e,i,n,s,r){"use strict";var c="history",d=a.Collection.extend(s.LoggableMixin).extend({_logNamespace:c,model:function(t,n){if("dataset"===t.history_content_type)return new e.HistoryDatasetAssociation(t,n);if("dataset_collection"===t.history_content_type){switch(t.collection_type){case"list":return new i.HistoryListDatasetCollection(t,n);case"paired":return new i.HistoryPairDatasetCollection(t,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(t,n);case"list:list":return new i.HistoryListOfListsDatasetCollection(t,n)}var s="Unknown collection_type: "+t.collection_type;return console.warn(s,t),{validationError:s}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},initialize:function(t,e){e=e||{},this.historyId=e.historyId,this.model.prototype.idAttribute="type_id",this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},running:function(){function t(t){return!t.inReadyState()}return new d(this.filter(t))},getByHid:function(t){return o.first(this.filter(function(e){return e.get("hid")===t}))},getVisible:function(t,e,i){i=i||[],this.debug("checking isVisible");var n=new d(this.filter(function(i){return i.isVisible(t,e)}));return o.each(i,function(t){o.isFunction(t)&&(n=new d(n.filter(t)))}),n},hidden:function(){function t(t){return t.hidden()}return new d(this.filter(t))},deleted:function(){function t(t){return t.get("deleted")}return new d(this.filter(t))},visibleAndUndeleted:function(){function t(t){ -return t.get("visible")&&!t.get("deleted")}return new d(this.filter(t))},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},fetch:function(t){return t=t||{},t.data=o.defaults(t.data||{},{v:"dev"}),a.Collection.prototype.fetch.call(this,t)},fetchUpdated:function(t,e){return e=e||{},e.traditional=!0,e.data=[{name:"v",value:"dev"}],t&&(e.data=e.data.concat(this._filtersFromMap({"update_time-ge":t.toISOString()}))),e.merge=!0,e.remove=!1,this.fetch(e)},_filtersFromMap:function(t){var e=[];return o.each(t,function(t,i){e.push({name:"q",value:i}),e.push({name:"qv",value:t})}),e},fetchAllDetails:function(t){t=t||{};var e={details:"all"};return t.data=t.data?o.extend(t.data,e):e,this.fetch(t)},fetchCollectionCounts:function(t){return t=t||{},t.data=o.defaults({keys:["type_id","element_count"].join(","),q:"history_content_type",qv:"dataset_collection"},t.data||{}),t.merge=!0,t.remove=!1,this.fetch(t)},ajaxQueue:function(t,e){var i=l.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var a=this.chain().reverse().map(function(o,l){return function(){var r=t.call(o,e);r.done(function(t){i.notify({curr:l,total:n,response:t,model:o})}),r.always(function(t){s.push(t),a.length?a.shift()():i.resolve(s)})}}).value();return a.shift()(),i},isCopyable:function(t){var e=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return o.isObject(t)&&t.id&&o.contains(e,t.model_class)},copy:function(t){var e,i,n;o.isString(t)?(e=t,n="hda",i="dataset"):(e=t.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,a=l.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:e,source:n,type:i})}).done(function(t){s.add([t])}).fail(function(t,o,l){s.trigger("error",s,a,{},"Error copying contents",{type:i,id:e,source:n})});return a},matches:function(t){return this.filter(function(e){return e.matches(t)})},createHDCA:function(t,e,n,s){var a=this,o={list:i.HistoryListDatasetCollection,paired:i.HistoryPairDatasetCollection},l=new o[e]({history_id:this.historyId,name:n,element_identifiers:t});return l.save().done(function(t){a.add(l)}).fail(function(t,e,i){a.trigger("error",t,e,i)})},clone:function(){var t=a.Collection.prototype.clone.call(this);return t.historyId=this.historyId,t},print:function(){var t=this;t.each(function(e){t.debug(e),e.elements&&t.debug("\t elements:",e.elements)})},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(2),i(1))},function(t,e,i){var n,s;(function(a,o,l,r){n=[i(6),i(5)],s=function(t,e){"use strict";var i="list",n=a.View.extend(t.LoggableMixin).extend({_logNamespace:i,initialize:function(t){this.expanded=t.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==t.fxSpeed?t.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(t){var e=this._buildNewRender();return this._setUpBehaviors(e),this._queueNewRender(e,t),this},_buildNewRender:function(){var t=o(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(t).replaceWith(this._renderDetails().show()),t},_queueNewRender:function(t,e){e=void 0===e?this.fxSpeed:e;var i=this;o(i).queue("fx",[function(t){this.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){this.$el.fadeIn(e,t)},function(t){this.trigger("rendered",i),t()}])},_swapNewRender:function(t){return this.$el.empty().attr("class",l.isFunction(this.className)?this.className():this.className).append(t.children())},_setUpBehaviors:function(t){t=t||this.$el,t.find("[title]").tooltip({placement:"bottom"})},$details:function(t){return t=t||this.$el,t.find("> .details")},_renderDetails:function(){var t=o(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(t),t},toggleExpanded:function(t){return t=void 0===t?!this.expanded:t,t?this.expand():this.collapse(),this},expand:function(){var t=this;return t._fetchModelDetails().always(function(){t._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?r.when():this.model.fetch()},_expand:function(){var t=this,e=t._renderDetails();t.$details().replaceWith(e),t.expanded=!0,t.$details().slideDown({duration:t.fxSpeed,step:function(){t.trigger("expanding",t)},complete:function(){t.trigger("expanded",t)}})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var t=this;t.expanded=!1,this.$details().slideUp({duration:t.fxSpeed,step:function(){t.trigger("collapsing",t)},complete:function(){t.trigger("collapsed",t)}})}}),s=n.extend(t.mixin(t.SelectableViewMixin,t.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){n.prototype.initialize.call(this,e),t.SelectableViewMixin.initialize.call(this,e),t.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(t){t?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var t=n.prototype._buildNewRender.call(this);return t.children(".warnings").replaceWith(this._renderWarnings()),t.children(".title-bar").replaceWith(this._renderTitleBar()),t.children(".primary-actions").append(this._renderPrimaryActions()),t.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),t},_swapNewRender:function(t){return n.prototype._swapNewRender.call(this,t),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var t=this,e=o('
    '),i=t.model.toJSON();return l.each(t.templates.warnings,function(n){e.append(o(n(i,t)))}),e},_renderTitleBar:function(){return o(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return o(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(t){t.stopPropagation(),t.altKey?(this.toggleSelect(t),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(t){var e=32,i=13;return!t||"keydown"!==t.type||t.keyCode!==e&&t.keyCode!==i||(this.toggleExpanded(),t.stopPropagation(),!1)},toString:function(){var t=this.model?this.model+"":"(no model)";return"ListItemView("+t+")"}}));s.prototype.templates=function(){var e=t.wrapTemplate(['
    ','
    ','
    ','',"
    ",'
    ','
    ','
    ',"
    "]),i={},n=t.wrapTemplate(['
    ','','
    ','<%- element.name %>',"
    ",'
    ',"
    "],"element"),s=t.wrapTemplate(['
    ']),a=t.wrapTemplate(['
    ']);return{el:e,warnings:i,titleBar:n,subtitle:s,details:a}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(t){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=t.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=t.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,t),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return o();var t=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,t)},_createFoldoutPanel:function(){var t=this.model,e=this._getFoldoutPanelClass(t),i=this._getFoldoutPanelOptions(t),n=new e(l.extend(i,{model:t}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(t,e){return e=e||this.$("> .details"),this.foldout=t.render(0),t.$("> .controls").hide(),e.append(t.$el)},expand:function(){var t=this;return t._fetchModelDetails().always(function(){"foldout"===t.foldoutStyle?t._expand():"drilldown"===t.foldoutStyle&&t._expandByDrilldown()})},_expandByDrilldown:function(){var t=this;t.listenTo(t.foldout,"close",function(){t.trigger("collapsed:drilldown",t,t.foldout)}),t.trigger("expanded:drilldown",t,t.foldout)}});return c.prototype.templates=function(){var e=t.wrapTemplate(['
    ',"
    "],"collection");return l.extend({},s.prototype.templates,{details:e})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(2),i(1))},function(t,e,i){var n,s;(function(a,o){n=[i(4),i(55),i(7),i(38),i(18),i(28)],s=function(t,e,i,n,s,l){return n.extend({initialize:function(t){var i=this;n.prototype.initialize.call(this,t),this.deferred=new e,t.inputs?this._buildForm(t):this.deferred.execute(function(e){i._buildModel(e,t,!0)}),t.listen_to_history&&parent.Galaxy&&parent.Galaxy.currHistoryPanel&&this.listenTo(parent.Galaxy.currHistoryPanel.collection,"change",function(){this.refresh()})},refresh:function(){var t=this;t.deferred.reset(),this.deferred.execute(function(e){t._updateModel(e)})},remove:function(){var t=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(t),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var i=this;this.options=t.merge(e,this.options),this.options=t.merge({icon:e.icon,title:""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:!this.options.hide_operations&&this._operations(),onchange:function(){i.refresh()}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append(a("
    ").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(e,n,s){var o=this;this.options.id=n.id,this.options.version=n.version;var l="",r={};n.job_id?l=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(l=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(r=a.extend({},Galaxy.params),n.version&&(r.tool_version=n.version))),t.get({url:l,data:r,success:function(t){return t=t.tool_model||t,t.display?(o._buildForm(t),!s&&o.message.update({status:"success",message:"Now you are using '"+o.options.name+"' version "+o.options.version+", id '"+o.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",t),void e.resolve()):void(window.location=Galaxy.root)},error:function(t,n){var s=t&&t.err_msg||"Uncaught error.";401==n.status?window.location=Galaxy.root+"user/login?"+a.param({redirect:Galaxy.root+"?tool_id="+o.options.id}):o.$el.is(":empty")?o.$el.prepend(new i.Message({message:s,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:s,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",t),e.reject()}})},_updateModel:function(e){var i=this,n=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",s={tool_id:this.options.id,tool_version:this.options.version,inputs:a.extend(!0,{},i.data.create())};this.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",s),t.request({type:"POST",url:n,data:s,success:function(t){i.update(t.tool_model||t),i.options.update&&i.options.update(t),i.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",t),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",t),e.reject()}})},_operations:function(){var t=this,e=this.options,n=new i.ButtonMenu({icon:"fa-cubes",title:!e.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!e.sustain_version&&e.versions&&e.versions.length>1)for(var s in e.versions){var a=e.versions[s];a!=e.version&&n.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){var i=e.id.replace(e.version,this.version),n=this.version;t.deferred.reset(),t.deferred.execute(function(e){t._buildModel(e,{id:i,version:n})})}})}else n.$el.hide();var o=new i.ButtonMenu({icon:"fa-caret-down",title:!e.narrow&&"Options"||null,tooltip:"View available options"});return e.biostar_url&&(o.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/p/new/post/")}}),o.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/local/search/page/?q="+e.name)}})),o.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+e.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&o.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+e.id+"/download"}}),e.requirements&&e.requirements.length>0&&o.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){!this.visible||t.portlet.collapsed?(this.visible=!0,t.portlet.expand(),t.message.update({persistent:!0,message:t._templateRequirements(e),status:"info"})):(this.visible=!1,t.message.update({message:""}))}}),e.sharable_url&&o.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(e.sharable_url)}}),{menu:o,versions:n}},_footer:function(){var t=this.options,e=a("
    ").append(this._templateHelp(t));if(t.citations){var i=a("
    "),n=new s.ToolCitationCollection;n.tool_id=t.id;var o=new l.CitationListView({el:i,collection:n});o.render(),n.fetch(),e.append(i)}return e},_templateHelp:function(t){var e=a("
    ").addClass("ui-form-help").append(t.help);return e.find("a").attr("target","_blank"),e},_templateRequirements:function(t){var e=t.requirements.length;if(e>0){var i="This tool requires ";o.each(t.requirements,function(t,n){i+=t.name+(t.version?" (Version "+t.version+")":"")+(n").attr("target","_blank").attr("href","https://wiki.galaxyproject.org/Tools/Requirements").text("here");return a("").append(i+". Click ").append(n).append(" for more information.")}return"No requirements found."}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(2))},function(t,e,i){var n,s;(function(a,o){n=[i(2),i(17),i(12),i(19)],s=function(t,e,i,n){"use strict";var s={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},l=a.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(t){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new l(this.toJSON())},set_value:function(t){this.set("value",t||"")}}),r=a.Collection.extend({model:l}),c=l.extend({}),d=l.extend({set_value:function(t){this.set("value",parseInt(t,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),h=d.extend({set_value:function(t){this.set("value",parseFloat(t))}}),u=l.extend({get_samples:function(){return t.map(this.get("options"),function(t){return t[0]})}});l.subModelTypes={integer:d,"float":h,data:c,select:u};var p=a.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(e){this.set("inputs",new r(t.map(e.inputs,function(t){var e=l.subModelTypes[t.type]||l;return new e(t)})))},toJSON:function(){var t=a.Model.prototype.toJSON.call(this);return t.inputs=this.get("inputs").map(function(t){return t.toJSON()}),t},remove_inputs:function(t){var e=this,i=e.get("inputs").filter(function(e){return t.indexOf(e.get("type"))!==-1});e.get("inputs").remove(i)},copy:function(t){var e=new p(this.toJSON());if(t){var i=new a.Collection;e.get("inputs").each(function(t){t.get_samples()&&i.push(t)}),e.set("inputs",i)}return e},apply_search_results:function(e){return t.indexOf(e,this.attributes.id)!==-1?this.show():this.hide(),this.is_visible()},set_input_value:function(t,e){this.get("inputs").find(function(e){return e.get("name")===t}).set("value",e)},set_input_values:function(e){var i=this;t.each(t.keys(e),function(t){i.set_input_value(t,e[t])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(n){var s=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),a=o.Deferred(),l=new e.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return o.when(l.go()).then(function(t){a.resolve(new i.DatasetCollection(t))}),a}});t.extend(p.prototype,s);var g=(a.View.extend({}),a.Collection.extend({model:p})),f=a.Model.extend(s),m=a.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){t.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(e){var i,n=!0;t.each(this.attributes.elems,function(t){t instanceof f?(i=t,i.hide()):t instanceof p&&t.apply_search_results(e)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});t.extend(m.prototype,s);var v=a.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var t=this.attributes.query;if(t.length");t.append(S.tool_link(this.model.toJSON()));var e=this.model.get("form_style",null);if("upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("regular"===e){var i=this;t.find("a").on("click",function(t){t.preventDefault();var e=new n.View({id:i.model.id,version:i.model.get("version")});e.deferred.execute(function(){Galaxy.app.display(e)})})}return this.$el.append(t),this}}),w=y.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(o("").text(this.model.attributes.text)),this}}),x=y.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){y.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(S.panel_section(this.model.toJSON()));var e=this.$el.find(".toolSectionBody");return t.each(this.model.attributes.elems,function(t){if(t instanceof p){var i=new b({model:t,className:"toolTitle"});i.render(),e.append(i.$el)}else if(t instanceof f){var n=new w({model:t});n.render(),e.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),C=a.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(S.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(t){return this.model.attributes.clear_key&&this.model.attributes.clear_key===t.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),$=a.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var t=this,e=new C({model:this.model.get("tool_search")});return e.render(),t.$el.append(e.$el),this.model.get("layout").each(function(e){if(e instanceof m){var i=new x({model:e});i.render(),t.$el.append(i.$el)}else if(e instanceof p){var n=new b({model:e,className:"toolTitleNoSection"});n.render(),t.$el.append(n.$el)}else if(e instanceof f){var s=new w({model:e});s.render(),t.$el.append(s.$el)}}),t.$el.find("a.tool-link").click(function(e){var i=o(this).attr("class").split(/\s+/)[0],n=t.model.get("tools").get(i);t.trigger("tool_link_click",e,n)}),this},handle_search_results:function(){var t=this.model.get("tool_search").get("results");t&&0===t.length?o("#search-no-results").show():o("#search-no-results").hide()}}),E=a.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(S.tool_form(this.model.toJSON()))}}),S=(a.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new $({collection:this.collection}),this.tool_form_view=new E},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,i){e.preventDefault(),t.show_tool(i)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),o("#left").width("650px")})}}),{tool_search:t.template(['',' ',''].join("")),panel_section:t.template(['
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    ",'