From 49783c21e853467e18d997bfde869ac4bbfbb2af Mon Sep 17 00:00:00 2001 From: guerler Date: Tue, 5 Dec 2017 16:42:15 -0500 Subject: [PATCH] Make client --- static/scripts/bundled/extended.bundled.js | 2 +- static/scripts/mvc/toolshed/repository-view.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/static/scripts/bundled/extended.bundled.js b/static/scripts/bundled/extended.bundled.js index c28c457f6748..1a1738767a32 100644 --- a/static/scripts/bundled/extended.bundled.js +++ b/static/scripts/bundled/extended.bundled.js @@ -46,4 +46,4 @@ s=n,l=e("
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    ").addClass("fa-icon-button fa fa-times").click(function(e){l.destroy()})),a.appendTo("#canvas-container");var u=e("#canvas-container").position(),h=e("#canvas-container").parent(),f=a.width(),p=a.height();return a.css({left:-u.left+h.width()/2-f/2,top:-u.top+h.height()/2-p/2}),d.prependTo(a.find(".toolFormTitle")),f+=d.width()+10,a.css("width",f),a.bind("dragstart",function(){r.workflow.activate_node(l)}).bind("dragend",function(){r.workflow.node_changed(this),r.workflow.fit_canvas_to_nodes(),r.canvas_manager.draw_overview()}).bind("dragclickonly",function(){r.workflow.activate_node(l)}).bind("drag",function(t,n){var i=e(this).offsetParent().offset(),r=n.offsetX-i.left,a=n.offsetY-i.top;e(this).css({left:r,top:a}),e(this).find(".terminal").each(function(){this.terminal.redraw()})}),l}})}).call(t,n(0),n(2),n(1))},286:function(e,t,n){"use strict";(function(e){function i(e,t){this.app=e,this.canvas_container=t,this.id_counter=0,this.nodes={},this.name=null,this.has_changes=!1,this.active_form_has_changes=!1,this.workflowOutputLabels={}}Object.defineProperty(t,"__esModule",{value:!0});var r=n(125),a=function(e){return e&&e.__esModule?e:{default:e}}(r),o=n(7),s=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}(o);e.extend(i.prototype,{canLabelOutputWith:function(e){return!e||!(e in this.workflowOutputLabels)},registerOutputLabel:function(e){e&&(this.workflowOutputLabels[e]=!0)},unregisterOutputLabel:function(e){e&&delete this.workflowOutputLabels[e]},updateOutputLabel:function(e,t){e&&this.unregisterOutputLabel(e),this.canLabelOutputWith(t)||s.warning("Workflow contains duplicate workflow output labels "+t+". This must be fixed before it can be saved."),t&&this.registerOutputLabel(t)},attemptUpdateOutputLabel:function(e,t,n){return!!this.canLabelOutputWith(n)&&(e.labelWorkflowOutput(t,n),e.nodeView.redrawWorkflowOutputs(),!0)},create_node:function(e,t,n){var i=this.app.prebuildNode(e,t,n);return this.add_node(i),this.fit_canvas_to_nodes(),this.app.canvas_manager.draw_overview(),this.activate_node(i),i},add_node:function(e){e.id=this.id_counter,e.element.attr("id","wf-node-step-"+e.id),this.id_counter++,this.nodes[e.id]=e,this.has_changes=!0,e.workflow=this},remove_node:function(e){this.active_node==e&&this.clear_active_node(),delete this.nodes[e.id],this.has_changes=!0},remove_all:function(){var t=this;e.each(this.nodes,function(e,n){n.destroy(),t.remove_node(n)})},rectify_workflow_outputs:function(){var t=!1,n=!1;if(e.each(this.nodes,function(i,r){r.workflow_outputs&&r.workflow_outputs.length>0&&(t=!0),e.each(r.post_job_actions,function(e,t){"HideDatasetAction"===t.action_type&&(n=!0)})}),!1!==t||!1!==n){var i=this;e.each(this.nodes,function(n,r){if("tool"===r.type){var a=!1;null===r.post_job_actions&&(r.post_job_actions={},a=!0);var o=[];e.each(r.post_job_actions,function(e,t){"HideDatasetAction"==t.action_type&&o.push(e)}),o.length>0&&e.each(o,function(e,t){a=!0,delete r.post_job_actions[t]}),t&&e.each(r.output_terminals,function(e,t){if(!0==!r.isWorkflowOutput(t.name)){a=!0;var n={action_type:"HideDatasetAction",output_name:t.name,action_arguments:{}};r.post_job_actions["HideDatasetAction"+t.name]=null,r.post_job_actions["HideDatasetAction"+t.name]=n}}),i.active_node==r&&!0===a&&i.reload_active_node()}})}},to_simple:function(){var t={};return e.each(this.nodes,function(n,i){var r={};e.each(i.input_terminals,function(t,n){r[n.name]=null;var i=[];e.each(n.connectors,function(e,t){if(t.handle1){var a={id:t.handle1.node.id,output_name:t.handle1.name},o=n.attributes.input.input_subworkflow_step_id;void 0!==o&&(a.input_subworkflow_step_id=o),i[e]=a,r[n.name]=i}})});var a={};i.post_job_actions&&e.each(i.post_job_actions,function(e,t){var n={action_type:t.action_type,output_name:t.output_name,action_arguments:t.action_arguments};a[t.action_type+t.output_name]=null,a[t.action_type+t.output_name]=n}),i.workflow_outputs||(i.workflow_outputs=[]);var o={id:i.id,type:i.type,content_id:i.content_id,tool_version:i.config_form.version,tool_state:i.tool_state,errors:i.errors,input_connections:r,position:e(i.element).position(),annotation:i.annotation,post_job_actions:i.post_job_actions,uuid:i.uuid,label:i.label,workflow_outputs:i.workflow_outputs};t[i.id]=o}),{steps:t}},from_simple:function(t,n){var i=void 0===n||n,r=this,o=0;i?r.name=t.name:o=Object.keys(r.nodes).length;var s=o,l=!1;e.each(t.steps,function(t,n){var a=r.app.prebuildNode(n.type,n.name,n.content_id);i||(n.uuid=null,e.each(n.workflow_outputs,function(e,t){t.uuid=null})),a.init_field_data(n),n.position&&a.element.css({top:n.position.top,left:n.position.left}),a.id=parseInt(n.id)+o,r.nodes[a.id]=a,s=Math.max(s,parseInt(t)+o),l||(a.workflow_outputs.length>0?l=!0:e.each(a.post_job_actions||[],function(e,t){"HideDatasetAction"===t.action_type&&(l=!0)}))}),r.id_counter=s+1,e.each(t.steps,function(t,n){var i=r.nodes[parseInt(t)+o];e.each(n.input_connections,function(t,n){n&&(e.isArray(n)||(n=[n]),e.each(n,function(e,n){var s=r.nodes[parseInt(n.id)+o],l=new a.default;l.connect(s.output_terminals[n.output_name],i.input_terminals[t]),l.redraw()}))}),l&&e.each(i.output_terminals,function(t,n){if(void 0===i.post_job_actions["HideDatasetAction"+n.name]){i.addWorkflowOutput(n.name);e(i.element).find(".callout."+n.name).find("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"),r.has_changes=!0}})})},check_changes_in_active_form:function(){this.active_form_has_changes&&(this.has_changes=!0,e("#right-content").find("form").submit(),this.active_form_has_changes=!1)},reload_active_node:function(){if(this.active_node){var e=this.active_node;this.clear_active_node(),this.activate_node(e)}},clear_active_node:function(){this.active_node&&(this.active_node.make_inactive(),this.active_node=null),document.activeElement.blur(),this.app.showAttributes()},activate_node:function(e){this.active_node!=e&&(this.check_changes_in_active_form(),this.clear_active_node(),this.app.showForm(e.config_form,e),e.make_active(),this.active_node=e)},node_changed:function(e,t){this.has_changes=!0,this.active_node==e&&t&&(this.check_changes_in_active_form(),this.app.showForm(e.config_form,e)),this.app.showWorkflowParameters()},layout:function(){this.check_changes_in_active_form(),this.has_changes=!0;var t={},n={};e.each(this.nodes,function(e,i){void 0===t[e]&&(t[e]=0),void 0===n[e]&&(n[e]=[])}),e.each(this.nodes,function(i,r){e.each(r.input_terminals,function(i,a){e.each(a.connectors,function(e,i){var a=i.handle1.node;t[r.id]+=1,n[a.id].push(r.id)})})});for(var i=[];;){var r=[];for(var a in t)0===t[a]&&r.push(a);if(0===r.length)break;i.push(r);for(var o in r){var s=r[o];delete t[s];for(var l in n[s])t[n[s][l]]-=1}}if(!t.length){var c=this.nodes,d=80;e.each(i,function(t,n){n.sort(function(t,n){return e(c[t].element).position().top-e(c[n].element).position().top});var i=0,r=30;e.each(n,function(t,n){var a=c[n],o=e(a.element);e(o).css({top:r,left:d}),i=Math.max(i,e(o).width()),r+=e(o).height()+30}),d+=i+80}),e.each(c,function(e,t){t.redraw()})}},bounds_for_all_nodes:function(){var t,n=1/0,i=-1/0,r=1/0,a=-1/0;return e.each(this.nodes,function(o,s){var l=e(s.element);t=l.position(),n=Math.min(n,t.left),i=Math.max(i,t.left+l.width()),r=Math.min(r,t.top),a=Math.max(a,t.top+l.width())}),{xmin:n,xmax:i,ymin:r,ymax:a}},fit_canvas_to_nodes:function(){function t(e,t){return Math.ceil(e/t)*t}function n(e,t){if(e3*t){return-(e-(Math.ceil(e%t/t)+1)*t)}return 0}var i=this.bounds_for_all_nodes(),r=this.canvas_container.position(),a=this.canvas_container.parent(),o=n(i.xmin,100),s=n(i.ymin,100);o=Math.max(o,r.left),s=Math.max(s,r.top);var l=r.left-o,c=r.top-s,d=t(i.xmax+100,100)+o,u=t(i.ymax+100,100)+s;d=Math.max(d,-l+a.width()),u=Math.max(u,-c+a.height()),this.canvas_container.css({left:l,top:c,width:d,height:u}),this.canvas_container.children().each(function(){var t=e(this).position();e(this).css("left",t.left+o),e(this).css("top",t.top+s)})}}),t.default=i}).call(t,n(0))},287:function(e,t,n){"use strict";(function(e){function n(e,t,n){this.app=e,this.cv=t,this.cc=this.cv.find("#canvas-container"),this.overview=n,this.oc=n.find("#overview-canvas"),this.ov=n.find("#overview-viewport"),this.init_drag(),this.init_copy_paste()}function i(e){this.panel=e}Object.defineProperty(t,"__esModule",{value:!0}),e.extend(n.prototype,{init_drag:function(){var t=this,n=function(e,n){e=Math.min(e,t.cv.width()/2),e=Math.max(e,-t.cc.width()+t.cv.width()/2),n=Math.min(n,t.cv.height()/2),n=Math.max(n,-t.cc.height()+t.cv.height()/2),t.cc.css({left:e,top:n}),t.cv.css({"background-position-x":e,"background-position-y":n}),t.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new i(this)});var r,a;this.cv.bind("click",function(){document.activeElement.blur()}).bind("dragstart",function(){var n=e(this).offset(),i=t.cc.position();a=i.top-n.top,r=i.left-n.left}).bind("drag",function(e,t){n(t.offsetX+r,t.offsetY+a)}).bind("dragend",function(){t.app.workflow.fit_canvas_to_nodes(),t.draw_overview()}),this.overview.click(function(e){if(t.overview.hasClass("blockaclick"))t.overview.removeClass("blockaclick");else{var i=t.cc.width(),r=t.cc.height(),a=t.oc.width(),o=t.oc.height(),s=e.pageX-t.oc.offset().left-t.ov.width()/2,l=e.pageY-t.oc.offset().top-t.ov.height()/2;n(-s/a*i,-l/o*r),t.app.workflow.fit_canvas_to_nodes(),t.draw_overview()}}),this.ov.bind("drag",function(e,i){var r=t.cc.width(),a=t.cc.height(),o=t.oc.width(),s=t.oc.height(),l=i.offsetX-t.overview.offset().left,c=i.offsetY-t.overview.offset().top;n(-l/o*r,-c/s*a)}).bind("dragend",function(){t.overview.addClass("blockaclick"),t.app.workflow.fit_canvas_to_nodes(),t.draw_overview()}),e("#overview-border").bind("drag",function(n,i){var r=e(this).offsetParent(),a=r.offset(),o=Math.max(r.width()-(i.offsetX-a.left),r.height()-(i.offsetY-a.top));e(this).css({width:o,height:o}),t.draw_overview()}),e("#overview-border div").bind("drag",function(){})},init_copy_paste:function(){var e=this;document.addEventListener("copy",function(t){""===window.getSelection().toString()&&(e.app.workflow.active_node&&t.clipboardData.setData("application/json",JSON.stringify({nodeId:e.app.workflow.active_node.id})),t.preventDefault())}),document.addEventListener("paste",function(t){if(document.activeElement&&"textarea"!==document.activeElement.type&&"text"!==document.activeElement.type){var n;try{n=JSON.parse(t.clipboardData.getData("application/json")).nodeId}catch(e){}n&&e.app.workflow.nodes.hasOwnProperty(n)&&e.app.workflow.nodes[n].clone(),t.preventDefault()}})},update_viewport_overlay:function(){var e=this.cc,t=this.cv,n=this.oc,i=this.ov,r=e.width(),a=e.height(),o=n.width(),s=n.height(),l=e.position();i.css({left:-l.left/r*o,top:-l.top/a*s,width:t.width()/r*o-2,height:t.height()/a*s-2})},draw_overview:function(){var t,n,i,r,a=e("#overview-canvas"),o=a.parent().parent().width(),s=a.get(0).getContext("2d"),l=e("#canvas-container").width(),c=e("#canvas-container").height(),d=this.cv.width(),u=this.cv.height();l0&&(s.fillStyle="#E8A92D",s.strokeStyle="#E8A92D"),s.fillRect(d,u,h,f),s.strokeRect(d,u,h,f)}),this.update_viewport_overlay()}}),e.extend(i.prototype,{test:function(t,n){var i=this;clearTimeout(this.timeout);var r=t.pageX,a=t.pageY,o=e(this.panel),s=o.position(),l=o.width(),c=o.height(),d=o.parent(),u=d.width(),h=d.height(),f=d.offset(),p=f.left,_=f.top,g=p+d.width(),m=_+d.height(),v=-(l-u/2),y=-(c-h/2),b=u/2,w=h/2,x=!1,k=0;r-5g?s.left>v&&(k=Math.min(23,s.left-v),o.css("left",s.left-k),x=!0):a-5<_?s.topm&&s.top>y&&(k=Math.min(23,s.top-v),o.css("top",s.top-k+"px"),x=!0),x&&(n(),this.timeout=setTimeout(function(){i.test(t,n)},50))},stop:function(){clearTimeout(this.timeout)}}),t.default=n}).call(t,n(0))},288:function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(289),c=a(l),d=e.Model.extend({initialize:function(e,t){this.app=e,this.element=t.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(e){return i.findWhere(this.workflow_outputs,{output_name:e})},isWorkflowOutput:function(e){return void 0!==this.getWorkflowOutput(e)},removeWorkflowOutput:function(e){for(;this.isWorkflowOutput(e);)this.workflow_outputs.splice(this.getWorkflowOutput(e),1)},addWorkflowOutput:function(e,t){if(!this.isWorkflowOutput(e)){var n={output_name:e};return t&&(n.label=t),this.workflow_outputs.push(n),!0}return!1},labelWorkflowOutput:function(e,t){var n=!1,i=null;if(this.isWorkflowOutput(e)){var r=this.getWorkflowOutput(e);i=r.label,r.label=t,n=i!=t}else n=this.addWorkflowOutput(e,t);return n&&(this.app.workflow.updateOutputLabel(i,t),this.markChanged(),this.nodeView.redrawWorkflowOutputs()),n},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(e){var t=[];return r.each(e,function(e,n){n.connectors.length>0&&t.push(n)}),t},hasConnectedOutputTerminals:function(){var e=this.output_terminals;for(var t in e)if(e[t].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var e=this.input_terminals;for(var t in e){var n=e[t];if(n.connectors.length>0&&n.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(e){var t=[];return r.each(e,function(e,n){n.mapOver().isCollection&&n.connectors.length>0&&t.push(n)}),t},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(e){var t=[];return r.each(e,function(e,n){n.mapOver().isCollection&&t.push(n)}),t},hasMappedOverInputTerminals:function(){var e=!1;return i.each(this.input_terminals,function(t){t.mapOver().isCollection&&(e=!0)}),e},redraw:function(){r.each(this.input_terminals,function(e,t){t.redraw()}),r.each(this.output_terminals,function(e,t){t.redraw()})},clone:function(){var e=this,t={name:this.name,label:this.label,annotation:this.annotation,post_job_actions:this.post_job_actions},n=this.app.workflow.create_node(this.type,this.name,this.content_id);s.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:{type:this.type,tool_id:this.content_id,inputs:this.tool_state},success:function(i){var r=Object.assign({},i,t);n.init_field_data(r),n.update_field_data(r),e.app.workflow.activate_node(n)}})},destroy:function(){r.each(this.input_terminals,function(e,t){t.destroy()}),r.each(this.output_terminals,function(e,t){t.destroy()}),this.app.workflow.remove_node(this),r(this.element).remove()},make_active:function(){r(this.element).addClass("toolForm-active")},make_inactive:function(){var e=this.element.get(0);!function(t){t.removeChild(e),t.appendChild(e)}(e.parentNode),r(e).removeClass("toolForm-active")},init_field_data:function(e){e.type&&(this.type=e.type),this.name=e.name,this.config_form=e.config_form,this.tool_version=this.config_form&&this.config_form.version,this.tool_state=e.tool_state,this.errors=e.errors,this.tooltip=e.tooltip?e.tooltip:"",this.annotation=e.annotation,this.post_job_actions=e.post_job_actions?e.post_job_actions:{},this.label=e.label,this.uuid=e.uuid,this.workflow_outputs=e.workflow_outputs?e.workflow_outputs:[];var t=this,n=new c.default({el:this.element[0],node:t});t.nodeView=n,r.each(e.data_inputs,function(e,t){n.addDataInput(t)}),e.data_inputs.length>0&&e.data_outputs.length>0&&n.addRule(),r.each(e.data_outputs,function(e,t){n.addDataOutput(t)}),n.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(e){var t=this,n=t.nodeView,a=[];if(r.each(n.outputViews,function(t,n){var r=n.output.name,o=e.data_outputs,s=!1;i.each(o,function(e){e.name==r&&(s=!0)}),!1===s&&a.push(r)}),i.each(a,function(e){i.each(n.outputViews[e].terminalElement.terminal.connectors,function(e){e&&e.destroy()}),n.outputViews[e].remove(),delete n.outputViews[e],delete t.output_terminals[e]}),r.each(t.workflow_outputs,function(e,n){n&&!t.output_terminals[n.output_name]&&t.workflow_outputs.splice(e,1)}),r.each(e.data_outputs,function(e,i){n.outputViews[i.name]?(t.output_terminals[i.name].datatypes=i.extensions,t.output_terminals[i.name].destroyInvalidConnections()):n.addDataOutput(i)}),this.tool_state=e.tool_state,this.config_form=e.config_form,this.tool_version=this.config_form&&this.config_form.version,this.errors=e.errors,this.annotation=e.annotation,this.label=e.label,"post_job_actions"in e){var o=e.post_job_actions;this.post_job_actions=o||{}}t.nodeView.renderToolErrors();var s=n.$("div.inputs"),l=n.newInputsDiv(),c={};i.each(e.data_inputs,function(e){var n=t.nodeView.addDataInput(e,l);c[e.name]=n}),i.each(i.difference(i.values(n.terminalViews),i.values(c)),function(e){e.el.terminal.destroy()}),n.terminalViews=c,t.nodeView.render(),1==e.data_outputs.length&&"collection_type"in e.data_outputs[0]&&n.updateDataOutput(e.data_outputs[0]),s.replaceWith(l),"workflow_outputs"in e&&(this.workflow_outputs=e.workflow_outputs?e.workflow_outputs:[]),this.markChanged(),this.redraw()},error:function(e){var t=r(this.element).find(".toolFormBody");t.find("div").remove();var n="
    "+e+"
    ";this.config_form=n,t.html(n),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});t.default=d}).call(t,n(2),n(1),n(0))},289:function(e,t,n){"use strict";(function(e,i){function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=n(1),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}(a),s=n(290),l=r(s),c=n(292),d=r(c);t.default=e.View.extend({initialize:function(e){this.node=e.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputViews={}},render:function(){this.renderToolLabel(),this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolLabel:function(){this.$(".nodeTitle").text(this.node.label||this.node.name)},renderToolErrors:function(){this.node.errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return i("
    ").addClass("inputs")},updateMaxWidth:function(e){this.output_width=Math.max(this.output_width,e)},addRule:function(){this.tool_body.append(i("
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s.default.OutputCollectionTerminal({element:this.el,collection_type:t,collection_type_source:n,datatypes:e.extensions})}});t.default={InputTerminalView:p,OutputTerminalView:m,InputCollectionTerminalView:_,OutputCollectionTerminalView:v}}).call(t,n(2),n(1),n(0))},291:function(e,t,n){"use strict";(function(e,n,i){function r(e){this.collectionType=e,this.isCollection=!0,this.rank=e.split(":").length}Object.defineProperty(t,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var a={isCollection:!1,canMatch:function(e){return!1},canMapOver:function(e){return!1},toString:function(){return"NullCollectionType[]"},append:function(e){return e},equal:function(e){return e===this}},o={isCollection:!0,canMatch:function(e){return a!==e},canMapOver:function(e){return!1},toString:function(){return"AnyCollectionType[]"},append:function(e){throw"Cannot append to ANY_COLLECTION_TYPE_DESCRIPTION"},equal:function(e){return e===this}};e.extend(r.prototype,{append:function(e){return e===a?this:e===o?otherCollectionType:new r(this.collectionType+":"+e.collectionType)},canMatch:function(e){return e!==a&&(e===o||e.collectionType==this.collectionType)},canMapOver:function(e){if(e===a)return!1;if(e===o)return!1;if(this.rank<=e.rank)return!1;var t=e.collectionType;return this._endsWith(this.collectionType,t)},effectiveMapOver:function(e){var t=e.collectionType;return new r(this.collectionType.substring(0,this.collectionType.length-t.length-1))},equal:function(e){return e.collectionType==this.collectionType},toString:function(){return"CollectionType["+this.collectionType+"]"},_endsWith:function(e,t){return-1!==e.indexOf(t,e.length-t.length)}});var s=n.Model.extend({initialize:function(e){this.mapOver=e.mapOver||a,this.terminal=e.terminal,this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(a)},setMapOver:function(e){this.mapOver=e,this.trigger("change")}}),l=n.Model.extend({initialize:function(e){this.element=e.element,this.connectors=[]},connect:function(e){this.connectors.push(e),this.node&&this.node.markChanged()},disconnect:function(t){this.connectors.splice(e.inArray(t,this.connectors),1),this.node&&(this.node.markChanged(),this.resetMappingIfNeeded())},redraw:function(){e.each(this.connectors,function(e,t){t.redraw()})},destroy:function(){e.each(this.connectors.slice(),function(e,t){t.destroy()})},destroyInvalidConnections:function(){i.each(this.connectors,function(e){e&&e.destroyIfInvalid()})},setMapOver:function(e){this.multiple||this.mapOver().equal(e)||(this.terminalMapping.setMapOver(e),i.each(this.node.output_terminals,function(t){t.setMapOver(e)}))},mapOver:function(){return this.terminalMapping?this.terminalMapping.mapOver:a},isMappedOver:function(){return this.terminalMapping&&this.terminalMapping.mapOver.isCollection},resetMapping:function(){this.terminalMapping.disableMapOver()},resetMappingIfNeeded:function(){}}),c=l.extend({initialize:function(e){l.prototype.initialize.call(this,e),this.datatypes=e.datatypes},resetMappingIfNeeded:function(){this.node.hasConnectedOutputTerminals()||this.node.hasConnectedMappedInputTerminals()||i.each(this.node.mappedInputTerminals(),function(e){e.resetMappingIfNeeded()}),!this.node.hasMappedOverInputTerminals()&&this.resetMapping()},resetMapping:function(){this.terminalMapping.disableMapOver(),i.each(this.connectors,function(e){var t=e.handle2;t&&(t.resetMappingIfNeeded(),e.destroyIfInvalid())})}}),d=l.extend({initialize:function(e){l.prototype.initialize.call(this,e),this.update(e.input)},canAccept:function(e){return!this._inputFilled()&&this.attachable(e)},resetMappingIfNeeded:function(){this.mapOver().isCollection&&((this.node.hasConnectedMappedInputTerminals()||!this.node.hasConnectedOutputTerminals())&&this.resetMapping())},resetMapping:function(){this.terminalMapping.disableMapOver(),this.node.hasMappedOverInputTerminals()||i.each(this.node.output_terminals,function(e){e.resetMapping()})},connected:function(){return 0!==this.connectors.length},_inputFilled:function(){var e;return this.connected()?this.multiple?this._collectionAttached()?inputsFilled=!0:e=!1:e=!0:e=!1,e},_collectionAttached:function(){if(this.connected()){var e=this.connectors[0].handle1;return!!e&&!!(e.isCollection||e.isMappedOver()||e.datatypes.indexOf("input_collection")>0)}return!1},_mappingConstraints:function(){if(!this.node)return[];var e=this.mapOver();if(e.isCollection)return[e];var t=[];return this.node.hasConnectedOutputTerminals()?t.push(i.first(i.values(this.node.output_terminals)).mapOver()):i.each(this.node.connectedMappedInputTerminals(),function(e){t.push(e.mapOver())}),t},_producesAcceptableDatatype:function(e){for(var t in this.datatypes){var n=this.datatypes[t];if("input"==n)return!0;var i=new Array;if(i=i.concat(e.datatypes),e.node.post_job_actions)for(var r in e.node.post_job_actions){var a=e.node.post_job_actions[r];"ChangeDatatypeAction"!=a.action_type||""!=a.output_name&&a.output_name!=e.name||!a.action_arguments||i.push(a.action_arguments.newtype)}for(var o in i){var s=i[o];if("input"==s||"_sniff_"==s||"input_collection"==s||window.workflow_globals.app.isSubType(i[o],n))return!0}}return!1},_otherCollectionType:function(e){var t=a;e.isCollection&&(t=e.collectionType);var n=e.mapOver();return n.isCollection&&(t=n.append(t)),t}}),u=d.extend({update:function(e){this.datatypes=e.extensions,this.multiple=e.multiple,this.collection=!1},connect:function(e){d.prototype.connect.call(this,e);var t=e.handle1;if(t){var n=this._otherCollectionType(t);n.isCollection&&this.setMapOver(n)}},attachable:function(e){var t=this._otherCollectionType(e),n=this.mapOver();if(t.isCollection){if(this.multiple)return!(this.connected()&&!this._collectionAttached())&&(1==t.rank&&this._producesAcceptableDatatype(e));if(n.isCollection&&n.canMatch(t))return this._producesAcceptableDatatype(e);return!!this._mappingConstraints().every(i.bind(t.canMatch,t))&&this._producesAcceptableDatatype(e)}return!n.isCollection&&this._producesAcceptableDatatype(e)}}),h=d.extend({update:function(e){this.multiple=!1,this.collection=!0,this.datatypes=e.extensions;var t=[];e.collection_types?i.each(e.collection_types,function(e){t.push(new r(e))}):t.push(o),this.collectionTypes=t},connect:function(e){d.prototype.connect.call(this,e);var t=e.handle1;if(t){var n=this._effectiveMapOver(t);this.setMapOver(n)}},_effectiveMapOver:function(e){var t=this.collectionTypes,n=this._otherCollectionType(e);if(!i.some(t,function(e){return e.canMatch(n)}))for(var r in t){var o=t[r];if(n.canMapOver(o)){var s=n.effectiveMapOver(o);if(s!=a)return s}}return a},_effectiveCollectionTypes:function(){var e=this.mapOver();return i.map(this.collectionTypes,function(t){return e.append(t)})},attachable:function(e){var t=this._otherCollectionType(e);if(t.isCollection){var n=this._effectiveCollectionTypes(),r=this.mapOver();if(i.some(n,function(e){return e.canMatch(t)}))return this._producesAcceptableDatatype(e);if(r.isCollection)return!1;if(i.some(this.collectionTypes,function(e){return t.canMapOver(e)})){var a=this._effectiveMapOver(e);if(!a.isCollection)return!1;if(this._mappingConstraints().every(a.canMatch))return this._producesAcceptableDatatype(e)}}return!1}}),f=l.extend({initialize:function(e){if(l.prototype.initialize.call(this,e),this.datatypes=e.datatypes,e.collection_type)this.collectionType=new r(e.collection_type);else{e.collection_type_source||console.log("Warning: No collection type or collection type source defined."),this.collectionType=o}this.isCollection=!0},update:function(e){var t;if(e.collection_type)t=new r(e.collection_type);else{e.collection_type_source||console.log("Warning: No collection type or collection type source defined."),t=o}t.collectionType!=this.collectionType.collectionType&&i.each(this.connectors,function(e){e.destroy()}),this.collectionType=t}});t.default={InputTerminal:u,OutputTerminal:c,InputCollectionTerminal:h,OutputCollectionTerminal:f,TerminalMapping:s,CollectionTypeDescription:r,NULL_COLLECTION_TYPE_DESCRIPTION:a,ANY_COLLECTION_TYPE_DESCRIPTION:o}}).call(t,n(0),n(2),n(1))},292:function(e,t,n){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var i=e.View.extend({className:"form-row dataRow input-data-row",initialize:function(e){this.input=e.input,this.nodeView=e.nodeView,this.terminalElement=e.terminalElement,this.$el.attr("name",this.input.name).html(this.input.label),e.skipResize||(this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),n("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()),this.$el.css({position:"",left:"",top:"",display:""}),this.$el.remove())}}),r=e.View.extend({className:"form-row dataRow",initialize:function(e){this.output=e.output,this.terminalElement=e.terminalElement,this.nodeView=e.nodeView;var t=this.output,i=t.name,r=this.nodeView.node;if(t.extensions.indexOf("input")>=0||t.extensions.indexOf("input_collection")>=0||(i=i+" ("+t.extensions.join(", ")+")"),this.$el.html(i),this.calloutView=null,["tool","subworkflow"].indexOf(r.type)>=0){var o=new a({label:i,output:t,node:r});this.calloutView=o,this.$el.append(o.el),this.$el.hover(function(){o.hoverImage()},function(){o.resetImage()})}this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),n("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()+17),this.$el.css({position:"",left:"",top:"",display:""}).detach()},redrawWorkflowOutput:function(){this.calloutView&&this.calloutView.resetImage()}}),a=e.View.extend({tagName:"div",initialize:function(e){this.label=e.label,this.node=e.node,this.output=e.output;var t=this,i=this.node;this.$el.attr("class","callout "+this.label).css({display:"none"}).append(n("
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All unmarked datasets will be hidden."}),this.$el.css({top:"50%",margin:"-8px 0px 0px 0px",right:8}),this.$el.show(),this.resetImage()},resetImage:function(){this.node.isWorkflowOutput(this.output.name)?this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"):this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")},hoverImage:function(){this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-yellow.png")}});t.default={DataInputView:i,DataOutputView:r}}).call(t,n(2),n(0))},293:function(e,t,n){"use strict";(function(e,i){function r(e){return e&&e.__esModule?e:{default:e}}function a(e){var t=e.model.attributes,n=t.workflow,i=t.node;t.inputs.unshift({type:"text",name:"__annotation",label:"Annotation",fixed:!0,value:i.annotation,area:!0,help:"Add an annotation or notes to this step. Annotations are available when a workflow is viewed."}),t.inputs.unshift({type:"text",name:"__label",label:"Label",value:i.label,help:"Add a step label.",fixed:!0,onchange:function(t){var r=!1;for(var a in n.nodes){var o=n.nodes[a];if(o.label&&o.label==t&&o.id!=i.id){r=!0;break}}var s=e.data.match("__label");e.element_list[s].model.set("error_text",r&&"Duplicate label. Please fix this before saving the workflow."),e.trigger("change")}})}function o(e,t,n,i){var r=i.node.post_job_actions;t=t||[],t.push(e);for(var a in e.inputs){var s=e.inputs[a];if(s.action){if(s.name="pja__"+n+"__"+s.action,s.pja_arg&&(s.name+="__"+s.pja_arg),s.payload)for(var l in s.payload)s.payload[s.name+"__"+l]=s.payload[l],delete s.payload[l];var c=r[s.action+n];if(c){for(var d in t)t[d].expanded=!0;s.pja_arg?s.value=c.action_arguments&&c.action_arguments[s.pja_arg]||s.value:s.value="true"}}s.inputs&&o(s,t.slice(0),n,i)}}function s(e,t){var n=[],i=[],r=t.datatypes,a=t.node,s=t.workflow;for(var l in r)n.push({0:r[l],1:r[l]});for(l in a.input_terminals)i.push(a.input_terminals[l].name);n.sort(function(e,t){return e.label>t.label?1:e.labelhere     for more information. Valid inputs are: '+i.join(", ")+"."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:n,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Add Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{action:"RemoveTagDatasetAction",pja_arg:"tags",label:"Remove Tags",type:"text",value:"",ignore:"",help:"This action will remove tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return o(d,[],e,t),d}function l(e){var t=e.model.attributes,n=t.inputs,i=t.node,r=i.post_job_actions,a=i.output_terminals&&Object.keys(i.output_terminals)[0];if(a){n.push({name:"pja__"+a+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(r["EmailAction"+a])),ignore:"false",help:"An email notification will be sent when the job has completed.",payload:{host:window.location.host}}),n.push({name:"pja__"+a+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(r["DeleteIntermediatesAction"+a])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var o in i.output_terminals)n.push(s(o,t))}}Object.defineProperty(t,"__esModule",{value:!0});var c=n(3),d=r(c),u=n(11),h=r(u),f=n(45),p=r(f),_=e.View.extend({initialize:function(e){var t=this,n=e.node;this.form=new h.default(d.default.merge(e,{onchange:function(){d.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:{id:n.id,type:n.type,content_id:n.content_id,inputs:t.form.data.create()},success:function(e){n.update_field_data(e)}})}})),a(this.form),this.form.render()}}),g=e.View.extend({initialize:function(e){var t=this,n=e.node;this.form=new p.default(d.default.merge(e,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",initialmodel:function(e,n){t._customize(n),e.resolve()},buildmodel:function(e,t){t.model.get("postchange")(e,t)},postchange:function(e,r){var a=r.model.attributes,o={tool_id:a.id,tool_version:a.version,type:"tool",inputs:i.extend(!0,{},r.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",o),d.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:o,success:function(i){r.model.set(i.config_form),t._customize(r),r.update(i.config_form),r.errors(i.config_form),n.update_field_data(i),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",i),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",t),e.reject()}})}}))},_customize:function(e){var t=e.model.attributes;d.default.deepeach(t.inputs,function(e){e.type&&(-1!=["data","data_collection"].indexOf(e.type)?(e.type="hidden",e.info="Data input '"+e.name+"' ("+d.default.textify(e.extensions)+")",e.value={__class__:"RuntimeValue"}):e.fixed||(e.collapsible_value={__class__:"RuntimeValue"},e.is_workflow=e.options&&0===e.options.length||-1!=["integer","float"].indexOf(e.type)))}),d.default.deepeach(t.inputs,function(e){"conditional"===e.type&&(e.test_param.collapsible_value=void 0)}),l(e),a(e)}});t.default={Default:_,Tool:g}}).call(t,n(2),n(0))},294:function(e,t,n){"use strict";(function(e,i){function r(e){return e&&e.__esModule?e:{default:e}}function a(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}Object.defineProperty(t,"__esModule",{value:!0});var o=n(1),s=a(o),l=n(295),c=a(l),d=n(27),u=r(d),h=n(3),f=r(h),p=n(37),_=r(p),g=n(41),m=r(g);n(40);var v=e.Model.extend({is_visible:function(e,t){var n=e.getBoundingClientRect(),r=i("svg")[0].getBoundingClientRect();return!(n.right<0||n.left>r.right||n.bottom<0||n.top>r.bottom)}}),y={drawTicks:function(e,t,n,i,r){var a=e.append("g").selectAll("g").data(t).enter().append("g").selectAll("g").data(n).enter().append("g").attr("class","tick").attr("transform",function(e){return"rotate("+(180*e.angle/Math.PI-90)+")translate("+e.radius+",0)"}),o=[],s=[],l=function(e){return e.angle>Math.PI?"end":null};return r?(o=[0,0,0,-4],s=[4,0,"",".35em"],l=null):(o=[1,0,4,0],s=[0,4,".35em",""]),a.append("line").attr("x1",o[0]).attr("y1",o[1]).attr("x2",o[2]).attr("y1",o[3]).style("stroke","#000"),a.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",l).attr("transform",i).text(function(e){return e.label})},formatNum:function(e,t){if(void 0===t&&(t=2),null===e)return null;var n=null;if(Math.abs(e)<1)n=e.toPrecision(t);else{var i=Math.round(e.toPrecision(t));e=Math.abs(e),e<1e3?n=i:e<1e6?n=Math.round((i/1e3).toPrecision(3)).toFixed(0)+"K":e<1e9&&(n=Math.round((i/1e6).toPrecision(3)).toFixed(0)+"M")}return n}},b=e.Model.extend({}),w=e.View.extend({className:"circster",initialize:function(e){this.genome=e.genome,this.label_arc_height=50,this.scale=1,this.circular_views=null,this.chords_views=null,this.model.get("drawables").on("add",this.add_track,this),this.model.get("drawables").on("remove",this.remove_track,this);var t=this.model.get("config");t.get("arc_dataset_height").on("change:value",this.update_track_bounds,this),t.get("track_gap").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(e){return"DiagonalHeatmapTrack"!==e.get("track_type")})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(e){return"DiagonalHeatmapTrack"===e.get("track_type")})},get_tracks_bounds:function(){var e=this.get_circular_tracks(),t=this.model.get("config").get_value("arc_dataset_height"),n=this.model.get("config").get_value("track_gap"),i=Math.min(this.$el.width(),this.$el.height())-20,r=i/2-e.length*(t+n)+n-this.label_arc_height,a=c.range(r,i/2,t+n);return s.map(a,function(e){return[e,e+t]})},render:function(){var e=this,t=e.$el.width(),n=e.$el.height(),i=this.get_circular_tracks(),r=this.get_chord_tracks(),a=e.model.get("config").get_value("total_gap"),o=this.get_tracks_bounds(),s=c.select(e.$el[0]).append("svg").attr("width",t).attr("height",n).attr("pointer-events","all").append("svg:g").call(c.behavior.zoom().on("zoom",function(){var t=c.event.scale;s.attr("transform","translate("+c.event.translate+") scale("+t+")"),e.scale!==t&&(e.zoom_drag_timeout&&clearTimeout(e.zoom_drag_timeout),e.zoom_drag_timeout=setTimeout(function(){},400))})).attr("transform","translate("+t/2+","+n/2+")").append("svg:g").attr("class","tracks");this.circular_views=i.map(function(t,n){var i=new M({el:s.append("g")[0],track:t,radius_bounds:o[n],genome:e.genome,total_gap:a});return i.render(),i}),this.chords_views=r.map(function(t){var n=new C({el:s.append("g")[0],track:t,radius_bounds:o[0],genome:e.genome,total_gap:a});return n.render(),n});var l=this.circular_views[this.circular_views.length-1].radius_bounds[1],d=[l,l+this.label_arc_height];this.label_track_view=new k({el:s.append("g")[0],track:new b,radius_bounds:d,genome:e.genome,total_gap:a}),this.label_track_view.render()},add_track:function(e){var t=this.model.get("config").get_value("total_gap");if("DiagonalHeatmapTrack"===e.get("track_type")){var n=this.circular_views[0].radius_bounds,i=new C({el:c.select("g.tracks").append("g")[0],track:e,radius_bounds:n,genome:this.genome,total_gap:t});i.render(),this.chords_views.push(i)}else{var r=this.get_tracks_bounds();s.each(this.circular_views,function(e,t){e.update_radius_bounds(r[t])}),s.each(this.chords_views,function(e){e.update_radius_bounds(r[0])});var a=this.circular_views.length,o=new M({el:c.select("g.tracks").append("g")[0],track:e,radius_bounds:r[a],genome:this.genome,total_gap:t});o.render(),this.circular_views.push(o)}},remove_track:function(e,t,n){var i=this.circular_views[n.index];this.circular_views.splice(n.index,1),i.$el.remove();var r=this.get_tracks_bounds();s.each(this.circular_views,function(e,t){e.update_radius_bounds(r[t])})},update_track_bounds:function(){var e=this.get_tracks_bounds();s.each(this.circular_views,function(t,n){t.update_radius_bounds(e[n])}),s.each(this.chords_views,function(t){t.update_radius_bounds(e[0])})}}),x=e.View.extend({tagName:"g",initialize:function(e){this.bg_stroke="#ddd",this.loading_bg_fill="#ffc",this.bg_fill="#ddd",this.total_gap=e.total_gap,this.track=e.track,this.radius_bounds=e.radius_bounds,this.genome=e.genome,this.chroms_layout=this._chroms_layout(),this.data_bounds=[],this.scale=1,this.parent_elt=c.select(this.$el[0])},get_fill_color:function(){var e=this.track.get("config").get_value("block_color");return e||(e=this.track.get("config").get_value("color")),e},render:function(){var e=this.parent_elt,t=this.chroms_layout,n=c.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),r=e.selectAll("g").data(t).enter().append("svg:g"),a=r.append("path").attr("d",n).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);a.append("title").text(function(e){return e.data.chrom});var o=this,s=o.track.get("data_manager"),l=!s||s.data_is_ready();i.when(l).then(function(){i.when(o._render_data(e)).then(function(){a.style("fill",o.bg_fill),o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(e){this.radius_bounds=e;var t=c.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1e3).attr("d",t),this._transition_chrom_data(),this._transition_labels()},update_scale:function(e){var t=this.scale;if(this.scale=e,!(e<=t)){var n=this,r=new v;return this.parent_elt.selectAll("path.chrom-data").filter(function(e,t){return r.is_visible(this)}).each(function(t,r){var a,o=c.select(this),l=o.attr("chrom"),d=n.genome.get_chrom_region(l),u=n.track.get("data_manager");u.can_get_more_detailed_data(d)&&(a=n.track.get("data_manager").get_more_detailed_data(d,"Coverage",0,e),i.when(a).then(function(e){o.remove(),n._update_data_bounds();var t=s.find(n.chroms_layout,function(e){return e.data.chrom===l}),i=n.get_fill_color();n._render_chrom_data(n.parent_elt,t,e).style("stroke",i).style("fill",i)}))}),n}},_transition_chrom_data:function(){var e=this.track,t=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data");if(n[0].length>0){var r=this;i.when(e.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){var a=s.reject(s.map(i,function(e,n){var i=null,a=r._get_path_function(t[n],e);return a&&(i=a(e.data)),i}),function(e){return null===e}),o=e.get("config").get_value("color");n.each(function(e,t){c.select(this).transition().duration(1e3).style("stroke",o).style("fill",o).attr("d",a[t])})})}},_transition_labels:function(){},_update_data_bounds:function(e){this.data_bounds;this.data_bounds=e||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome)),this._transition_chrom_data()},_render_data:function(e){var t=this,n=this.chroms_layout,r=this.track,a=i.Deferred();return i.when(r.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){t.data_bounds=t.get_data_bounds(i),r.get("config").set_value("min_value",t.data_bounds[0],{silent:!0}),r.get("config").set_value("max_value",t.data_bounds[1],{silent:!0});var o=s.zip(n,i);s.each(o,function(n){var i=n[0],r=n[1];return t._render_chrom_data(e,i,r)});var l=t.get_fill_color();t.parent_elt.selectAll("path.chrom-data").style("stroke",l).style("fill",l),a.resolve(e)}),a},_render_chrom_data:function(e,t,n){},_get_path_function:function(e,t){},_chroms_layout:function(){var e=this.genome.get_chroms_info(),t=c.layout.pie().value(function(e){return e.len}).sort(null),n=t(e),i=2*Math.PI*this.total_gap/e.length;return s.map(n,function(e,t){var n=e.endAngle-i;return e.endAngle=n>e.startAngle?n:e.startAngle,e})}}),k=x.extend({initialize:function(e){x.prototype.initialize.call(this,e),this.innerRadius=this.radius_bounds[0],this.radius_bounds[0]=this.radius_bounds[1],this.bg_stroke="#fff",this.bg_fill="#fff",this.min_arc_len=.05},_render_data:function(e){var t=this,n=e.selectAll("g");n.selectAll("path").attr("id",function(e){return"label-"+e.data.chrom}),n.append("svg:text").filter(function(e){return e.endAngle-e.startAngle>t.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(e){return"#label-"+e.data.chrom}).attr("startOffset","25%").text(function(e){return e.data.chrom});var i=function(e){var n=(e.endAngle-e.startAngle)/e.value,i=c.range(0,e.value,25e6).map(function(i,r){return{radius:t.innerRadius,angle:i*n+e.startAngle,label:0===r?0:r%3?null:t.formatNum(i)}});return i.length<4&&(i[i.length-1].label=t.formatNum(Math.round((i[i.length-1].angle-e.startAngle)/n))),i},r=function(e){return e.angle>Math.PI?"rotate(180)translate(-16)":null},a=s.filter(this.chroms_layout,function(e){return e.endAngle-e.startAngle>t.min_arc_len});this.drawTicks(this.parent_elt,a,i,r)}});s.extend(k.prototype,y);var j=x.extend({initialize:function(e){x.prototype.initialize.call(this,e);var t=this.track.get("config");t.get("min_value").on("change:value",this._update_min_max,this),t.get("max_value").on("change:value",this._update_min_max,this),t.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var e=this.track.get("config"),t=[e.get_value("min_value"),e.get_value("max_value")];this._update_data_bounds(t),this.parent_elt.selectAll(".min_max").text(function(e,n){return t[n]})},_quantile:function(e,t){return e.sort(c.ascending),c.quantile(e,t)},_render_chrom_data:function(e,t,n){var i=this._get_path_function(t,n);return i?e.datum(n.data).append("path").attr("class","chrom-data").attr("chrom",t.data.chrom).attr("d",i):null},_get_path_function:function(e,t){if("string"==typeof t||!t.data||0===t.data.length)return null;var n=c.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(!0),i=c.scale.linear().domain([0,t.data.length]).range([e.startAngle,e.endAngle]),r=c.svg.line.radial().interpolate("linear").radius(function(e){return n(e[1])}).angle(function(e,t){return i(t)});return c.svg.area.radial().interpolate(r.interpolate()).innerRadius(n(0)).outerRadius(r.radius()).angle(r.angle())},render_labels:function(){var e=this,t=function(){return"rotate(90)"},n=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),t,!0).classed("min_max",!0);s.each(n,function(t){i(t).click(function(){new _.default.ConfigSettingCollectionView({collection:e.track.get("config")}).render_in_modal("Configure Track")})})},_transition_labels:function(){if(0!==this.data_bounds.length){var e=this,t=s.filter(this.chroms_layout,function(e){return e.endAngle-e.startAngle>.08}),n=s.filter(t,function(e,t){return t%3==0}),i=s.flatten(s.map(n,function(t){return e._data_bounds_ticks_fn()(t)}));this.parent_elt.selectAll("g.tick").data(i).transition().attr("transform",function(e){return"rotate("+(180*e.angle/Math.PI-90)+")translate("+e.radius+",0)"})}},_data_bounds_ticks_fn:function(){var e=this;return visibleChroms=0,function(t){return[{radius:e.radius_bounds[0],angle:t.startAngle,label:e.formatNum(e.data_bounds[0])},{radius:e.radius_bounds[1],angle:t.startAngle,label:e.formatNum(e.data_bounds[1])}]}},get_data_bounds:function(e){}});s.extend(j.prototype,y);var M=j.extend({get_data_bounds:function(e){var t=s.flatten(s.map(e,function(e){return e?s.map(e.data,function(e){return parseInt(e[1],10)||0}):0}));return[s.min(t),this._quantile(t,.98)||s.max(t)]}}),C=x.extend({render:function(){var e=this;i.when(e.track.get("data_manager").data_is_ready()).then(function(){i.when(e.track.get("data_manager").get_genome_wide_data(e.genome)).then(function(t){var n=[],i=e.genome.get_chroms_info();s.each(t,function(t,r){var a=i[r].chrom,o=s.map(t.data,function(t){var n=e._get_region_angle(a,t[1]),i=e._get_region_angle(t[3],t[4]);return{source:{startAngle:n,endAngle:n+.01},target:{startAngle:i,endAngle:i+.01}}});n=n.concat(o)}),e.parent_elt.append("g").attr("class","chord").selectAll("path").data(n).enter().append("path").style("fill",e.get_fill_color()).attr("d",c.svg.chord().radius(e.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(e){this.radius_bounds=e,this.parent_elt.selectAll("path").transition().attr("d",c.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(e,t){var n=s.find(this.chroms_layout,function(t){return t.data.chrom===e});return n.endAngle-(n.endAngle-n.startAngle)*(n.data.len-t)/n.data.len}}),S=e.View.extend({initialize:function(){f.default.cssLoadFile("static/style/circster.css");var e=new u.default.Genome(galaxy_config.app.genome),t=new u.default.GenomeVisualization(galaxy_config.app.viz_config);t.get("config").add([{key:"arc_dataset_height",label:"Arc Dataset Height",type:"int",value:25,view:"circster"},{key:"track_gap",label:"Gap Between Tracks",type:"int",value:5,view:"circster"},{key:"total_gap",label:"Gap [0-1]",type:"float",value:.4,view:"circster",hidden:!0}]),new w({el:i("#center .unified-panel-body"),genome:e,model:t}).render(),i("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var n=m.default.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){u.default.select_datasets({dbkey:t.get("dbkey")},function(e){t.add_tracks(e)})}},{icon_class:"gear",title:"Settings",on_click:function(){new _.default.ConfigSettingCollectionView({collection:t.get("config")}).render_in_modal("Configure Visualization")}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"}),i.ajax({url:Galaxy.root+"visualization/save",type:"POST",dataType:"json",data:{id:t.get("vis_id"),title:t.get("title"),dbkey:t.get("dbkey"),type:"trackster",vis_json:JSON.stringify(t)}}).success(function(e){Galaxy.modal.hide(),t.set("vis_id",e.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. 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o=n(7),s=a(o),l=n(13),c=a(l),d=n(299),u=a(d),h=e.View.extend({el:"#folder_items_element",progress:0,progressStep:1,folderContainer:null,current_sort_order:"asc",current_sort_key:"name",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .folder_row":"selectClickedRow","click .sort-folder-name":"sortColumnClicked","click .sort-folder-file_ext":"sortColumnClicked","click .sort-folder-description":"sortColumnClicked","click .sort-folder-state":"sortColumnClicked"},collection:null,defaults:{include_deleted:!1,page_count:null,show_page:null},initialize:function(e){this.options=i.defaults(this.options||{},this.defaults,e),this.modal=null,this.rowViews={},this.collection=new c.default.Folder,this.listenTo(this.collection,"add",this.renderOne),this.listenTo(this.collection,"remove",this.removeOne),this.listenTo(this.collection,"sort",this.rePaint),this.listenTo(this.collection,"reset",this.rePaint),this.fetchFolder()},fetchFolder:function(e){var e=e||{};this.options.include_deleted=e.include_deleted;var t=this;this.folderContainer=new c.default.FolderContainer({id:this.options.id}),this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents",this.options.include_deleted&&(this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"),this.folderContainer.fetch({success:function(e){t.folder_container=e,t.render()},error:function(e,t){void 0!==t.responseJSON?s.default.error(t.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):s.default.error("An error occurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},render:function(e){this.options=i.extend(this.options,e);var t=this.templateFolder();r(".tooltip").hide();var n,a=this.folderContainer.attributes.metadata.full_path;if(n=1===a.length?0:a[a.length-2][0],this.$el.html(t({path:this.folderContainer.attributes.metadata.full_path,parent_library_id:this.folderContainer.attributes.metadata.parent_library_id,id:this.options.id,upper_folder_id:n,order:this.current_sort_order})),this.options.dataset_id){var o=i.findWhere(self.rowViews,{id:this.options.dataset_id});o?o.showDatasetDetails():s.default.error("Requested dataset not found. Showing folder instead.")}else(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.paginate();r("#center [data-toggle]").tooltip(),r("#center").css("overflow","auto")},paginate:function(e){this.options=i.extend(this.options,e),(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_items_count=this.folder_container.get("folder").models.length,this.options.page_count=Math.ceil(this.options.total_items_count/Galaxy.libraries.preferences.get("folder_page_size"));var t=Galaxy.libraries.preferences.get("folder_page_size")*(this.options.show_page-1),n=null;n=this.folder_container.get("folder").models.slice(t,t+Galaxy.libraries.preferences.get("folder_page_size")),this.options.items_shown=n.length,Galaxy.libraries.preferences.get("folder_page_size")*this.options.show_page>this.options.total_items_count+Galaxy.libraries.preferences.get("folder_page_size")&&(n=[]),Galaxy.libraries.folderToolbarView.renderPaginator(this.options),this.collection.reset(n)},rePaint:function(e){this.options=i.extend(this.options,e),this.removeAllRows(),this.renderAll(),this.checkEmptiness()},addAll:function(e){i.each(e,function(e){Galaxy.libraries.folderListView.collection.add(e,{current_sort_order:!1})}),r("#center [data-toggle]").tooltip(),this.checkEmptiness(),this.postRender()},postRender:function(){var e=this.folderContainer.attributes.metadata;e.contains_file_or_folder=void 0!==this.collection.findWhere({type:"file"})||void 0!==this.collection.findWhere({type:"folder"}),Galaxy.libraries.folderToolbarView.configureElements(e)},renderAll:function(){var e=this;i.each(this.collection.models.reverse(),function(t){e.renderOne(t)}),this.postRender()},renderOne:function(e){this.options.contains_file_or_folder=!0,e.set("folder_id",this.id);var t=new u.default.FolderRowView({model:e});this.rowViews[e.get("id")]=t,this.$el.find("#first_folder_item").after(t.el)},removeOne:function(e){this.$el.find("tr").filter(function(){return r(this).data("id")&&r(this).data("id")===e.id}).remove()},removeAllRows:function(){r(".library-row").remove()},checkEmptiness:function(){0===this.$el.find(".dataset_row").length&&0===this.$el.find(".folder_row").length?this.$el.find(".empty-folder-message").show():this.$el.find(".empty-folder-message").hide()},sortColumnClicked:function(e){e.preventDefault(),this.current_sort_order="asc"===this.current_sort_order?"desc":"asc",this.current_sort_key=e.currentTarget.className.replace("sort-folder-",""),this.collection.sortFolder(this.current_sort_key,this.current_sort_order),this.renderSortIcon()},selectAll:function(e){var t=e.target.checked,n=this;r(":checkbox","#folder_list_body").each(function(){this.checked=t;var e=r(this).closest("tr");t?n.makeDarkRow(e):n.makeWhiteRow(e)})},selectClickedRow:function(e){var t,n,i="";t=r(e.target).closest("tr"),"input"===e.target.localName?(i=e.target,n="input"):"td"===e.target.localName&&(i=t.find(":checkbox")[0],n="td"),i.checked?"td"===n?(i.checked="",this.makeWhiteRow(t)):"input"===n&&this.makeDarkRow(t):"td"===n?(i.checked="selected",this.makeDarkRow(t)):"input"===n&&this.makeWhiteRow(t)},makeDarkRow:function(e){e.removeClass("light").addClass("dark"),e.find("a").removeClass("light").addClass("dark"),e.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file"),e.find(".fa-folder-o").removeClass("fa-folder-o").addClass("fa-folder")},makeWhiteRow:function(e){e.removeClass("dark").addClass("light"),e.find("a").removeClass("dark").addClass("light"),e.find(".fa-file").removeClass("fa-file").addClass("fa-file-o"),e.find(".fa-folder").removeClass("fa-folder").addClass("fa-folder-o")},renderSortIcon:function(){"asc"===this.current_sort_order?(r('[class*="sort-icon"]').removeClass("fa-sort-alpha-desc").removeClass("fa-sort-alpha-asc"),r(".sort-icon-"+this.current_sort_key).addClass("fa-sort-alpha-asc")):r(".sort-icon-"+this.current_sort_key).addClass("fa-sort-alpha-desc")},templateFolder:function(){return i.template(['
      ','
    1. Libraries
      2. ',"<% _.each(path, function(path_item) { %>","<% if (path_item[0] != id) { %>",'
    2. <%- path_item[1] %>
      3. ',"<% } else { %>",'
    3. <%- path_item[1] %>
      4. ',"<% } %>","<% }); %>","
    ",'',"",'','','','','','','','',' ',"",'','',"","","","","","","","","","","","
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    ",'" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..',"
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Click this to see it.","",{onclick:function(){var e=t.model.get("folder_id");window.location=Galaxy.root+"library/list#folders/"+e+"/datasets/"+t.id}})},error:function(e,t){void 0!==t.responseJSON?s.default.error("Dataset was not undeleted. "+t.responseJSON.err_msg):s.default.error("An error occured! Dataset was not undeleted. Please try again.")}})},undeleteFolder:function(e){r(".tooltip").hide();var t=r(e.target).closest("tr").data("id"),n=Galaxy.libraries.folderListView.collection.get(t);n.url=n.urlRoot+n.id+"?undelete=true",n.destroy({success:function(e,n){Galaxy.libraries.folderListView.collection.remove(t);var i=new c.default.FolderAsModel(n);Galaxy.libraries.folderListView.collection.add(i),Galaxy.libraries.folderListView.collection.sortFolder("name","asc"),s.default.success("Folder undeleted.")},error:function(e,t){void 0!==t.responseJSON?s.default.error("Folder was not undeleted. "+t.responseJSON.err_msg):s.default.error("An error occured! Folder was not undeleted. Please try again.")}})},startModifications:function(){this.options.edit_mode=!0,this.repaint()},cancelModifications:function(){this.options.edit_mode=!1,this.repaint()},saveModifications:function(){var e=Galaxy.libraries.folderListView.collection.get(this.$el.data("id")),t=!1,n=this.$el.find(".input_folder_name").val();if(void 0!==n&&n!==e.get("name")){if(!(n.length>2))return void s.default.warning("Folder name has to be at least 3 characters long.");e.set("name",n),t=!0}var i=this.$el.find(".input_folder_description").val();if(void 0!==i&&i!==e.get("description")&&(e.set("description",i),t=!0),t){var r=this;e.save(null,{patch:!0,success:function(e){r.options.edit_mode=!1,r.repaint(e),s.default.success("Changes to folder saved.")},error:function(e,t){void 0!==t.responseJSON?s.default.error(t.responseJSON.err_msg):s.default.error("An error occured while attempting to update the folder.")}})}else this.options.edit_mode=!1,this.repaint(e),s.default.info("Nothing has changed.")},repaint:function(){r(".tooltip").hide();var e=this.$el;this.render(),e.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},templateRowFolder:function(){return i.template(['',"",'',"",'',"<% if(!edit_mode) { %>","",'<%- content_item.get("name") %>',"","",'<%- content_item.get("description") %>',"","<% } else if(edit_mode){ %>",'','',"<% } %>","folder","","",'<%= _.escape(content_item.get("update_time")) %>',"","","","<% if(edit_mode) { %>",'",'","<% } else if (!edit_mode){%>",'",'','","","<% } %>","",""].join(""))},templateRowFile:function(){return i.template(['',"",'',"",'','',"","",'/datasets/<%- content_item.id %>" class="library-dataset">','<%- content_item.get("name") %>',"","",'<%- content_item.get("message") %>','<%= _.escape(content_item.get("file_ext")) %>','<%= _.escape(content_item.get("file_size")) %>','<%= _.escape(content_item.get("update_time")) %>',"",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) %>',"<% } %>","","",'<% if (content_item.get("is_unrestricted")) { %>','',"<% } %>",'<% if (content_item.get("is_private")) { %>','',"<% } %>",'<% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %>','',"<% } %>",'<% if (content_item.get("can_manage")) { %>','/datasets/<%- content_item.id %>/permissions">','","","<% } %>","",""].join(""))},templateRowDeletedFile:function(){return i.template(['',"",'',"","",'','<%- content_item.get("name") %>',"","",'<%- content_item.get("message") %>',"","",'<%= _.escape(content_item.get("file_ext")) %>',"","",'<%= _.escape(content_item.get("file_size")) %>',"","",'<%= _.escape(content_item.get("update_time")) %>',"","",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) %>',"<% } %>","","",'','","",""].join(""))},templateRowDeletedFolder:function(){return i.template(['',"",'',"","",'','<%- content_item.get("name") %>',"","",'<%- content_item.get("description") %>',"","","folder","","","",'<%= _.escape(content_item.get("update_time")) %>',"","","",'','","",""].join(""))}});t.default={FolderRowView:h}}).call(t,n(2),n(1),n(0))},300:function(e,t,n){"use strict";(function(e,i){function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=n(7),o=r(a),s=n(13),l=r(s),c=n(301),d=r(c),u=n(1),h=r(u),f=e.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},defaults:{page_count:null,show_page:null,all_fetched:!1},initialize:function(e){this.options=h.default.defaults(this.options||{},e,this.defaults);var t=this;this.modal=null,this.collection=new l.default.Libraries,this.collection.url=this.collection.urlRoot+"?deleted=false",this.collection.fetch({success:function(){t.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})},render:function(e){this.options=h.default.extend(this.options,e),this.setElement("#libraries_element");var t=this.templateLibraryList(),n=null,r=null,a=function(e){return!0===e.get("public")};if(i(".tooltip").hide(),void 0!==e&&(r=void 0!==e.models?e.models:null),null!==this.collection&&null===r)this.sortLibraries(),n=Galaxy.libraries.preferences.get("with_deleted")?this.collection.models:this.collection.where({deleted:!1}),Galaxy.libraries.preferences.get("without_restricted")&&(n=h.default.filter(n,a));else if(null!==r){if(Galaxy.libraries.preferences.get("with_deleted"))n=r;else{var o=function(e){return!1===e.get("deleted")};n=h.default.filter(r,o)}Galaxy.libraries.preferences.get("without_restricted")&&(n=h.default.filter(n,a))}else n=[];(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_libraries_count=n.length;var s=Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1);this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size")),this.options.total_libraries_count>0&&sthis.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size")&&(n=[]),this.$el.html(t({length:1,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options),this.renderRows(n)):(this.$el.html(t({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),i("#center [data-toggle]").tooltip(),i("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var e=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){e.options.all_fetched=!0,e.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})}},renderRows:function(e){for(var t=0;t',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","
    ","There are no libraries matching your search. Try different keyword.","
    ","<% } else{ %>","
    ","There are no libraries visible to you here. If you expected some to show up please consult the",' library security wikipage',' or visit the Galaxy support site.',"
    ","<% }%>","<% } else{ %>",'',"",'",'',' ','',"",'',"","
    ','',"name","",'',"descriptionsynopsis
    ","<% }%>","
    "].join(""))}});t.default={LibraryListView:f}}).call(t,n(2),n(0))},301:function(e,t,n){"use strict";(function(e,i,r){Object.defineProperty(t,"__esModule",{value:!0});var a=n(7),o=function(e){return e&&e.__esModule?e:{default:e}}(a),s=e.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library"},edit_mode:!1,element_visibility_config:{upload_library_btn:!1,edit_library_btn:!1,permission_library_btn:!1,save_library_btn:!1,cancel_library_btn:!1,delete_library_btn:!1,undelete_library_btn:!1},initialize:function(e){this.render(e)},render:function(e){void 0===e&&(e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))),this.prepareButtons(e);var t=this.templateRow();return this.setElement(t({library:e,button_config:this.element_visibility_config,edit_mode:this.edit_mode})),this.$el.show(),this},repaint:function(e){i(".tooltip").hide();var t=this.$el;this.render(),t.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){var t=this.element_visibility_config;!1===this.edit_mode?(t.save_library_btn=!1,t.cancel_library_btn=!1,t.delete_library_btn=!1,!0===e.get("deleted")?(t.undelete_library_btn=!0,t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1):!1===e.get("deleted")&&(t.save_library_btn=!1,t.cancel_library_btn=!1,t.undelete_library_btn=!1,!0===e.get("can_user_add")&&(t.upload_library_btn=!0),!0===e.get("can_user_modify")&&(t.edit_library_btn=!0),!0===e.get("can_user_manage")&&(t.permission_library_btn=!0))):!0===this.edit_mode&&(t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1,t.save_library_btn=!0,t.cancel_library_btn=!0,t.delete_library_btn=!0,t.undelete_library_btn=!1),this.element_visibility_config=t},edit_button_clicked:function(){this.edit_mode=!0,this.repaint()},cancel_library_modification:function(){this.edit_mode=!1,this.repaint()},save_library_modification:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=!1,n=this.$el.find(".input_library_name").val();if(void 0!==n&&n!==e.get("name")){if(!(n.length>2))return void o.default.warning("Library name has to be at least 3 characters long.");e.set("name",n),t=!0}var i=this.$el.find(".input_library_description").val();void 0!==i&&i!==e.get("description")&&(e.set("description",i),t=!0);var r=this.$el.find(".input_library_synopsis").val();if(void 0!==r&&r!==e.get("synopsis")&&(e.set("synopsis",r),t=!0),t){var a=this;e.save(null,{patch:!0,success:function(e){a.edit_mode=!1,a.repaint(e),o.default.success("Changes to library saved.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while attempting to update the library.")}})}else this.edit_mode=!1,this.repaint(e),o.default.info("Nothing has changed.")},delete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.destroy({success:function(e){e.set("deleted",!0),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,!1===Galaxy.libraries.preferences.get("with_deleted")?(i(".tooltip").hide(),t.repaint(e),t.$el.remove()):!0===Galaxy.libraries.preferences.get("with_deleted")&&t.repaint(e),o.default.success("Library has been marked deleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured during deleting the library.")}})},undelete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.url=e.urlRoot+e.id+"?undelete=true",e.destroy({success:function(e){e.set("deleted",!1),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,t.repaint(e),o.default.success("Library has been undeleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while undeleting the library.")}})},templateRow:function(){return r.template(['" style="display:none;" data-id="<%- library.get("id") %>">',"<% if(!edit_mode) { %>",'<% if(library.get("deleted")) { %>','<%- library.get("name") %>',"<% } else { %>",'"><%- library.get("name") %>',"<% } %>",'<% if(library.get("description")) { %>','<% if( (library.get("description")).length> 80 ) { %>','"><%= _.escape(library.get("description")).substring(0, 80) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("description"))%>',"<% } %>","<% } else { %>","","<% } %>",'<% if(library.get("synopsis")) { %>','<% if( (library.get("synopsis")).length> 120 ) { %>','"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("synopsis"))%>',"<% } %>","<% } else { %>","","<% } %>","<% } else if(edit_mode){ %>",'','','',"<% } %>",'','<% if( (library.get("public")) 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e=this.templateToolBar(),t=!1,n=!0;Galaxy.user&&(t=Galaxy.user.isAdmin(),n=Galaxy.user.isAnonymous()),this.$el.html(e({admin_user:t,anon_user:n})),t&&(this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted"),this.$el.find("#exclude_restricted_chk")[0].checked=Galaxy.libraries.preferences.get("without_restricted"))},renderPaginator:function(e){this.options=i.extend(this.options,e);var t=this.templatePaginator();this.$el.find("#library_paginator").html(t({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown,library_page_size:Galaxy.libraries.preferences.get("library_page_size")}))},createLibraryFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this;this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New 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t=r(".library-search-input").val();this.options.search_term=t,Galaxy.libraries.libraryListView.searchLibraries(t)},templateToolBar:function(){return i.template(['
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t=this.templatePaginator();r("body").find(".folder-paginator").html(t({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown,folder_page_size:Galaxy.libraries.preferences.get("folder_page_size")}))},configureElements:function(e){this.options=i.extend(this.options,e),!0===this.options.can_add_library_item?r(".add-library-items").show():r(".add-library-items").hide(),!0===this.options.contains_file_or_folder&&Galaxy.user?Galaxy.user.isAnonymous()?(r(".dataset-manipulation").show(),r(".logged-dataset-manipulation").hide()):(r(".logged-dataset-manipulation").show(),r(".dataset-manipulation").show()):(r(".logged-dataset-manipulation").hide(),r(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this,n=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:n(),buttons:{Create:function(){t.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var t=this.serialize_new_folder();if(this.validate_new_folder(t)){var n,i=new h.default.FolderAsModel,r=e.history.fragment.split("/");n=r.indexOf("page")>-1?r[r.length-3]:r[r.length-1],i.url=i.urlRoot+n,i.save(t,{success:function(e){Galaxy.modal.hide(),d.default.success("Folder created."),e.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(e)},error:function(e,t){Galaxy.modal.hide(),void 0!==t.responseJSON?d.default.error(t.responseJSON.err_msg):d.default.error("An error occurred.")}})}else d.default.error("Folder's name is 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e=this.modal.$("input[name=history_name]").val(),t=this;if(""!==e)r.post(Galaxy.root+"api/histories",{name:e}).done(function(e){t.options.last_used_history_id=e.id,t.processImportToHistory(e.id,e.name)}).fail(function(e,t,n){d.default.error("An error occurred.")}).always(function(){t.modal.enableButton("Import")});else{var n=r("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=n;var i=r("select[name=dataset_import_bulk] option:selected").text();this.processImportToHistory(n,i),this.modal.enableButton("Import")}},processImportToHistory:function(e,t){var n=[],i=[];this.findCheckedRows().each(function(){var e=r(this).closest("tr").data("id");"F"==e.substring(0,1)?i.push(e):n.push(e)});for(var o=[],s=n.length-1;s>=0;s--){var l=n[s],c=new h.default.HistoryItem;c.url=c.urlRoot+e+"/contents",c.content=l,c.source="library",o.push(c)}for(var s=i.length-1;s>=0;s--){var d=i[s],c=new 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    ','
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s=Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1);this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size")),this.options.total_libraries_count>0&&sthis.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size")&&(n=[]),this.$el.html(t({length:1,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options),this.renderRows(n)):(this.$el.html(t({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),i("#center [data-toggle]").tooltip(),i("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var e=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){e.options.all_fetched=!0,e.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})}},renderRows:function(e){for(var t=0;t',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","
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t=this.element_visibility_config;!1===this.edit_mode?(t.save_library_btn=!1,t.cancel_library_btn=!1,t.delete_library_btn=!1,!0===e.get("deleted")?(t.undelete_library_btn=!0,t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1):!1===e.get("deleted")&&(t.save_library_btn=!1,t.cancel_library_btn=!1,t.undelete_library_btn=!1,!0===e.get("can_user_add")&&(t.upload_library_btn=!0),!0===e.get("can_user_modify")&&(t.edit_library_btn=!0),!0===e.get("can_user_manage")&&(t.permission_library_btn=!0))):!0===this.edit_mode&&(t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1,t.save_library_btn=!0,t.cancel_library_btn=!0,t.delete_library_btn=!0,t.undelete_library_btn=!1),this.element_visibility_config=t},edit_button_clicked:function(){this.edit_mode=!0,this.repaint()},cancel_library_modification:function(){this.edit_mode=!1,this.repaint()},save_library_modification:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=!1,n=this.$el.find(".input_library_name").val();if(void 0!==n&&n!==e.get("name")){if(!(n.length>2))return void o.default.warning("Library name has to be at least 3 characters long.");e.set("name",n),t=!0}var i=this.$el.find(".input_library_description").val();void 0!==i&&i!==e.get("description")&&(e.set("description",i),t=!0);var r=this.$el.find(".input_library_synopsis").val();if(void 0!==r&&r!==e.get("synopsis")&&(e.set("synopsis",r),t=!0),t){var a=this;e.save(null,{patch:!0,success:function(e){a.edit_mode=!1,a.repaint(e),o.default.success("Changes to library saved.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while attempting to update the library.")}})}else this.edit_mode=!1,this.repaint(e),o.default.info("Nothing has changed.")},delete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.destroy({success:function(e){e.set("deleted",!0),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,!1===Galaxy.libraries.preferences.get("with_deleted")?(i(".tooltip").hide(),t.repaint(e),t.$el.remove()):!0===Galaxy.libraries.preferences.get("with_deleted")&&t.repaint(e),o.default.success("Library has been marked deleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured during deleting the library.")}})},undelete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.url=e.urlRoot+e.id+"?undelete=true",e.destroy({success:function(e){e.set("deleted",!1),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,t.repaint(e),o.default.success("Library has been undeleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while undeleting the library.")}})},templateRow:function(){return r.template(['" style="display:none;" data-id="<%- library.get("id") %>">',"<% if(!edit_mode) { %>",'<% if(library.get("deleted")) { %>','<%- library.get("name") %>',"<% } else { %>",'"><%- library.get("name") %>',"<% } %>",'<% if(library.get("description")) { %>','<% if( (library.get("description")).length> 80 ) { %>','"><%= _.escape(library.get("description")).substring(0, 80) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("description"))%>',"<% } %>","<% } else { %>","","<% } %>",'<% if(library.get("synopsis")) { %>','<% if( (library.get("synopsis")).length> 120 ) { %>','"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("synopsis"))%>',"<% } %>","<% } else { %>","","<% } %>","<% } else if(edit_mode){ %>",'','','',"<% } %>",'','<% if( (library.get("public")) 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t=r(".library-search-input").val();this.options.search_term=t,Galaxy.libraries.libraryListView.searchLibraries(t)},templateToolBar:function(){return i.template(['
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    ',"User with any of these roles can add items to this library (folders and datasets).","
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    ','",'','
    ',"
    "].join("")),templatePanelSelectOptions:i.template(["<% _.each(sections, function(section) { %>",'',"<% }); %>"].join(""))});t.default={RepoDetails:m}}).call(t,n(2),n(1),n(0))},311:function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(17),s=a(o),l=n(18),c=a(l),d=e.View.extend({el:"#center",defaults:[{}],initialize:function(e){var t=this;this.model=new s.default.RepoQueue,this.listenTo(this.model,"sync",this.render),this.model.fetch(),t.render()},render:function(e){var t=this,n=t.templateRepoQueue,r=t.model.models;t.$el.html(n({title:"Repository Installation Queue",repositories:r,queue:c.default.queueLength()})),i("#center").css("overflow","auto"),t.bindEvents()},bindEvents:function(){var t=this;i(".install_one").on("click",function(){var e=t.loadFromQueue(i(this).attr("data-repokey"));t.installFromQueue(e,i(this).attr("data-repokey"))}),i(".remove_one").on("click",function(){var e=i(this).attr("data-repokey"),t=JSON.parse(localStorage.repositories);if(t.hasOwnProperty(e)){var n=t[e].repository.id;delete t[e],i("#queued_repository_"+n).remove()}localStorage.repositories=JSON.stringify(t)}),i("#clear_queue").on("click",function(){localStorage.repositories="{}"}),i("#from_workflow").on("click",function(){e.history.navigate("workflows",{trigger:!0,replace:!0})})},installFromQueue:function(t,n){var r=Object();r.install_tool_dependencies=t.install_tool_dependencies,r.install_repository_dependencies=t.install_repository_dependencies,r.install_resolver_dependencies=t.install_resolver_dependencies,r.tool_panel_section=t.tool_panel_section,r.shed_tool_conf=t.shed_tool_conf,r.repositories=JSON.stringify([[t.repository.id,t.changeset_revision]]),r.tool_shed_repository_ids=JSON.stringify([t.repository.id]),r.tool_shed_url=n.split("|")[0],r.changeset=t.changeset_revision;var a=Galaxy.root+"api/tool_shed_repositories/install?async=True";if(i("#queued_repository_"+t.repository.id).remove(),localStorage.repositories){void 0===n&&(n=c.default.queueKey(t));var o=JSON.parse(localStorage.repositories);o.hasOwnProperty(n)&&(delete o[n],localStorage.repositories=JSON.stringify(o))}i.post(a,r,function(t){var n=JSON.parse(t),r=n.repositories,a="status/r/"+r.join("|");i.post(Galaxy.root+"admin_toolshed/install_repositories",n,function(e){console.log("Initializing repository installation succeeded")}),e.history.navigate(a,{trigger:!0,replace:!0})})},loadFromQueue:function(e){var t=JSON.parse(localStorage.repositories);if(t.hasOwnProperty(e))return t[e]},reDraw:function(e){this.$el.empty(),this.initialize(e),this.model.fetch(),this.render(e)},templateRepoQueue:r.template(['
    ','
    <%= title %>
    ','
    Repository Queue (<%= queue %>)
    ',"
    ",'
    ','','',"",'','','','','','',"","","","<% _.each(repositories, function(repository) { %>",'">','','','','','",'","","<% }); %>","","
    NameOwnerRevisionToolShedInstall
    <%= repository.get("repository").name %><%= repository.get("repository").owner %><%= repository.get("changeset_revision") %><%= repository.get("tool_shed_url") %>','" type="submit" id="install_repository_<%= repository.get("id") %>" name="install_repository" value="Install now" />',"','" type="submit" id="unqueue_repository_<%= repository.get("id") %>" name="unqueue_repository" value="Remove from queue" />',"
    ",'',"
    "].join(""))});t.default={RepoQueueView:d}}).call(t,n(2),n(0),n(1))},312:function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(17),s=a(o),l=n(18),c=a(l),d=e.View.extend({el:"#center",initialize:function(e){this.options=i.defaults(this.options||[{}],e,this.defaults),this.model=new s.default.RepoStatus,this.listenTo(this.model,"sync",this.render),this.model.url+="?repositories="+this.options.repositories.join("|"),this.model.fetch(),this.timer=setInterval(function(e){var t=["installed","error"],n=!0;i.some(e.model.models,function(e){repo_id=e.get("id");var i=e.get("status").toLowerCase();if(-1===t.indexOf(i))return n=!1,!0}),n?clearInterval(e.timer):e.model.fetch()},2e3,this)},close:function(){clearInterval(this.timer)},render:function(e){this.options=i.extend(this.options,e);var t=this.templateRepoStatus;this.$el.html(t({title:"Repository Status",repositories:this.model.models,queue:c.default.queueLength()})),r("#center").css("overflow","auto"),this.bindEvents()},bindEvents:function(){},reDraw:function(e){this.$el.empty(),this.initialize(e)},templateRepoStatus:i.template(['
    ','
    <%= title %>
    ','
    Repository Queue (<%= queue %>)
    ',"
    ",'",'','',"",'','','','','',"","",'',"<% _.each(repositories, function(repository) { %>","","","","","","","","<% }); %>","",'',"
    NameDescriptionOwnerRevisionInstallation Status
    ",'
    ','","
    ","    		",'
    ','","
    ","    		",'
    ','","
    ","    		",'
    ','","
    ","    		",'
    ','","
    ","
    "].join(""))});t.default={RepoStatus:d}}).call(t,n(2),n(1),n(0))},313:function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(17),s=a(o),l=n(18),c=a(l),d=e.View.extend({el:"#center",defaults:[{}],initialize:function(e){var t=this;this.model=new s.default.WorkflowTools,this.listenTo(this.model,"sync",this.render),this.model.fetch(),t.render()},render:function(e){var t=this,n=t.templateWorkflows,r=t.model.models;t.$el.html(n({title:"Workflows Missing Tools",workflows:r,queue:c.default.queueLength()})),i("#center").css("overflow","auto"),t.bindEvents()},bindEvents:function(){var t,n=this;i(".show_wf_repo").on("click",function(){var n=i(this).attr("data-toolids"),r=i(this).attr("data-shed"),a=Galaxy.root+"api/tool_shed/repository",o={tool_ids:n};i.get(a,o,function(n){t=n.repository.id;var i="repository/s/"+r.replace(/:/g,"%3a").replace(/\//g,"%2f")+"/r/"+n.repository.id;e.history.navigate(i,{trigger:!0,replace:!0})})}),i(".queue_wf_repo").on("click",function(){var e=i(this),n=e.attr("data-toolids"),r=e.attr("data-shed"),a=Galaxy.root+"api/tool_shed/repository",o={tool_ids:n};i.get(a,o,function(n){t=n.repository.id,o={tool_shed_url:r,repository_id:t},i.get(a,o,function(t){var n=Object.keys(t.repository.metadata),i=n[0],a=t.repository.metadata[i];a.tool_shed_url=r,c.default.addToQueue(a),e.remove()})})}),i("#from_workflow").on("click",n.loadWorkflows)},reDraw:function(e){this.$el.empty(),this.initialize(e)},templateWorkflows:r.template(['
    ','
    <%= title %>
    ','
    Repository Queue (<%= queue %>)
    ',"
    ",'",'','',"",'','','','','','',"","","","<% _.each(workflows, function(workflow) { %>","",'",'",'','','','","","<% }); %>","",""].join(""))});t.default={Workflows:d}}).call(t,n(2),n(0),n(1))},61:function(e,t,n){"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.default={tool:"fa-wrench",data_input:"fa-file-o",data_collection_input:"fa-folder-o",subworkflow:"fa-sitemap fa-rotate-270",pause:"fa-pause"}}},[284]); \ No newline at end of file diff --git a/static/scripts/mvc/toolshed/repository-view.js b/static/scripts/mvc/toolshed/repository-view.js index c1c8e15e698e..f4d374e912ad 100644 --- a/static/scripts/mvc/toolshed/repository-view.js +++ b/static/scripts/mvc/toolshed/repository-view.js @@ -1 +1 @@ -define("mvc/toolshed/repository-view",["exports","mvc/toolshed/toolshed-model","libs/jquery/jstree","utils/utils","mvc/ui/ui-modal","mvc/form/form-view","mvc/toolshed/util"],function(e,t,o,i,n,l,s){"use strict";function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var d=a(t),r=(a(o),a(i)),c=a(n),p=a(l),h=a(s),u=Backbone.View.extend({el:"#center",initialize:function(e){this.options=_.defaults(this.options||{},this.defaults),this.model=new d.default.RepositoryCollection,this.listenTo(this.model,"sync",this.render);var t=e.tool_shed.replace(/\//g,"%2f");this.model.url+="?tool_shed_url="+t+"&repository_id="+e.repository_id,this.model.tool_shed_url=e.tool_shed.replace(/%2f/g,"/"),this.model.tool_shed=t,this.model.category=e.repository_id,this.model.fetch()},render:function(e){var t=this.templateRepoDetails,o=this.model.models[0];this.options={repository:o.get("repository"),tool_shed:this.model.tool_shed,queue:h.default.queueLength()};var i=Object.keys(this.options.repository.metadata);this.options.current_changeset=this.options.current_changeset||i[i.length-1],this.options.current_metadata=this.options.repository.metadata[this.options.current_changeset],this.options.current_metadata.tool_shed_url=this.model.tool_shed_url,this.options.tools=this.options.current_metadata.tools,this.options.repository_dependencies_template=this.templateRepoDependencies,this.options.repository_dependency_template=this.templateRepoDependency,this.options.tps_template_global_select=this.templateGlobalSectionSelect,this.options.tps_template_tool_select=this.templateToolSectionSelect,this.options.tps_select_options=this.templatePanelSelectOptions,this.options.tool_dependencies=o.get("tool_dependencies"),this.options.shed_tool_conf=this.templateShedToolConf({shed_tool_confs:o.get("shed_conf")}),console.log(o.get("shed_conf")),this.options.panel_section_dict=o.get("panel_section_dict"),this.options.api_url=Galaxy.root+"api/tool_shed_repositories/install?async=True",this.options=_.extend(this.options,e),this.$el.html(t(this.options)),this.checkInstalled(this.options.current_metadata),this.bindEvents(),$("#center").css("overflow","auto")},bindEvents:function(){var e=this;$("#changeset").on("change",function(){e.options.current_changeset=$("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset],e.checkInstalled(e.options.current_metadata),e.reDraw()}),$("#tool_panel_section_select").on("change",function(){e.tpsSelection()}),$("#install_repository").on("click",function(t){$("#repository_installation");t.preventDefault();var o={};o.repositories=JSON.stringify([[$("#install_repository").attr("data-tsrid"),$("#changeset").find("option:selected").val()]]),o.tool_shed_repository_ids=JSON.stringify([$("#install_repository").attr("data-tsrid")]),o.tool_shed_url=e.model.tool_shed_url,o.install_tool_dependencies=$("#install_tool_dependencies").val(),o.install_repository_dependencies=$("#install_repository_dependencies").val(),o.install_resolver_dependencies=$("#install_resolver_dependencies").val();e.panelSelect(o);o.tool_panel_section=JSON.stringify(e.panelSelect(o)),o.shed_tool_conf=$("select[name='shed_tool_conf']").find("option:selected").val(),o.changeset=$("#changeset").find("option:selected").val();var i=$("#repository_installation").attr("action");e.prepareInstall(o,i)}),$("#queue_install").on("click",function(t){e.options.current_changeset=$("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset];e.options.current_changeset;var o={};_.each(Object.keys(e.options.current_metadata),function(t){o[t]||(o[t]=e.options.current_metadata[t])}),o.install_tool_dependencies=$("#install_tool_dependencies").val(),o.install_repository_dependencies=$("#install_repository_dependencies").val(),o.install_resolver_dependencies=$("#install_resolver_dependencies").val(),o.tool_panel_section=JSON.stringify(e.panelSelect({})),o.shed_tool_conf=$("select[name='shed_tool_conf']").find("option:selected").val(),o.tool_shed_url=e.model.tool_shed_url,"/"==o.tool_shed_url.substr(-1)&&(o.tool_shed_url=o.tool_shed_url.substr(0,o.tool_shed_url.length-1)),h.default.addToQueue(o),e.checkInstalled(o)}),$(".tool_panel_section_picker").on("change",function(){$(this).find("option:selected").val()==$("#tool_panel_section_select").find("option:selected").val()?$(this).attr("default","active"):$(this).removeAttr("default")}),$(function(){$("#repository_dependencies").jstree()}),$(".tool_form").on("click",function(){var t=$(this).attr("data-guid"),o=($(this).attr("data-clean"),$(this).attr("data-name")),i=$(this).attr("data-desc"),n=e.model.tool_shed_url,l=$("#repository_details").attr("data-tsrid"),s=$("#changeset").find("option:selected").val(),a=Galaxy.root+"api/tool_shed/tool_json",d={guid:t,tool_shed_url:n,tsr_id:l,changeset:s};$.get(a,d,function(e){e.cls="ui-portlet-plain";var t=new p.default(e);r.default.deepeach(e.inputs,function(e){e.type&&-1!=["data","data_collection"].indexOf(e.type)&&(e.type="hidden",e.info="Data input '"+e.name+"' ("+r.default.textify(e.extensions)+")")});var n=new c.default.View,l=""+o+" "+i;n.show({closing_events:!0,title:l,body:t.$el,buttons:{Close:function(){n.hide()}}})})})},checkInstalled:function(e){var t=this,o={name:e.name,owner:e.owner},i=!1;t.repoQueued(e);$.get(Galaxy.root+"api/tool_shed_repositories",o,function(o){for(var n=0;n','
    Repository information for <%= repository.name %> from <%= repository.owner %>
    ','
    Repository Queue (<%= queue %>)
    ',"",'
    ','
    ','','','
    ','
    Changeset
    ','
    ','",'','','
    Please select a revision and review the settings below before installing.
    ',"
    ","
    ","<%= shed_tool_conf %>","<% if (current_metadata.has_repository_dependencies) { %>",'
    Repository dependencies for <%= current_changeset %>
    ','
    ','

    ','','',"

    ","<% current_metadata.repository_dependency_template = repository_dependency_template; %>",'
    ','
    ','',"Repository dependencies – installation of these additional repositories is required","","
    ","<%= repository_dependencies_template(current_metadata) %>","
    ","
    ","<% } %>","<% if (current_metadata.includes_tool_dependencies) { %>",'
    Tool dependencies
    ','
    ','

    ','','',"

    ",'

    ','','',"

    ",'
    WorkflowsTool IDsShedNameOwnerActions
    ','
      ','<% _.each(workflow.get("workflows"), function(name) { %>','
    • <%= name %>
      • ',"<% }); %>","
    ","    		','
      ','<% _.each(workflow.get("tools"), function(tool) { %>','
    • <%= tool %>
      • ',"<% }); %>","
    ","    		<%= workflow.get("shed") %><%= workflow.get("repository") %><%= workflow.get("owner") %>','
      ','
    • ','" data-owner="<%= workflow.get("owner") %>" data-repo="<%= workflow.get("repository") %>" data-toolids="<%= workflow.get("tools").join(",") %>" value="Show Repository" />
      • ',"
    ","
    ',"",'','',"","","","",'',"<% _.each(tool_dependencies[current_changeset], function(dependency) { %>",'','","","","","<% }); %>","","
    NameVersionType
    ',"<%= dependency.name %><%= dependency.version %><%= dependency.type %>
    ","
    ","
    ","<% } %>","<% if (current_metadata.includes_tools_for_display_in_tool_panel) { %>",'
    Tools – click the name to preview the tool and use the pop-up menu to inspect all metadata
    ','
    ','
    ','',"",'','',"","","","",'',"<% _.each(current_metadata.tools, function(tool) { %>",'','","",'','","","<% }); %>","","
    NameDescriptionVersion<%= tps_template_global_select({tps: panel_section_dict, tps_select_options: tps_select_options}) %>
    ','","<%= tool.description %><%= tool.version %>',"<%= tps_template_tool_select({tool: tool, tps: panel_section_dict, tps_select_options: tps_select_options}) %>","
    ","
    ","
    ","<% } %>","","
    "].join("")),templateRepoDependencies:_.template(['
    Repository Dependencies
    ','
    ',"
      ","
    • Repository installation requires the following","<% if (has_repository_dependencies) { %>","<% _.each(repository_dependencies, function(dependency) { %>","<% dependency.repository_dependency_template = repository_dependency_template; %>","<%= repository_dependency_template(dependency) %>","<% }); %>","<% } %>","
      • ","
    ","
    "].join("")),templateRepoDependency:_.template(['
  • ',"Repository <%= repository.name %> revision <%= changeset_revision %> owned by <%= repository.owner %>","<% if (has_repository_dependencies) { %>",'
      ',"<% _.each(repository_dependencies, function(dependency) { %>","<% dependency.repository_dependency_template = repository_dependency_template; %>","<%= repository_dependency_template(dependency) %>","<% }); %>","
    ","<% } %>","
    • "].join("")),templateShedToolConf:_.template(['
    Shed tool configuration file:
    ','
    ','
    ','",'
    Select the file whose tool_path setting you want used for installing repositories.
    ',"
    ","
    "].join("")),templateToolDependency:_.template(["<% if (has_repository_dependencies) { %>","<% _.each(repository_dependencies, function(dependency) { %>","<% if (dependency.includes_tool_dependencies) { %>","<% dependency.tool_dependency_template = tool_dependency_template %>","<%= tool_dependency_template(dependency) %>","<% } %>","<% }); %>","<% } %>"].join("")),templateGlobalSectionCreate:_.template(['
    ','
    ','','','
    ',"Add a new tool panel section to contain the installed tools (optional).","
    ","
    ","
    "].join("")),templateGlobalSectionSelect:_.template(['
    ','
    Tool Panel Section
    ','
    ','
    ','",'','
    ',"Select an existing tool panel section to contain the installed tools (optional).","
    ","
    ","
    ","
    "].join("")),templateToolSectionCreate:_.template(['
    ','','',"
    "].join("")),templateToolSectionSelect:_.template(['
    ','",'','
    ',"
    "].join("")),templatePanelSelectOptions:_.template(["<% _.each(sections, function(section) { %>",'',"<% }); %>"].join(""))});e.default={RepoDetails:u}}); \ No newline at end of file +define("mvc/toolshed/repository-view",["exports","mvc/toolshed/toolshed-model","libs/jquery/jstree","utils/utils","mvc/ui/ui-modal","mvc/form/form-view","mvc/toolshed/util"],function(e,t,o,i,n,l,s){"use strict";function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var d=a(t),r=(a(o),a(i)),c=a(n),p=a(l),h=a(s),u=Backbone.View.extend({el:"#center",initialize:function(e){this.options=_.defaults(this.options||{},this.defaults),this.model=new d.default.RepositoryCollection,this.listenTo(this.model,"sync",this.render);var t=e.tool_shed.replace(/\//g,"%2f");this.model.url+="?tool_shed_url="+t+"&repository_id="+e.repository_id,this.model.tool_shed_url=e.tool_shed.replace(/%2f/g,"/"),this.model.tool_shed=t,this.model.category=e.repository_id,this.model.fetch()},render:function(e){var t=this.templateRepoDetails,o=this.model.models[0];this.options={repository:o.get("repository"),tool_shed:this.model.tool_shed,queue:h.default.queueLength()};var i=Object.keys(this.options.repository.metadata);this.options.current_changeset=this.options.current_changeset||i[i.length-1],this.options.current_metadata=this.options.repository.metadata[this.options.current_changeset],this.options.current_metadata.tool_shed_url=this.model.tool_shed_url,this.options.tools=this.options.current_metadata.tools,this.options.repository_dependencies_template=this.templateRepoDependencies,this.options.repository_dependency_template=this.templateRepoDependency,this.options.tps_template_global_select=this.templateGlobalSectionSelect,this.options.tps_template_tool_select=this.templateToolSectionSelect,this.options.tps_select_options=this.templatePanelSelectOptions,this.options.tool_dependencies=o.get("tool_dependencies"),this.options.shed_tool_conf=this.templateShedToolConf({shed_tool_confs:o.get("shed_conf")}),this.options.panel_section_dict=o.get("panel_section_dict"),this.options.api_url=Galaxy.root+"api/tool_shed_repositories/install?async=True",this.options=_.extend(this.options,e),this.$el.html(t(this.options)),this.checkInstalled(this.options.current_metadata),this.bindEvents(),$("#center").css("overflow","auto")},bindEvents:function(){var e=this;$("#changeset").on("change",function(){e.options.current_changeset=$("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset],e.checkInstalled(e.options.current_metadata),e.reDraw()}),$("#tool_panel_section_select").on("change",function(){e.tpsSelection()}),$("#install_repository").on("click",function(t){$("#repository_installation");t.preventDefault();var o={};o.repositories=JSON.stringify([[$("#install_repository").attr("data-tsrid"),$("#changeset").find("option:selected").val()]]),o.tool_shed_repository_ids=JSON.stringify([$("#install_repository").attr("data-tsrid")]),o.tool_shed_url=e.model.tool_shed_url,o.install_tool_dependencies=$("#install_tool_dependencies").val(),o.install_repository_dependencies=$("#install_repository_dependencies").val(),o.install_resolver_dependencies=$("#install_resolver_dependencies").val();e.panelSelect(o);o.tool_panel_section=JSON.stringify(e.panelSelect(o)),o.shed_tool_conf=$("select[name='shed_tool_conf']").find("option:selected").val(),o.changeset=$("#changeset").find("option:selected").val();var i=$("#repository_installation").attr("action");e.prepareInstall(o,i)}),$("#queue_install").on("click",function(t){e.options.current_changeset=$("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset];e.options.current_changeset;var o={};_.each(Object.keys(e.options.current_metadata),function(t){o[t]||(o[t]=e.options.current_metadata[t])}),o.install_tool_dependencies=$("#install_tool_dependencies").val(),o.install_repository_dependencies=$("#install_repository_dependencies").val(),o.install_resolver_dependencies=$("#install_resolver_dependencies").val(),o.tool_panel_section=JSON.stringify(e.panelSelect({})),o.shed_tool_conf=$("select[name='shed_tool_conf']").find("option:selected").val(),o.tool_shed_url=e.model.tool_shed_url,"/"==o.tool_shed_url.substr(-1)&&(o.tool_shed_url=o.tool_shed_url.substr(0,o.tool_shed_url.length-1)),h.default.addToQueue(o),e.checkInstalled(o)}),$(".tool_panel_section_picker").on("change",function(){$(this).find("option:selected").val()==$("#tool_panel_section_select").find("option:selected").val()?$(this).attr("default","active"):$(this).removeAttr("default")}),$(function(){$("#repository_dependencies").jstree()}),$(".tool_form").on("click",function(){var t=$(this).attr("data-guid"),o=($(this).attr("data-clean"),$(this).attr("data-name")),i=$(this).attr("data-desc"),n=e.model.tool_shed_url,l=$("#repository_details").attr("data-tsrid"),s=$("#changeset").find("option:selected").val(),a=Galaxy.root+"api/tool_shed/tool_json",d={guid:t,tool_shed_url:n,tsr_id:l,changeset:s};$.get(a,d,function(e){e.cls="ui-portlet-plain";var t=new p.default(e);r.default.deepeach(e.inputs,function(e){e.type&&-1!=["data","data_collection"].indexOf(e.type)&&(e.type="hidden",e.info="Data input '"+e.name+"' ("+r.default.textify(e.extensions)+")")});var n=new c.default.View,l=""+o+" "+i;n.show({closing_events:!0,title:l,body:t.$el,buttons:{Close:function(){n.hide()}}})})})},checkInstalled:function(e){var t=this,o={name:e.name,owner:e.owner},i=!1;t.repoQueued(e);$.get(Galaxy.root+"api/tool_shed_repositories",o,function(o){for(var n=0;n','
    Repository information for <%= repository.name %> from <%= repository.owner %>
    ','
    Repository Queue (<%= queue %>)
    ',"
    ",'
    ','
    ','','','
    ','
    Changeset
    ','
    ','",'','','
    Please select a revision and review the settings below before installing.
    ',"
    ","
    ","<%= shed_tool_conf %>","<% if (current_metadata.has_repository_dependencies) { %>",'
    Repository dependencies for <%= current_changeset %>
    ','
    ','

    ','','',"

    ","<% current_metadata.repository_dependency_template = repository_dependency_template; %>",'
    ','
    ','',"Repository dependencies – installation of these additional repositories is required","","
    ","<%= repository_dependencies_template(current_metadata) %>","
    ","
    ","<% } %>","<% if (current_metadata.includes_tool_dependencies) { %>",'
    Tool dependencies
    ','
    ','

    ','','',"

    ",'

    ','','',"

    ",'
    ','
    ','',"Tool dependencies – repository tools require handling of these dependencies","","
    ",'',"",'','',"","","","",'',"<% _.each(tool_dependencies[current_changeset], function(dependency) { %>",'','","","","","<% }); %>","","
    NameVersionType
    ',"<%= dependency.name %><%= dependency.version %><%= dependency.type %>
    ","
    ","
    ","<% } %>","<% if (current_metadata.includes_tools_for_display_in_tool_panel) { %>",'
    Tools – click the name to preview the tool and use the pop-up menu to inspect all metadata
    ','
    ','
    ','',"",'','',"","","","",'',"<% _.each(current_metadata.tools, function(tool) { %>",'','","",'','","","<% }); %>","","
    NameDescriptionVersion<%= tps_template_global_select({tps: panel_section_dict, tps_select_options: tps_select_options}) %>
    ','","<%= tool.description %><%= tool.version %>',"<%= tps_template_tool_select({tool: tool, tps: panel_section_dict, tps_select_options: tps_select_options}) %>","
    ","
    ","
    ","<% } %>","
    ","
    "].join("")),templateRepoDependencies:_.template(['
    Repository Dependencies
    ','
    ',"
      ","
    • Repository installation requires the following","<% if (has_repository_dependencies) { %>","<% _.each(repository_dependencies, function(dependency) { %>","<% dependency.repository_dependency_template = repository_dependency_template; %>","<%= repository_dependency_template(dependency) %>","<% }); %>","<% } %>","
      • ","
    ","
    "].join("")),templateRepoDependency:_.template(['
  • ',"Repository <%= repository.name %> revision <%= changeset_revision %> owned by <%= repository.owner %>","<% if (has_repository_dependencies) { %>",'
      ',"<% _.each(repository_dependencies, function(dependency) { %>","<% dependency.repository_dependency_template = repository_dependency_template; %>","<%= repository_dependency_template(dependency) %>","<% }); %>","
    ","<% } %>","
    • "].join("")),templateShedToolConf:_.template(['
    Shed tool configuration file:
    ','
    ','
    ','",'
    Select the file whose tool_path setting you want used for installing repositories.
    ',"
    ","
    "].join("")),templateToolDependency:_.template(["<% if (has_repository_dependencies) { %>","<% _.each(repository_dependencies, function(dependency) { %>","<% if (dependency.includes_tool_dependencies) { %>","<% dependency.tool_dependency_template = tool_dependency_template %>","<%= tool_dependency_template(dependency) %>","<% } %>","<% }); %>","<% } %>"].join("")),templateGlobalSectionCreate:_.template(['
    ','
    ','','','
    ',"Add a new tool panel section to contain the installed tools (optional).","
    ","
    ","
    "].join("")),templateGlobalSectionSelect:_.template(['
    ','
    Tool Panel Section
    ','
    ','
    ','",'','
    ',"Select an existing tool panel section to contain the installed tools (optional).","
    ","
    ","
    ","
    "].join("")),templateToolSectionCreate:_.template(['
    ','','',"
    "].join("")),templateToolSectionSelect:_.template(['
    ','",'','
    ',"
    "].join("")),templatePanelSelectOptions:_.template(["<% _.each(sections, function(section) { %>",'',"<% }); %>"].join(""))});e.default={RepoDetails:u}}); \ No newline at end of file