From 450735a6c6e60a21166922448aac80a3aaab70b1 Mon Sep 17 00:00:00 2001 From: "istemi.bahceci" Date: Wed, 21 Dec 2016 16:08:08 +0200 Subject: [PATCH] Preparing for release --- public/bin/base.min.css | 2 +- public/bin/base.min.js | 2 +- public/index.html | 30 ++++++++++++++-------------- public/src/css/sass/base.scss | 4 ++++ public/src/js/NotificationFactory.js | 2 +- 5 files changed, 22 insertions(+), 18 deletions(-) diff --git a/public/bin/base.min.css b/public/bin/base.min.css index 774bf85e..2b6d6373 100644 --- a/public/bin/base.min.css +++ b/public/bin/base.min.css @@ -4,4 +4,4 @@ * Licensed under the MIT license - http://opensource.org/licenses/MIT * * Copyright (c) 2016 Daniel Eden - 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.list-group-item.active:hover{background-color:#1abc9c!important}.edgePaletteWrapper .edge-palette .list-group-item{padding:7px 5px}.edgePaletteWrapper .edge-palette a{margin-bottom:5px;border-radius:6px;font-size:12px}.edgePaletteWrapper .edge-palette a img{width:30px}footer{background-color:#eee;color:#393939;height:100%}.pageContentWrapper{margin-bottom:70px}.navbar-nav>.open>a,.navbar-nav>.open>a:focus,.navbar-nav>.open>a:hover{color:#fff!important;background-color:#1abc9c!important;border-left-color:transparent}.navbar-nav>.open>.dropdown-menu>li>a{color:#fff!important;border-radius:4px!important;font-size:12px!important}.navbar-nav>.open>.dropdown-menu{background-color:#2f4154!important}.navbar-nav>li>.dropdown-menu,.navbar-nav>li>.dropdown-submenu{border-radius:4px!important;border:none}.navbar-nav>.open>.dropdown-menu>li>a:focus,.navbar-nav>.open>.dropdown-menu>li>a:hover{color:#fff;background-color:#1abc9c}.navbar{border-radius:0 0 6px 6px;background-color:#2f4154;border:none!important;margin-bottom:10px!important}.navbar-nav a{transition:all .2s linear}.navbar-nav>li>a{color:#fff!important;font-weight:500!important;font-size:12px}.navbar-nav>li>a:hover{color:#1abc9c!important}.navbar-brand{color:#fff!important;font-size:16px;font-weight:700}.pnl{margin-bottom:10px;border-radius:6px;box-shadow:0 1px 1px rgba(0,0,0,.15),0 -1px 1px rgba(0,0,0,.15)}.pnl .pnl-header{background-color:#1abc9c;border-top-left-radius:6px;border-top-right-radius:6px;padding:8px 5px 5px;color:#fff;font-size:12px;font-weight:900}.pnl .pnl-body{background-color:#eff0f2;padding:4px 2px;border-bottom-left-radius:6px;border-bottom-right-radius:6px}.pnl .pnl-body .buttonContainer>button{border:none!important}.pnl .pnl-body .dragButtonContainer{width:115px;margin-left:auto;margin-right:auto}.customMargins{margin-left:3%!important;margin-right:3%!important}.leftPanelFix{padding-left:0}.hiddenfile{width:0;height:0;overflow:hidden}.buttonContainer{margin-bottom:5px}.buttonContainer button{font-size:12px;width:85%}.cyContainer{border:3px solid #1abc9c;height:850px;border-radius:6px;padding-right:0!important;padding-left:0!important;width:100%;margin-left:10px}#cy{height:100%}.btn:focus{background-color:#fff!important} \ No newline at end of file diff --git a/public/bin/base.min.js b/public/bin/base.min.js index 1c1b0ca9..2f29863a 100644 --- a/public/bin/base.min.js +++ b/public/bin/base.min.js @@ -45,7 +45,7 @@ var targetNode=_CoSELayout.idToLNode[edge.data("target")];var e1=gm.add(_CoSELay if(parts.length>0){return parts[0]}return""},parseDelimitedInfo:function(info,delimiter,separator,formatter){if(info==undefined||info==null){return info}var text="";var parts=info.split(delimiter);if(parts.length>0){if(formatter){text=formatter(parts[0])}else{text=parts[0]}}for(var i=1;iPlease Wait Loading Cancer Studies");this.$el.find("#cancerDropDown").append(this.cachedLoadingTemplate)},updateCancerStudies:function(cancerStudies){this.cancerStudies=cancerStudies;this.updateView()},updateView:function(){var self=this;this.$el.find("#cancerDropDown").empty();this.$el.find("#dataTypeSelection").empty();this.$el.find("#cancerDropDown").append("

Select Cancer Study

");var cancerStudiesDropDown=$('');for(var cancerName in this.cancerStudies){cancerStudiesDropDown.append("")}$("#cancerDropDown").append(cancerStudiesDropDown);cancerStudiesDropDown.selectpicker({liveSearch:true,container:"body",liveSearchPlaceholder:"Search Cancer Study"});$("#cancerSelectBox").change(function(){self.$el.find("#dataTypeSelection").empty();self.$el.find("#dataTypeSelection").append(self.cachedLoadingTemplate);var key=$(this).find("option:selected").attr("key");self.currenCancerStudy=self.cancerStudies[key];var createDataTypeSelectionCallback=function(cancerData){self.$el.find("#dataTypeSelection").empty();var dataTypes={};for(var obj in cancerData){var dataType=self.portalAccessor.getDataType(obj);dataTypes[dataType]=cancerData[obj]}self.$el.find("#dataTypeSelection").append("

Data Types

");for(var obj in dataTypes){var newCheckbox=$('
'+""+"
");newCheckbox.find('input[type="checkbox"]').on("click",function(evt){var checkedNum=self.$el.find('input[type="checkbox"]:checked').length;if(checkedNum>=1)self.showSubmitButton();else if(checkedNum==0)self.hideSubmitButton()});self.$el.find("#dataTypeSelection").append(newCheckbox)}};self.portalAccessor.getSupportedGeneticProfiles(key,createDataTypeSelectionCallback)})},render:function(){this.hideSubmitButton();if(!this.cancerStudies){this.$el.modal("show");return}this.updateView();this.$el.modal("show")},hideSubmitButton:function(){$("#getProfileData").hide()},showSubmitButton:function(){$("#getProfileData").show()},fetchProfileData:function(){var checkedDataTypes=this.$el.find('input[type="checkbox"]:checked');var geneSymbols=window.editorActionsManager.getGeneSymbols();var self=this;for(var i=0;iThere is currently no data to show');this.$el.find("#save-genomic").hide()},saveHandler:function(event){var dataMap={};this.$el.find(".genomicDataContentDiv label").each(function(){var jqEl=$(this);var cancerType=jqEl.text();var isChecked=jqEl.find("input").is(":checked");dataMap[cancerType]=isChecked});this.editorActionsManagerRef.updateGenomicDataVisibility(dataMap);this.$el.modal("toggle")},notify:function(data){this.$el.find(".genomicDataContentDiv").empty();var cancerTypes=this.editorActionsManagerRef.genomicDataOverlayManager.visibleGenomicDataMapByType;if(cancerTypes&&Object.keys(cancerTypes).length===0){this.renderEmptyView()}else{this.$el.find(".genomicDataContentDiv").append('

Data Set To Show:

');var checkboxDiv=$('
');for(var cancerType in cancerTypes){var checkboxContent=$('");checkboxContent.find("input").attr("checked",cancerTypes[cancerType]);checkboxDiv.append(checkboxContent)}this.$el.find(".genomicDataContentDiv").append(checkboxDiv);this.$el.find("#save-genomic").show()}}});module.exports=genomicDataExplorer},{}],176:[function(require,module,exports){var gridOptionsView=Backbone.View.extend({currentProperties:null,events:{"click #applyGridOptions":"saveProperties"},initialize:function(options){this.defaultGridGuideOptions={snapToGrid:false,discreteDrag:false,guidelines:true,resize:false,gridSpacing:20,parentPadding:false,drawGrid:false,guidelinesStackOrder:4,guidelinesTolerance:2,guidelinesStyle:{lineWidth:2,strokeStyle:"#000000",lineDash:[7,15]}};this.copyProperties(this.defaultGridGuideOptions);cy.gridGuide(this.currentProperties)},copyProperties:function(params){this.currentProperties=_.clone(params)},render:function(){var templateProperties=_.clone(this.currentProperties);this.template=_.template($("#gridOptionsTemplate").html());var tplContent=this.template(templateProperties);this.$el.empty();this.$el.append(tplContent);this.delegateEvents()},saveProperties:function(event){this.currentProperties.gridSpacing=Number(this.$el.find("#gridSize").val());this.currentProperties.drawGrid=this.$el.find("#showGrid").is(":checked");this.currentProperties.guidelines=this.$el.find("#showGuides").is(":checked");this.currentProperties.snapToGrid=this.$el.find("#snapToGrid").is(":checked");this.currentProperties.guidelinesStyle.strokeStyle=this.$el.find('input[type="color"]').val();cy.gridGuide(this.currentProperties);this.$el.modal("toggle")},changeParameters:function(){this.$el.find("#gridSize").val(this.currentProperties.gridSize);this.$el.find("#showGrid")[0].checked=this.currentProperties.showGrid;this.$el.find("#showGuides")[0].checked=this.currentProperties.showGuides;this.$el.find('input[type="color"]').val(this.currentProperties.guidelinesStyle.strokeStyle)},defaultLayoutHandler:function(event){},notify:function(){}});module.exports=gridOptionsView},{}],177:[function(require,module,exports){var layoutProps=Backbone.View.extend({currentLayoutProperties:null,events:{"click #save-layout":"saveLayoutHandler","click #default-layout":"defaultLayoutHandler"},initialize:function(options){this.editorActionsManagerRef=options.editorActionsManager;this.copyProperties(this.editorActionsManagerRef.layoutProperties);this.editorActionsManagerRef.registerObserver(this)},copyProperties:function(params){this.currentLayoutProperties=_.clone(params)},render:function(){var templateProperties=_.clone(this.currentLayoutProperties);this.template=_.template($("#layoutPropertiesTemplate").html());var tplContent=this.template(templateProperties);this.$el.empty();this.$el.append(tplContent);this.delegateEvents()},saveLayoutHandler:function(event){this.currentLayoutProperties.nodeRepulsion=Number(this.$el.find("#node-repulsion").val());this.currentLayoutProperties.nodeOverlap=Number(this.$el.find("#node-overlap").val());this.currentLayoutProperties.idealEdgeLength=Number(this.$el.find("#ideal-edge-length").val());this.currentLayoutProperties.edgeElasticity=Number(this.$el.find("#edge-elasticity").val());this.currentLayoutProperties.nestingFactor=Number(this.$el.find("#nesting-factor").val());this.currentLayoutProperties.gravity=Number(this.$el.find("#gravity").val());this.currentLayoutProperties.numIter=Number(this.$el.find("#num-iter").val());this.currentLayoutProperties.gravityRangeCompound=Number(this.$el.find("#comp-gravRange").val());this.currentLayoutProperties.gravityCompound=Number(this.$el.find("#comp-grav").val());this.currentLayoutProperties.gravityRange=Number(this.$el.find("#grav-range").val());this.currentLayoutProperties.tile=this.$el.find("#tile").is(":checked");this.currentLayoutProperties.animate=this.$el.find("#animate").is(":checked");this.currentLayoutProperties.randomize=!this.$el.find("#randomize").is(":checked");this.editorActionsManagerRef.saveLayoutProperties(this.currentLayoutProperties);this.$el.modal("toggle")},changeParameters:function(){this.$el.find("#node-repulsion").val(this.currentLayoutProperties.nodeRepulsion);this.$el.find("#node-overlap").val(this.currentLayoutProperties.nodeOverlap);this.$el.find("#ideal-edge-length").val(this.currentLayoutProperties.idealEdgeLength);this.$el.find("#edge-elasticity").val(this.currentLayoutProperties.edgeElasticity);this.$el.find("#nesting-factor").val(this.currentLayoutProperties.nestingFactor);this.$el.find("#gravity").val(this.currentLayoutProperties.gravity);this.$el.find("#comp-gravRange").val(this.currentLayoutProperties.gravityRangeCompound);this.$el.find("#comp-grav").val(this.currentLayoutProperties.gravityCompound);this.$el.find("#grav-range").val(this.currentLayoutProperties.gravityRange);this.$el.find("#num-iter").val(this.currentLayoutProperties.numIter);this.$el.find("#tile")[0].checked=this.currentLayoutProperties.tile;this.$el.find("#animate")[0].checked=this.currentLayoutProperties.animate;this.$el.find("#randomize")[0].checked=!this.currentLayoutProperties.randomize},defaultLayoutHandler:function(event){this.copyProperties(this.editorActionsManagerRef.defaultLayoutProperties);this.changeParameters()},notify:function(){this.copyProperties(this.editorActionsManagerRef.layoutProperties);this.changeParameters()}});module.exports=layoutProps},{}],178:[function(require,module,exports){var pathwayDetails=Backbone.View.extend({currentLayoutProperties:null,events:{"click #savePathwayDetails":"saveHandler"},initialize:function(options){this.properties={pathwayName:"pathway.txt",pathwayTitle:"New Pathway",pathwayDescription:""}},saveHandler:function(event){this.properties.pathwayName=this.$el.find("#pName").val();this.properties.pathwayTitle=this.$el.find("#pTitle").val();this.properties.pathwayDescription=this.$el.find("#pDesc").val();this.$el.modal("toggle")},updatePathwayProperties:function(data){this.properties.pathwayName=data.fileName;this.properties.pathwayTitle=data.pathwayTitle;this.properties.pathwayDescription=data.pathwayDescription},copyProperties:function(params){this.currentLayoutProperties=_.clone(params)},render:function(){this.template=_.template($("#pathwayDetailsTemplate").html());var tplContent=this.template(this.properties);this.$el.empty();this.$el.append(tplContent);this.delegateEvents();this.$el.find("input").on("keypress",function(e){if(e.keyCode==13){e.preventDefault()}});return this}});module.exports=pathwayDetails},{}],179:[function(require,module,exports){var WelcomePageView=Backbone.View.extend({cachedTpl:_.template($("#welcomePageTemplate").html()),events:{"click #localUsage":"localUsageHandler","click #collaborativeUsage":"collaborativeUsageHandler","click .continueButton":"continueButtonHandler"},initialize:function(options){this.localUsageCallback=options.localUsageCallback;this.collaborativeUsageCallback=options.collaborativeUsageCallback;this.modelSelectionMap={NONE:-1,LOCAL:0,COLLAB:1};this.modelSelection=this.modelSelectionMap.NONE},render:function(){this.$el.empty();this.$el.append(this.cachedTpl());this.$el.find("#localUsage").popover({container:"body",content:"Create a pathway individually",placement:"left",delay:100,trigger:"manual"});this.$el.find("#collaborativeUsage").popover({container:"body",html:true,content:function(){return $("#collaborativePopoverContent").html()},placement:"right",delay:200,trigger:"manual"})},localUsageHandler:function(event){if(this.modelSelection==this.modelSelectionMap.LOCAL)return;$(".popover").popover("hide");this.$el.find(".welcomePageCheckable").removeClass("active");$(event.currentTarget).addClass("active");this.$el.find("#localUsage").popover("show");this.$el.find(".continueRow").css("visibility","visible");this.modelSelection=this.modelSelectionMap.LOCAL},collaborativeUsageHandler:function(event){if(this.modelSelection==this.modelSelectionMap.COLLAB)return;$(".popover").popover("hide");this.$el.find(".welcomePageCheckable").removeClass("active");$(event.currentTarget).addClass("active");this.$el.find("#collaborativeUsage").popover("show");this.$el.find(".continueRow").css("visibility","visible");this.modelSelection=this.modelSelectionMap.COLLAB},continueButtonHandler:function(event){$(".popover").hide();var self=this;this.$el.find(".welcomePageLoading").show();function postHandler(){self.postSuccess()}if(this.modelSelection!=this.modelSelectionMap.NONE){if(this.modelSelection==this.modelSelectionMap.LOCAL){this.localUsageCallback(postHandler)}else if(this.modelSelection==this.modelSelectionMap.COLLAB){this.collaborativeUsageCallback(postHandler)}}},postSuccess:function(){this.$el.empty();this.$el.fadeOut(800)}});module.exports=WelcomePageView},{}],180:[function(require,module,exports){module.exports=function(){"use strict";var CxtMenu=function(cy,editorActionsManager){this.cy=cy;this.editorActionsManager=editorActionsManager;this.init()};CxtMenu.prototype.init=function(){var classRef=this;var options={menuItems:[{id:"remove",title:"Delete",selector:"node, edge",onClickFunction:function(event){var ele=event.cyTarget;var selectedElements=cy.nodes(":selected").union(ele);classRef.editorActionsManager.removeElement(selectedElements)},disabled:false,hasTrailingDivider:true,coreAsWell:false},{id:"addSelected",title:"Add selected into this",selector:"node",onClickFunction:function(event){var ele=event.cyTarget;var selectedNodes=cy.nodes(":selected");var containerType=ele.data("type");var validNodes=cy.collection();if(ele._private.data["type"]==="GENE"||selectedNodes.size()<1){return}else{var notValid=false;selectedNodes.forEach(function(tmpNode,i){if(ele.id()==tmpNode.id()){notValid=true;return false}if(tmpNode.isParent()){notValid=isChildren(tmpNode,ele);if(notValid){return false}}});if(notValid){return}}selectedNodes.forEach(function(tmpNode,i){if(containerType=="FAMILY"||containerType=="COMPLEX"){if(tmpNode.data("type")!="COMPARTMENT"&&tmpNode.data("type")!="PROCESS"){validNodes=validNodes.add(tmpNode)}}else{validNodes=validNodes.add(tmpNode)}});var compId=ele.id();classRef.editorActionsManager.changeParents(validNodes,compId)},disabled:false,hasTrailingDivider:true,coreAsWell:false},{id:"removeSelected",title:"Remove selected from parent",selector:"node",onClickFunction:function(event){var ele=event.cyTarget;var selectedNodes=cy.nodes(":selected").union(ele);var notValid=false;selectedNodes.forEach(function(tmpNode,i){if(tmpNode.isParent()){notValid=isChildren(tmpNode,ele);if(notValid){return false}}});if(notValid){return}classRef.editorActionsManager.changeParents(selectedNodes,null)},disabled:false,hasTrailingDivider:true,coreAsWell:false},{id:"performLayout",title:"Perform Layout",coreAsWell:true,onClickFunction:function(event){classRef.editorActionsManager.performLayout()},disabled:false,hasTrailingDivider:true}],menuItemClasses:[],contextMenuClasses:[]};this.cy.contextMenus(options)};window.edgeAddingMode=false;function isChildren(node,queryNode){var parent=queryNode.parent()[0];while(parent){if(parent.id()==node.id()){return true}parent=parent.parent()[0]}return false}return CxtMenu}()},{}],181:[function(require,module,exports){module.exports=function($,$$){"use strict";var NodeAdd=function(editorActionsManager){this.editorActionsManager=editorActionsManager;this.initNodeAdd()};NodeAdd.prototype.initNodeAdd=function(){var nodeAddClass=this;var defaults={height:30,width:30,padding:5,backgroundColorDiv:"#fbfbfb",borderColorDiv:"#fff",borderWidthDiv:"0px",borderRadiusDiv:"5px",icon:"",nodeParams:function(){return{}}};$.fn.cytoscapeNodeadd=function(params){var options=$.extend(true,{},defaults,params);var fn=params;var functions={destroy:function(){var $this=$(this);$this.find(".ui-cytoscape-nodeadd").remove()},init:function(){return $(this).each(function(){var components=options.components;for(var index in components){var component=components[index];var dragContainer=component.container;var explanationText=component.explanationText;var $nodeadd=$('
');dragContainer.append($nodeadd);var $nodeDragHandle=$('
');$nodeadd.append($nodeDragHandle);$nodeDragHandle.bind("mousedown",function(e){e.stopPropagation();e.preventDefault()});dragContainer.find(".ui-cytoscape-nodeadd-nodediv").css({background:options.backgroundColorDiv,border:options.borderWidthDiv+" solid "+options.borderColorDiv,"border-radius":options.borderRadiusDiv});dragContainer.find("#ui-cytoscape-nodeadd-icon").draggable({helper:"clone",cursor:"pointer"})}var $container=$(this);$container.droppable({activeClass:"ui-state-highlight",drop:function(event,ui){$container.removeClass("ui-state-highlight");var currentOffset=$container.offset();var relX=event.pageX-currentOffset.left;var relY=event.pageY-currentOffset.top;var nodeType=$(ui.helper).attr("nodeType").toUpperCase();var cy=$container.cytoscape("get");var nodeMap={};var parentMap={};cy.nodes().forEach(function(node,i){var nodeBbox=node.renderedBoundingBox();if(relX<=nodeBbox.x2&&relX>=nodeBbox.x1&&(relY<=nodeBbox.y2&&relY>=nodeBbox.y1)&&node.data().type!="GENE"){if(node.children().length>0){parentMap[node.id()]=true}if(parentMap[node._private.data.parent]){delete nodeMap[node._private.data.parent]}nodeMap[node.id()]=node}});var parent=nodeMap[Object.keys(nodeMap)[0]];var nodeData={type:nodeType,name:"New "+$(ui.helper).attr("nodeType")};if(parent){if(parent.data().type=="FAMILY"||parent.data().type=="COMPLEX"){if(nodeType!="COMPARTMENT"&&nodeType!="PROCESS"){nodeData.parent=parent.id()}}else{nodeData.parent=parent.id()}}relX=relX/cy.zoom()+cy.extent().x1;relY=relY/cy.zoom()+cy.extent().y1;nodeAddClass.editorActionsManager.addNode(nodeData,{x:relX,y:relY})}})})}};if(functions[fn]){return functions[fn].apply(this,Array.prototype.slice.call(arguments,1))}else if(typeof fn=="object"||!fn){return functions.init.apply(this,arguments)}else{$.error("No such function `"+fn+"` for jquery.cytoscapenodeadd")}return $(this)};$.fn.cynodeadd=$.fn.cytoscapeNodeadd;$$("core","nodeadd",function(options){var cy=this;$(cy.container()).cytoscapeNodeadd(options)})};return NodeAdd}(window.$,window.cytoscape)},{}],182:[function(require,module,exports){var edgeHandleDefaults={preview:true,stackOrder:4,handleSize:10,handleColor:"#1abc9c",handleLineType:"ghost",handleLineWidth:1,handleNodes:"node",hoverDelay:1,cxt:false,enabled:false,toggleOffOnLeave:true,edgeType:function(sourceNode,targetNode){return"flat"},loopAllowed:function(node){return false},nodeLoopOffset:-50,nodeParams:function(sourceNode,targetNode){return{}},edgeParams:function(sourceNode,targetNode,i){return{}},start:function(sourceNode){var type=this.getGlobalEdgeType();cy.edgehandles("option","ghostEdgeType",type)},complete:function(sourceNode,targetNodes,addedEntities){cy.remove(addedEntities);window.editorActionsManager.addEdge({source:sourceNode.id(),target:targetNodes[0].id(),type:this.getGlobalEdgeType()})},stop:function(sourceNode){$(".edge-palette a").blur().removeClass("active");window.edgeAddingMode==-1;cy.edgehandles("disable")},getGlobalEdgeType:function(){var type="NONE";if(window.edgeAddingMode==1){type="ACTIVATES"}else if(window.edgeAddingMode==2){type="INHIBITS"}else if(window.edgeAddingMode==3){type="INDUCES"}else if(window.edgeAddingMode==4){type="REPRESSES"}else if(window.edgeAddingMode==5){type="BINDS"}return type}};module.exports=edgeHandleDefaults},{}],183:[function(require,module,exports){var GenomicDataOverlayManager=require("./GenomicDataOverlayManager.js");var SVGExporter=require("./SVGExporter.js");module.exports=function(){"use strict";var EditorActionsManager=function(isCollaborative,realtimeManager,cyInst){this.cy=cyInst;this.isCollaborative=isCollaborative;if(this.isCollaborative&&realtimeManager)this.realTimeManager=realtimeManager;this.defaultLayoutProperties={name:"cose-bilkent",nodeRepulsion:4500,nodeOverlap:10,idealEdgeLength:50,edgeElasticity:.45,nestingFactor:.1,gravity:.15,numIter:2500,tile:true,animate:"end",randomize:false,gravityRangeCompound:1.5,gravityCompound:1,gravityRange:1.5};this.FIT_CONSTANT=50;this.layoutProperties=_.clone(this.defaultLayoutProperties);this.observers=[];this.genomicDataOverlayManager=new GenomicDataOverlayManager;this.svgExporter=new SVGExporter;this.selecteNodeStack={};window.undoRedoManager=cy.undoRedo();window.undoRedoManager.action("changePositions",this.doChangePosition,this.undoChangePosition);window.undoRedoManager.action("changeName",this.doChangename,this.undoChangeName)};EditorActionsManager.prototype.doChangename=function(args){var currentName=args.node.data("name");var newArgs={node:args.node,newName:args.newName,oldName:currentName};args.node.data("name",args.newName);args.node.css("content",args.newName);return newArgs};EditorActionsManager.prototype.undoChangeName=function(args){var currentName=args.node.data("name");var newArgs={node:args.node,newName:args.oldName,oldName:currentName};args.node.data("name",args.oldName);args.node.css("content",args.oldName);return newArgs};EditorActionsManager.prototype.doChangePosition=function(movedNodes){var newMovedNodes=[];for(var i=0;i0){children.forEach(function(childNode,i){lockedNodes[childNode.id()]=true});removedEles=removedEles.union(removeNodes(children))}removedEles=removedEles.union(nodes.remove());self.cy.nodes().updateCompoundBounds();return removedEles}var removedEles=removeNodes(eles);window.undoRedoManager.do("remove",removedEles);for(var i=0;i0){ele.data.source=cySourceNode.id()}if(cyTargetNode.length>0){ele.data.target=cyTargetNode.id()}if(cyTargetNode.length<0&&cySourceNode.length<0){continue}var edgesBtw=cy.filter('edge[source = "'+cySourceNode.id()+'"][target = "'+cyTargetNode.id()+'"]');var isFound=false;edgesBtw.forEach(function(edge,i){if(edge.data().type==ele.data.type){isFound=true;return false}});if(!isFound){delete ele.data.id;edgesToBeAdded.push(ele)}}cy.add(edgesToBeAdded)};EditorActionsManager.prototype.fitGraph=function(){if(this.isCollaborative){cy.fit(this.FIT_CONSTANT);var newState={zoomLevel:cy.zoom(),panLevel:cy.pan()};this.updateGlobalOptions(newState)}else{cy.fit(this.FIT_CONSTANT)}};EditorActionsManager.prototype.loadFile=function(nodes,edges){if(this.isCollaborative){this.loadfileRealTime(nodes,edges)}else{this.loadFileCy(nodes,edges)}this.fitGraph()};EditorActionsManager.prototype.loadFileCy=function(nodes,edges){this.removeElementCy(cy.elements());this.addNodesCy(nodes);this.addEdgesCy(edges)};EditorActionsManager.prototype.loadfileRealTime=function(nodes,edges){this.realTimeManager.loadGraph(nodes,edges)};EditorActionsManager.prototype.removeAllElements=function(){if(this.isCollaborative){this.realTimeManager.removeAllElements()}else{cy.remove(cy.elements())}};EditorActionsManager.prototype.changeName=function(ele,newName){if(this.isCollaborative){this.realTimeManager.changeName(ele,newName)}else{this.changeNameCy(ele,newName)}};EditorActionsManager.prototype.changeNameCy=function(ele,newName){var currentName=ele.data("name");var args={node:ele,oldName:currentName,newName:newName};window.undoRedoManager.do("changeName",args)};EditorActionsManager.prototype.updateElementCallback=function(ele,id){var nodeID=id;var cyEle=this.cy.$("#"+nodeID);cyEle.position({x:ele.x,y:ele.y});this.changeNameCy(cyEle,ele.name)};EditorActionsManager.prototype.getGenomicDataSVG=function(node){return this.genomicDataOverlayManager.generateSVGForNode(node)};EditorActionsManager.prototype.removeGenomicData=function(){if(this.isCollaborative){this.realTimeManager.clearGenomicData();this.realTimeManager.clearGenomicVisData()}else{this.genomicDataOverlayManager.removeGenomicData();this.genomicDataOverlayManager.removeGenomicVisData();this.genomicDataOverlayManager.hideGenomicData();this.genomicDataOverlayManager.notifyObservers()}};EditorActionsManager.prototype.addGenomicData=function(genomicData){if(this.isCollaborative){this.removeGenomicData();var parsedGenomicData=this.genomicDataOverlayManager.prepareGenomicDataRealTime(genomicData);var genomicDataMap=parsedGenomicData.genomicDataMap;var visibilityMap=parsedGenomicData.visibilityMap;this.realTimeManager.addGenomicData("genomicData",genomicDataMap);this.realTimeManager.addGenomicVisibilityData("visMap",visibilityMap)}else{this.genomicDataOverlayManager.addGenomicDataLocally(genomicData)}};EditorActionsManager.prototype.addPortalGenomicData=function(genomicData){if(this.isCollaborative){this.genomicDataOverlayManager.addPortalGenomicData(genomicData);this.realTimeManager.addGenomicData("genomicData",this.genomicDataOverlayManager.genomicDataMap);this.realTimeManager.addGenomicVisibilityData("visMap",this.genomicDataOverlayManager.visibleGenomicDataMapByType)}else{this.genomicDataOverlayManager.addPortalGenomicData(genomicData)}};EditorActionsManager.prototype.realTimeGenomicDataHandler=function(event){var newData=event.newValue;var geneSymbol=event.property;if(newData){this.genomicDataOverlayManager.addGenomicData(newData)}else{this.genomicDataOverlayManager.removeGenomicData(geneSymbol)}};EditorActionsManager.prototype.realTimeGenomicDataVsibilityHandler=function(event){var data=event.newValue;if(data){this.genomicDataOverlayManager.addGenomicVisData(data)}else{this.genomicDataOverlayManager.removeGenomicVisData(data)}this.genomicDataOverlayManager.showGenomicData();this.genomicDataOverlayManager.notifyObservers()};return EditorActionsManager}()},{"./GenomicDataOverlayManager.js":185,"./SVGExporter.js":195}],184:[function(require,module,exports){var SaveLoadUtilities=require("./SaveLoadUtility.js");module.exports=function($){"use strict";function b64toBlob(b64Data,contentType,sliceSize){contentType=contentType||"";sliceSize=sliceSize||512;var byteCharacters=atob(b64Data);var byteArrays=[];for(var offset=0;offset0?"<0.5":Math.round(percent);var text=textPercent+"%";var fontSize=14;var textLength=text.length;var xOffset=w/2-textLength*4;var yOffset=fontSize/3;var svgText=document.createElementNS(svgNameSpace,"text");svgText.setAttribute("x",x+xOffset);svgText.setAttribute("y",y+h/2+yOffset);svgText.setAttribute("font-family","Arial");svgText.setAttribute("font-size",fontSize);svgText.innerHTML=text;parentSVG.appendChild(overlayRect);parentSVG.appendChild(svgText)}return svg};function getRequiredWidthForGenomicData(genomicDataBoxCount){var term=genomicDataBoxCount>3?genomicDataBoxCount-3:0;return 150+term*35}GenomicDataOverlayManager.prototype.showGenomicData=function(){var self=this;var genomicDataBoxCount=this.countVisibleGenomicDataByType();if(genomicDataBoxCount<1){this.hideGenomicData();return}cy.style().selector('node[type="GENE"]').style("width",function(ele){return getRequiredWidthForGenomicData(genomicDataBoxCount)}).style("text-margin-y",function(ele){var nodeLabel=ele.data("name");if(!(nodeLabel in self.genomicDataMap))return 0;return-15}).style("background-image",function(ele){var dataURI="data:image/svg+xml,";return dataURI+self.generateSVGForNode(ele).outerHTML}).update()};GenomicDataOverlayManager.prototype.parseGenomicData=function(genomicData){this.genomicDataMap={};this.cancerTypes=[];this.visibleGenomicDataMapByType={};var lines=genomicData.split("\n");var metaLineColumns=lines[0].split(" ");for(var i=1;i0){mappedArr[mappedElem.parent().id()].childNodes.push(mappedElem)}else{tree.push(mappedElem)}}return tree};GraphUtilities.prototype.createGraphHierarchyRealTime=function(nodes){var tree=[];var mappedArr={};for(var i=0,len=nodes.length;i');textInput.change(function(){var nodeID=$(this).find("input").attr("nodeid");var cyNode=self.cy.$("#"+nodeID)[0];var newName=$(this).find("input").val();window.editorActionsManager.changeName(cyNode,newName)});var wrapper=$("
");var row=$('
Name:
');row.append(textInput);wrapper.append(row);if(ele.data().type==="GENE"){var entrezGeneButton=$('
');entrezGeneButton.find("button").on("click",function(event){event.preventDefault();var nodeID=$(this).attr("nodeid");var nodeSymbol=self.cy.$("#"+nodeID)[0]._private.data["name"];var parent=$(this).parent();parent.empty().append('');var formData=new FormData;formData.append("query",nodeSymbol);var request=new XMLHttpRequest;request.onreadystatechange=function(){if(request.readyState===XMLHttpRequest.DONE){if(request.status===200){var jsonData=JSON.parse(request.responseText);if(jsonData.count>0){var backboneView=new BackboneView({model:jsonData.geneInfo[0]}).render().html();parent.empty().append(backboneView)}else{parent.empty().append("There is no extra information for this gene")}}else{parent.empty().append("An error occured while retrieving the data")}}};request.open("POST","/getBioGeneData");request.send(formData)});wrapper.append(entrezGeneButton)}return wrapper};QtipManager.prototype.addQtipToElements=function(eles){var self=this;eles.forEach(function(node,i){var qTipOpts={content:{text:function(){return self.generateQtipContentHTML(this)},title:function(){return capitalizeFirstLetter(node.data().type.toLowerCase())+" Details"}},position:{my:"top center",at:"bottom center"},style:{classes:"qtip-tipsy qtip-rounded",width:400}};node.qtip(qTipOpts)})};function capitalizeFirstLetter(string){return string.charAt(0).toUpperCase()+string.slice(1)}return QtipManager}(window.$)},{"./BackboneViews/BioGeneView.js":173}],193:[function(require,module,exports){module.exports=function(){"use strict";var RealTimeManager=function(postFileLoadCallback){this.clientId="122039910543-b7u74aijsqne9iv5rk2tgm3529ped4d0.apps.googleusercontent.com";this.NODEMAP_NAME="nodes";this.EDGEMAP_NAME="edges";this.LAYOUT_PROPS_NAME="layoutProperties";this.GLOBAL_OPTS_NAME="globalOptions";this.GENOMIC_DATA_MAP_NAME="genomicDataMap";this.VISIBLE_GENOMIC_DATA_MAP_NAME="visibleGenomicDataMapByType";this.realtimeUtils=new utils.RealtimeUtils({clientId:this.clientId});this.postFileLoad=postFileLoadCallback};RealTimeManager.prototype.authorize=function(callbackFunction,isModal){this.realtimeUtils.authorize(function(response){callbackFunction(response)},isModal)};RealTimeManager.prototype.initRealTimeAPI=function(){var id=this.realtimeUtils.getParam("id");this.registerTypes();var self=this;var initFileCallback=function(model){self.onFileInitialize(model)};var loadFileCallback=function(model){self.onFileLoaded(model)};if(id){this.realtimeUtils.load(id.replace("/",""),loadFileCallback,initFileCallback)}else{this.realtimeUtils.createAppFile("New Graph",function(createResponse){var result=createResponse.result;window.history.pushState(null,null,"?id="+result.id);self.realtimeUtils.load(result.id,loadFileCallback,initFileCallback)})}};RealTimeManager.prototype.onFileInitialize=function(model){var root=model.getRoot();var nodeMap=model.createMap();var edgeMap=model.createMap();var layoutProperties=model.create(LayoutPropertiesR,window.editorActionsManager.layoutProperties); +});return tpMostNodes}var NodeObj=function(nodeObj){this.nodeRef=nodeObj;this.children=[]};var connectedEdges=eles.connectedEdges();function traverseNodes(eles,rootNodeObj){eles.forEach(function(ele,index){connectedEdges=connectedEdges.union(ele.connectedEdges());if(ele.isParent()){rootNodeObj.children.push(new NodeObj(ele));var lengthOfChildrenArray=rootNodeObj.children.length;traverseNodes(ele.children(),rootNodeObj.children[lengthOfChildrenArray-1])}else{rootNodeObj.children.push(new NodeObj(ele))}})}var topMostNodes=getTopLevelParents(eles);var rootNodeR=new NodeObj(null);traverseNodes(topMostNodes,rootNodeR);this.realTimeManager.changeParent(rootNodeR,newParentId,connectedEdges)};EditorActionsManager.prototype.moveElements=function(ele,position){var classRef=this;if(this.isCollaborative){ele.forEach(function(ele,index){classRef.realTimeManager.moveElement(ele)})}};EditorActionsManager.prototype.handleChangePositionByAlignment=function(movedNodeArr){window.undoRedoManager.do("changePositions",movedNodeArr)};EditorActionsManager.prototype.mergeGraph=function(nodes,edges){if(this.isCollaborative){this.realTimeManager.mergeGraph(nodes,edges)}else{this.mergeGraphCy(nodes,edges)}this.fitGraph()};EditorActionsManager.prototype.mergeGraphCy=function(nodes,edges){var nodesToBeAdded=[];var edgesToBeAdded=[];var nodeMap={};for(var index in nodes){var ele=nodes[index];nodeMap[ele.data.id]=ele;if(cy.filter('node[name = "'+ele.data.name+'"]').length<=0){delete ele.data.id;nodesToBeAdded.push(ele)}}cy.add(nodesToBeAdded);for(var index in edges){var ele=edges[index];var sourceNode=nodeMap[ele.data.source];var targetNode=nodeMap[ele.data.target];var cySourceNode=cy.nodes('[name="'+sourceNode.data.name+'"]');var cyTargetNode=cy.nodes('[name="'+targetNode.data.name+'"]');if(cySourceNode.length>0){ele.data.source=cySourceNode.id()}if(cyTargetNode.length>0){ele.data.target=cyTargetNode.id()}if(cyTargetNode.length<0&&cySourceNode.length<0){continue}var edgesBtw=cy.filter('edge[source = "'+cySourceNode.id()+'"][target = "'+cyTargetNode.id()+'"]');var isFound=false;edgesBtw.forEach(function(edge,i){if(edge.data().type==ele.data.type){isFound=true;return false}});if(!isFound){delete ele.data.id;edgesToBeAdded.push(ele)}}cy.add(edgesToBeAdded)};EditorActionsManager.prototype.fitGraph=function(){if(this.isCollaborative){cy.fit(this.FIT_CONSTANT);var newState={zoomLevel:cy.zoom(),panLevel:cy.pan()};this.updateGlobalOptions(newState)}else{cy.fit(this.FIT_CONSTANT)}};EditorActionsManager.prototype.loadFile=function(nodes,edges){if(this.isCollaborative){this.loadfileRealTime(nodes,edges)}else{this.loadFileCy(nodes,edges)}this.fitGraph()};EditorActionsManager.prototype.loadFileCy=function(nodes,edges){this.removeElementCy(cy.elements());this.addNodesCy(nodes);this.addEdgesCy(edges)};EditorActionsManager.prototype.loadfileRealTime=function(nodes,edges){this.realTimeManager.loadGraph(nodes,edges)};EditorActionsManager.prototype.removeAllElements=function(){if(this.isCollaborative){this.realTimeManager.removeAllElements()}else{cy.remove(cy.elements())}};EditorActionsManager.prototype.changeName=function(ele,newName){if(this.isCollaborative){this.realTimeManager.changeName(ele,newName)}else{this.changeNameCy(ele,newName)}};EditorActionsManager.prototype.changeNameCy=function(ele,newName){var currentName=ele.data("name");var args={node:ele,oldName:currentName,newName:newName};window.undoRedoManager.do("changeName",args)};EditorActionsManager.prototype.updateElementCallback=function(ele,id){var nodeID=id;var cyEle=this.cy.$("#"+nodeID);cyEle.position({x:ele.x,y:ele.y});this.changeNameCy(cyEle,ele.name)};EditorActionsManager.prototype.getGenomicDataSVG=function(node){return this.genomicDataOverlayManager.generateSVGForNode(node)};EditorActionsManager.prototype.removeGenomicData=function(){if(this.isCollaborative){this.realTimeManager.clearGenomicData();this.realTimeManager.clearGenomicVisData()}else{this.genomicDataOverlayManager.removeGenomicData();this.genomicDataOverlayManager.removeGenomicVisData();this.genomicDataOverlayManager.hideGenomicData();this.genomicDataOverlayManager.notifyObservers()}};EditorActionsManager.prototype.addGenomicData=function(genomicData){if(this.isCollaborative){this.removeGenomicData();var parsedGenomicData=this.genomicDataOverlayManager.prepareGenomicDataRealTime(genomicData);var genomicDataMap=parsedGenomicData.genomicDataMap;var visibilityMap=parsedGenomicData.visibilityMap;this.realTimeManager.addGenomicData("genomicData",genomicDataMap);this.realTimeManager.addGenomicVisibilityData("visMap",visibilityMap)}else{this.genomicDataOverlayManager.addGenomicDataLocally(genomicData)}};EditorActionsManager.prototype.addPortalGenomicData=function(genomicData){if(this.isCollaborative){this.genomicDataOverlayManager.addPortalGenomicData(genomicData);this.realTimeManager.addGenomicData("genomicData",this.genomicDataOverlayManager.genomicDataMap);this.realTimeManager.addGenomicVisibilityData("visMap",this.genomicDataOverlayManager.visibleGenomicDataMapByType)}else{this.genomicDataOverlayManager.addPortalGenomicData(genomicData)}};EditorActionsManager.prototype.realTimeGenomicDataHandler=function(event){var newData=event.newValue;var geneSymbol=event.property;if(newData){this.genomicDataOverlayManager.addGenomicData(newData)}else{this.genomicDataOverlayManager.removeGenomicData(geneSymbol)}};EditorActionsManager.prototype.realTimeGenomicDataVsibilityHandler=function(event){var data=event.newValue;if(data){this.genomicDataOverlayManager.addGenomicVisData(data)}else{this.genomicDataOverlayManager.removeGenomicVisData(data)}this.genomicDataOverlayManager.showGenomicData();this.genomicDataOverlayManager.notifyObservers()};return EditorActionsManager}()},{"./GenomicDataOverlayManager.js":185,"./SVGExporter.js":195}],184:[function(require,module,exports){var SaveLoadUtilities=require("./SaveLoadUtility.js");module.exports=function($){"use strict";function b64toBlob(b64Data,contentType,sliceSize){contentType=contentType||"";sliceSize=sliceSize||512;var byteCharacters=atob(b64Data);var byteArrays=[];for(var offset=0;offset0?"<0.5":Math.round(percent);var text=textPercent+"%";var fontSize=14;var textLength=text.length;var xOffset=w/2-textLength*4;var yOffset=fontSize/3;var svgText=document.createElementNS(svgNameSpace,"text");svgText.setAttribute("x",x+xOffset);svgText.setAttribute("y",y+h/2+yOffset);svgText.setAttribute("font-family","Arial");svgText.setAttribute("font-size",fontSize);svgText.innerHTML=text;parentSVG.appendChild(overlayRect);parentSVG.appendChild(svgText)}return svg};function getRequiredWidthForGenomicData(genomicDataBoxCount){var term=genomicDataBoxCount>3?genomicDataBoxCount-3:0;return 150+term*35}GenomicDataOverlayManager.prototype.showGenomicData=function(){var self=this;var genomicDataBoxCount=this.countVisibleGenomicDataByType();if(genomicDataBoxCount<1){this.hideGenomicData();return}cy.style().selector('node[type="GENE"]').style("width",function(ele){return getRequiredWidthForGenomicData(genomicDataBoxCount)}).style("text-margin-y",function(ele){var nodeLabel=ele.data("name");if(!(nodeLabel in self.genomicDataMap))return 0;return-15}).style("background-image",function(ele){var dataURI="data:image/svg+xml,";return dataURI+self.generateSVGForNode(ele).outerHTML}).update()};GenomicDataOverlayManager.prototype.parseGenomicData=function(genomicData){this.genomicDataMap={};this.cancerTypes=[];this.visibleGenomicDataMapByType={};var lines=genomicData.split("\n");var metaLineColumns=lines[0].split(" ");for(var i=1;i0){mappedArr[mappedElem.parent().id()].childNodes.push(mappedElem)}else{tree.push(mappedElem)}}return tree};GraphUtilities.prototype.createGraphHierarchyRealTime=function(nodes){var tree=[];var mappedArr={};for(var i=0,len=nodes.length;i');textInput.change(function(){var nodeID=$(this).find("input").attr("nodeid");var cyNode=self.cy.$("#"+nodeID)[0];var newName=$(this).find("input").val();window.editorActionsManager.changeName(cyNode,newName)});var wrapper=$("
");var row=$('
Name:
');row.append(textInput);wrapper.append(row);if(ele.data().type==="GENE"){var entrezGeneButton=$('
');entrezGeneButton.find("button").on("click",function(event){event.preventDefault();var nodeID=$(this).attr("nodeid");var nodeSymbol=self.cy.$("#"+nodeID)[0]._private.data["name"];var parent=$(this).parent();parent.empty().append('');var formData=new FormData;formData.append("query",nodeSymbol);var request=new XMLHttpRequest;request.onreadystatechange=function(){if(request.readyState===XMLHttpRequest.DONE){if(request.status===200){var jsonData=JSON.parse(request.responseText);if(jsonData.count>0){var backboneView=new BackboneView({model:jsonData.geneInfo[0]}).render().html();parent.empty().append(backboneView)}else{parent.empty().append("There is no extra information for this gene")}}else{parent.empty().append("An error occured while retrieving the data")}}};request.open("POST","/getBioGeneData");request.send(formData)});wrapper.append(entrezGeneButton)}return wrapper};QtipManager.prototype.addQtipToElements=function(eles){var self=this;eles.forEach(function(node,i){var qTipOpts={content:{text:function(){return self.generateQtipContentHTML(this)},title:function(){return capitalizeFirstLetter(node.data().type.toLowerCase())+" Details"}},position:{my:"top center",at:"bottom center"},style:{classes:"qtip-tipsy qtip-rounded",width:400}};node.qtip(qTipOpts)})};function capitalizeFirstLetter(string){return string.charAt(0).toUpperCase()+string.slice(1)}return QtipManager}(window.$)},{"./BackboneViews/BioGeneView.js":173}],193:[function(require,module,exports){module.exports=function(){"use strict";var RealTimeManager=function(postFileLoadCallback){this.clientId="122039910543-b7u74aijsqne9iv5rk2tgm3529ped4d0.apps.googleusercontent.com";this.NODEMAP_NAME="nodes";this.EDGEMAP_NAME="edges";this.LAYOUT_PROPS_NAME="layoutProperties";this.GLOBAL_OPTS_NAME="globalOptions";this.GENOMIC_DATA_MAP_NAME="genomicDataMap";this.VISIBLE_GENOMIC_DATA_MAP_NAME="visibleGenomicDataMapByType";this.realtimeUtils=new utils.RealtimeUtils({clientId:this.clientId});this.postFileLoad=postFileLoadCallback};RealTimeManager.prototype.authorize=function(callbackFunction,isModal){this.realtimeUtils.authorize(function(response){callbackFunction(response)},isModal)};RealTimeManager.prototype.initRealTimeAPI=function(){var id=this.realtimeUtils.getParam("id");this.registerTypes();var self=this;var initFileCallback=function(model){self.onFileInitialize(model)};var loadFileCallback=function(model){self.onFileLoaded(model)};if(id){this.realtimeUtils.load(id.replace("/",""),loadFileCallback,initFileCallback)}else{this.realtimeUtils.createAppFile("New Graph",function(createResponse){var result=createResponse.result;window.history.pushState(null,null,"?id="+result.id);self.realtimeUtils.load(result.id,loadFileCallback,initFileCallback)})}};RealTimeManager.prototype.onFileInitialize=function(model){var root=model.getRoot();var nodeMap=model.createMap();var edgeMap=model.createMap();var layoutProperties=model.create(LayoutPropertiesR,window.editorActionsManager.layoutProperties); var globalOptions=model.create(GlobalOptionsR,window.editorActionsManager.getGlobalOptions());var genomicDataMap=model.createMap();var genomicDataVisibilityMap=model.createMap();root.set(this.NODEMAP_NAME,nodeMap);root.set(this.EDGEMAP_NAME,edgeMap);root.set(this.LAYOUT_PROPS_NAME,layoutProperties);root.set(this.GLOBAL_OPTS_NAME,globalOptions);root.set(this.GENOMIC_DATA_MAP_NAME,genomicDataMap);root.set(this.VISIBLE_GENOMIC_DATA_MAP_NAME,genomicDataVisibilityMap)};RealTimeManager.prototype.onFileLoaded=function(doc){var model=doc.getModel();var root=model.getRoot();var nodeMap=root.get(this.NODEMAP_NAME);var edgeMap=root.get(this.EDGEMAP_NAME);var realTimeLayoutProperties=root.get(this.LAYOUT_PROPS_NAME);var globalOptions=root.get(this.GLOBAL_OPTS_NAME);var genomicDataMap=root.get(this.GENOMIC_DATA_MAP_NAME);var visDataMap=root.get(this.VISIBLE_GENOMIC_DATA_MAP_NAME);var nodeMapEntries=nodeMap.values();var edgeMapEntries=edgeMap.values();window.editorActionsManager.addNewElementsLocally(nodeMapEntries,edgeMapEntries);window.editorActionsManager.updateLayoutPropertiesCallback(realTimeLayoutProperties);window.editorActionsManager.changeGlobalOptions(globalOptions);window.editorActionsManager.genomicDataOverlayManager.genomicDataMap=genomicDataMap.get("genomicData");window.editorActionsManager.genomicDataOverlayManager.visibleGenomicDataMapByType=visDataMap.get("visMap");window.editorActionsManager.genomicDataOverlayManager.showGenomicData();window.editorActionsManager.genomicDataOverlayManager.notifyObservers();cy.fit(50);this.realTimeDoc=doc;var nodeAddRemoveHandler=function(event){window.editorActionsManager.realTimeNodeAddRemoveEventCallBack(event)};var edgeAddRemoveHandler=function(event){window.editorActionsManager.realTimeEdgeAddRemoveEventCallBack(event)};var genomicDataAddRemoveHandler=function(event){window.editorActionsManager.realTimeGenomicDataHandler(event)};var genomicDataVisibilityChangeHandler=function(event){window.editorActionsManager.realTimeGenomicDataVsibilityHandler(event)};root.get(this.NODEMAP_NAME).addEventListener(gapi.drive.realtime.EventType.VALUE_CHANGED,nodeAddRemoveHandler);root.get(this.EDGEMAP_NAME).addEventListener(gapi.drive.realtime.EventType.VALUE_CHANGED,edgeAddRemoveHandler);root.get(this.GENOMIC_DATA_MAP_NAME).addEventListener(gapi.drive.realtime.EventType.VALUE_CHANGED,genomicDataAddRemoveHandler);root.get(this.VISIBLE_GENOMIC_DATA_MAP_NAME).addEventListener(gapi.drive.realtime.EventType.VALUE_CHANGED,genomicDataVisibilityChangeHandler);this.postFileLoad()};RealTimeManager.prototype.clearGenomicData=function(){var model=this.realTimeDoc.getModel();var root=model.getRoot();var genomicMap=root.get(this.GENOMIC_DATA_MAP_NAME);var genomicMapKeys=genomicMap.keys();model.beginCompoundOperation();for(var i in genomicMapKeys){genomicMap.delete(genomicMapKeys[i])}model.endCompoundOperation()};RealTimeManager.prototype.clearGenomicVisData=function(){var model=this.realTimeDoc.getModel();var root=model.getRoot();var map=root.get(this.VISIBLE_GENOMIC_DATA_MAP_NAME);var mapKeys=map.keys();model.beginCompoundOperation();for(var i in mapKeys){map.delete(mapKeys[i])}model.endCompoundOperation()};RealTimeManager.prototype.addGenomicData=function(_key,geneData){var model=this.realTimeDoc.getModel();var root=model.getRoot();var genomicMap=root.get(this.GENOMIC_DATA_MAP_NAME);genomicMap.set(_key,geneData)};RealTimeManager.prototype.addGenomicVisibilityData=function(cancerType,isVisible){var model=this.realTimeDoc.getModel();var root=model.getRoot();var map=root.get(this.VISIBLE_GENOMIC_DATA_MAP_NAME);map.set(cancerType,isVisible)};RealTimeManager.prototype.addNewNode=function(nodeData,posData){var model=this.realTimeDoc.getModel();var root=model.getRoot();var nodeMap=root.get(this.NODEMAP_NAME);var newNode=model.create(NodeR,{name:nodeData.name,type:nodeData.type,parent:nodeData.parent});if(posData){newNode.x=posData.x;newNode.y=posData.y}var realTimeGeneratedID=this.getCustomObjId(newNode);nodeMap.set(realTimeGeneratedID,newNode)};RealTimeManager.prototype.addNewEdge=function(edgeData){var model=this.realTimeDoc.getModel();var root=model.getRoot();var edgeMap=root.get(this.EDGEMAP_NAME);var newEdge=model.create(EdgeR,{type:edgeData.type,source:edgeData.source,target:edgeData.target});var realTimeGeneratedID=this.getCustomObjId(newEdge);edgeMap.set(realTimeGeneratedID,newEdge)};RealTimeManager.prototype.removeElement=function(elementID){var model=this.realTimeDoc.getModel();var root=model.getRoot();var edgeMap=root.get(this.EDGEMAP_NAME);var nodeMap=root.get(this.NODEMAP_NAME);if(nodeMap.has(elementID)){nodeMap.delete(elementID)}else if(edgeMap.has(elementID)){edgeMap.delete(elementID)}else{throw new Error("Element does not exists in Real Time")}};RealTimeManager.prototype.moveElement=function(ele){var model=this.realTimeDoc.getModel();var root=model.getRoot();var nodeMap=root.get(this.NODEMAP_NAME);var elementID=ele.id();var newPos=ele.position();if(nodeMap.has(elementID)){var tmpNode=nodeMap.get(elementID);model.beginCompoundOperation();tmpNode.x=newPos.x;tmpNode.y=newPos.y;model.endCompoundOperation()}else{throw new Error("Element does not exists in nodes !!! ")}};RealTimeManager.prototype.changeName=function(ele,newName){var model=this.realTimeDoc.getModel();var root=model.getRoot();var nodeMap=root.get(this.NODEMAP_NAME);var elementID=ele.id();if(nodeMap.has(elementID)){var tmpNode=nodeMap.get(elementID);model.beginCompoundOperation();tmpNode.name=newName;model.endCompoundOperation()}else{throw new Error("Element does not exists in nodes !!! ")}};RealTimeManager.prototype.changeParent=function(rootNode,newParentId,connectedEdges){var model=this.realTimeDoc.getModel();var root=model.getRoot();var nodeMap=root.get(this.NODEMAP_NAME);var nodeLookupTable={};var self=this;function traverseFromRoot(rootNode,parId){var refNode=rootNode.nodeRef;var children=rootNode.children;var newParentId=parId;if(refNode){var refNodeId=refNode.id();var nodeData=refNode.data();var posData=refNode.position();var newNodeData={name:nodeData.name,type:nodeData.type,x:posData.x,y:posData.y};if(parId){newNodeData.parent=parId}self.removeElement(refNodeId);var newNode=model.create(NodeR,newNodeData);var newNodeId=self.getCustomObjId(newNode);nodeMap.set(newNodeId,newNode);newParentId=newNodeId;nodeLookupTable[refNodeId]=newNodeId}for(var i in children){var childNode=children[i];traverseFromRoot(childNode,newParentId)}}traverseFromRoot(rootNode,newParentId);connectedEdges.forEach(function(edge,index){var edgeData=edge.data();self.removeElement(edge.id());var newSource=nodeLookupTable[edgeData.source];var newTarget=nodeLookupTable[edgeData.target];if(newSource){edgeData.source=newSource}if(newTarget){edgeData.target=newTarget}self.addNewEdge(edgeData)})};RealTimeManager.prototype.removeAllElements=function(){var model=this.realTimeDoc.getModel();var root=model.getRoot();var nodeMap=root.get(this.NODEMAP_NAME);var edgeMap=root.get(this.EDGEMAP_NAME);var nodeMapKeys=nodeMap.keys();var edgeMapKeys=edgeMap.keys();for(var index in nodeMapKeys){this.removeElement(nodeMapKeys[index])}for(var index in edgeMapKeys){this.removeElement(edgeMapKeys[index])}};RealTimeManager.prototype.loadGraph=function(nodes,edges){var model=this.realTimeDoc.getModel();var root=model.getRoot();var nodeMap=root.get(this.NODEMAP_NAME);var edgeMap=root.get(this.EDGEMAP_NAME);this.removeAllElements();var that=this;var oldIdNewIdMap={};function traverseTree(node,newParentId){node.data.x=node.position.x;node.data.y=node.position.y;if(newParentId){var parent=node.data.parent;if(parent){node.data.parent=newParentId}}var newNode=model.create(NodeR,node.data);var newNodeId=that.getCustomObjId(newNode);oldIdNewIdMap[node.data.id]=newNodeId;nodeMap.set(newNodeId,newNode);if(node.children.length>0){for(var i in node.children){var tmpNode=node.children[i];traverseTree(tmpNode,newNodeId)}}}var tree=window.GraphUtilities.createGraphHierarchyRealTime(nodes);for(var i in tree){var rootLevelNode=tree[i];traverseTree(rootLevelNode)}for(var i in edges){var edge=edges[i];edge.data.source=oldIdNewIdMap[edge.data.source];edge.data.target=oldIdNewIdMap[edge.data.target];var newEdge=model.create(EdgeR,edge.data);var newEdgeID=this.getCustomObjId(newEdge);edgeMap.set(newEdgeID,newEdge)}};RealTimeManager.prototype.mergeGraph=function(nodes,edges){var model=this.realTimeDoc.getModel();var root=model.getRoot();var nodeMap=root.get(this.NODEMAP_NAME);var edgeMap=root.get(this.EDGEMAP_NAME);var realTimeNodeMap=nodeMap.items();var realTimeNodeLookupTable={};var realTimeNodeNameLookupTable={};var oldIdNewIdMap={};var that=this;for(var i in realTimeNodeMap){var nodeMapItem=realTimeNodeMap[i];realTimeNodeLookupTable[nodeMapItem[0]]=nodeMapItem[1];realTimeNodeNameLookupTable[nodeMapItem[1].name]=nodeMapItem[1]}function traverseTree(node,newParentId){if(!(node.data.name in realTimeNodeNameLookupTable)){node.data.x=node.position.x;node.data.y=node.position.y;if(newParentId){var parent=node.data.parent;if(parent){node.data.parent=newParentId}}var newNode=model.create(NodeR,node.data);var newNodeId=that.getCustomObjId(newNode);oldIdNewIdMap[node.data.id]=newNodeId;nodeMap.set(newNodeId,newNode);if(node.children.length>0){for(var i in node.children){var tmpNode=node.children[i];traverseTree(tmpNode,newNodeId)}}}else{var sameNameNode=realTimeNodeNameLookupTable[node.data.name];var sameNodeId=that.getCustomObjId(sameNameNode);oldIdNewIdMap[node.data.id]=sameNodeId;if(node.children.length>0){for(var i in node.children){var tmpNode=node.children[i];traverseTree(tmpNode,sameNodeId)}}}}var tree=window.GraphUtilities.createGraphHierarchyRealTime(nodes);for(var i in tree){var rootLevelNode=tree[i];traverseTree(rootLevelNode,rootLevelNode.data.id)}for(var i in edges){var edge=edges[i];edge.data.source=oldIdNewIdMap[edge.data.source];edge.data.target=oldIdNewIdMap[edge.data.target];var newEdge=model.create(EdgeR,edge.data);var newEdgeID=this.getCustomObjId(newEdge);edgeMap.set(newEdgeID,newEdge)}};RealTimeManager.prototype.updateLayoutProperties=function(newLayoutProperties){var model=this.realTimeDoc.getModel();var root=model.getRoot();var layoutPropertiesR=root.get(this.LAYOUT_PROPS_NAME);model.beginCompoundOperation();for(var property in newLayoutProperties){if(newLayoutProperties.hasOwnProperty(property)){layoutPropertiesR[property]=newLayoutProperties[property]}}model.endCompoundOperation()};RealTimeManager.prototype.updateGlobalOptions=function(newOptions){var model=this.realTimeDoc.getModel();var root=model.getRoot();var globalOptions=root.get(this.GLOBAL_OPTS_NAME);model.beginCompoundOperation();for(var property in globalOptions){if(newOptions.hasOwnProperty(property)){globalOptions[property]=newOptions[property]}}model.endCompoundOperation()};RealTimeManager.prototype.getCustomObjId=function(object){return gapi.drive.realtime.custom.getId(object)};RealTimeManager.prototype.registerTypes=function(){this.createRealTimeObjectDefinitions()};RealTimeManager.prototype.createGraphHierarchy=function(nodes){var tree=[];var mappedArr={};for(var i=0,len=nodes.length;i0){var id=files[0].id;successHandler(id)}else{var createProps={resource:{name:appFName,mimeType:"application/vnd.google-apps.folder"}};driveAPI.files.create(createProps).then(function(resp){var newFolderId=resp.result.id;successHandler(newFolderId)},function(err){console.log(err)})}},function(err){console.log(err)})}},shareRealTimeFile:function(fileId){window.gapi.client.drive.permissions.create({resource:{type:"anyone",role:"writer",allowFileDiscovery:false},fileId:fileId}).then(function(resp){console.log("File shared succesfully !")},function(reason){console.log("An Error happened: "+reason.result.error.message)})},load:function(documentId,onFileLoaded,initializeModel){var that=this;window.gapi.drive.realtime.load(documentId,function(doc){onFileLoaded(doc)},initializeModel,this.onError.bind(this))},onError:function(error){if(error.type==window.gapi.drive.realtime.ErrorType.TOKEN_REFRESH_REQUIRED){this.authorizer.authorize(function(){console.log("Error, auth refreshed")},false)}else if(error.type==window.gapi.drive.realtime.ErrorType.CLIENT_ERROR){alert("An Error happened: "+error.message);window.location.href="/"}else if(error.type==window.gapi.drive.realtime.ErrorType.NOT_FOUND){alert("The file was not found. It does not exist or you do not have "+"read access to the file.");window.location.href="/"}else if(error.type==window.gapi.drive.realtime.ErrorType.FORBIDDEN){alert("You do not have access to this file. Try having the owner share"+"it with you from Google Drive.");window.location.href="/"}}};utils.RealtimeAuthorizer=function(realtimeUtil){this.util=realtimeUtil;this.handleAuthResult=this.handleAuthResult.bind(this);this.token=null};utils.RealtimeAuthorizer.prototype={start:function(onAuthComplete,usePopup){var that=this;window.gapi.load("auth:client,drive-realtime,drive-share",{callback:function(){that.authorize(onAuthComplete,usePopup)}});if(this.authTimer){window.clearTimeout(this.authTimer)}this.refreshAuth()},authorize:function(onAuthComplete,usePopup){this.onAuthComplete=onAuthComplete;window.gapi.auth.authorize({client_id:this.util.clientId,scope:this.util.scopes,immediate:!usePopup},this.handleAuthResult)},handleAuthResult:function(authResult){if(authResult&&!authResult.error){this.token=authResult.access_token}this.onAuthComplete(authResult)},refreshAuth:function(){var that=this;this.authTimer=setTimeout(function(){that.authorize(function(){console.log("Refreshed Auth Token")},false);that.refreshAuth()},this.util.refreshInterval)}}}()},{}],195:[function(require,module,exports){var SaveLoadUtilities=require("./SaveLoadUtility.js");module.exports=function(){var SVGExporter=function(){this.SVGNameSpace="http://www.w3.org/2000/svg";this.svg=document.createElementNS(this.SVGNameSpace,"svg");this.NODE_FILL_COLOR="rgb(255,255,255)";this.FAMILY_FILL_COLOR="rgb(255,255,255)";this.FAMILY_STROKE_COLOR="rgb(204,204,204)";this.NODE_STROKE_COLOR="rgb(0,0,0)";this.COMPARTMENT_STROKE_WIDTH=2;this.NODE_STROKE_WIDTH=1;this.NODE_OPACITY=.5;this.ROUNDING_FACTOR=6;this.GENOMICDATA_LABEL_Y_OFFSET=-15;this.EDGE_WIDTH=1;this.T_WIDTH=2;this.T_HEIGHT=8;this.T_ARROW_HEAD_OFFSET=2;this.TRIANGLE_ARROW_HEAD_HEIGHT=8;this.TRIANGLE_ARROW_HEAD_WIDTH=8;this.DASH_PARAMETERS="5, 3";this.COMPOUND_MARGIN=8;this.NODE_FONT_SIZE=14};SVGExporter.prototype.resetSVG=function(){this.svg=document.createElementNS(this.SVGNameSpace,"svg")};SVGExporter.prototype.exportGraph=function(nodes,edges){this.resetSVG();var cyBounds=cy.extent();this.svg.setAttribute("viewBox",cyBounds.x1+" "+cyBounds.y1+" "+cyBounds.w+" "+cyBounds.h);var that=this;var nodeMap={};var nodeTree=window.GraphUtilities.createGraphHierarchy(nodes);var traverseFunction=function(node){nodeMap[node.id()]=node;var genomicDataSVG=window.editorActionsManager.getGenomicDataSVG(node).children;that.svg.appendChild(that.createRect(node));var labelOffset=genomicDataSVG&&genomicDataSVG.length>0?that.GENOMICDATA_LABEL_Y_OFFSET:0;that.svg.appendChild(that.createText(node,labelOffset));if(genomicDataSVG){while(genomicDataSVG.length>0){var elemSVG=genomicDataSVG[0];var nodePosition=node.position();var svgX=elemSVG.getAttribute("x");var svgY=elemSVG.getAttribute("y");elemSVG.setAttribute("x",nodePosition.x-node.width()/2+parseFloat(svgX));elemSVG.setAttribute("y",nodePosition.y-node.height()/2+parseFloat(svgY));that.svg.appendChild(elemSVG)}}if(node.childNodes){for(var i in node.childNodes){traverseFunction(node.childNodes[i])}}};for(var i in nodeTree){var rootLevelNode=nodeTree[i];traverseFunction(rootLevelNode)}edges.forEach(function(edge){var source=nodeMap[edge.source().id()];var target=nodeMap[edge.target().id()];that.drawEdge(edge,source,target)});return this.svg.outerHTML};SVGExporter.prototype.drawEdge=function(edge,source,target){var edgeType=edge.data().type;var sourceRectangle={x:source.position().x,y:source.position().y,width:source.width(),height:source.height()};var targetRectangle={x:target.position().x,y:target.position().y,width:target.width(),height:target.height()};if(source.isParent()){sourceRectangle.width+=this.COMPOUND_MARGIN;sourceRectangle.height+=this.COMPOUND_MARGIN}if(target.isParent()){targetRectangle.width+=this.COMPOUND_MARGIN;targetRectangle.height+=this.COMPOUND_MARGIN}var clipPoints=this.findClippingPoints(sourceRectangle,targetRectangle);var unitV=unitVector({x:clipPoints.targetClipPoints.x-clipPoints.sourceClipPoints.x,y:clipPoints.targetClipPoints.y-clipPoints.sourceClipPoints.y});var inverseUnitV=scale(unitV,-1);var targetX=clipPoints.targetClipPoints.x;var targetY=clipPoints.targetClipPoints.y;if(edgeType=="ACTIVATES"||edgeType=="INDUCES"){targetX=clipPoints.targetClipPoints.x+this.TRIANGLE_ARROW_HEAD_HEIGHT*inverseUnitV.x;targetY=clipPoints.targetClipPoints.y+this.TRIANGLE_ARROW_HEAD_HEIGHT*inverseUnitV.y;var point1Vector=rotateVector(unitV,Math.PI/2);var point2Vector=rotateVector(unitV,-Math.PI/2);point1Vector=scale(point1Vector,this.TRIANGLE_ARROW_HEAD_WIDTH/2);point2Vector=scale(point2Vector,this.TRIANGLE_ARROW_HEAD_WIDTH/2);var point1X=targetX+point1Vector.x;var point1Y=targetY+point1Vector.y;var point2X=targetX+point2Vector.x;var point2Y=targetY+point2Vector.y;var polySVG=document.createElementNS(this.SVGNameSpace,"polygon");polySVG.setAttribute("points",point1X+","+point1Y+","+point2X+","+point2Y+","+clipPoints.targetClipPoints.x+","+clipPoints.targetClipPoints.y);this.svg.appendChild(polySVG)}else if(edgeType=="INHIBITS"||edgeType=="REPRESSES"){targetX=clipPoints.targetClipPoints.x+this.T_ARROW_HEAD_OFFSET*inverseUnitV.x;targetY=clipPoints.targetClipPoints.y+this.T_ARROW_HEAD_OFFSET*inverseUnitV.y;var point1Vector=rotateVector(unitV,Math.PI/2);var point2Vector=rotateVector(unitV,-Math.PI/2);point1Vector=scale(point1Vector,this.T_HEIGHT/2);point2Vector=scale(point2Vector,this.T_HEIGHT/2);var point1X=targetX+point1Vector.x;var point1Y=targetY+point1Vector.y;var point2X=targetX+point2Vector.x;var point2Y=targetY+point2Vector.y;var lineSVG=document.createElementNS(this.SVGNameSpace,"line");lineSVG.setAttribute("x1",point1X);lineSVG.setAttribute("y1",point1Y);lineSVG.setAttribute("x2",point2X);lineSVG.setAttribute("y2",point2Y);lineSVG.setAttribute("stroke-width",this.T_WIDTH);lineSVG.setAttribute("stroke","black");this.svg.appendChild(lineSVG)}var lineSVG=document.createElementNS(this.SVGNameSpace,"line");lineSVG.setAttribute("x1",clipPoints.sourceClipPoints.x);lineSVG.setAttribute("y1",clipPoints.sourceClipPoints.y);lineSVG.setAttribute("x2",targetX);lineSVG.setAttribute("y2",targetY);lineSVG.setAttribute("stroke-width",this.EDGE_WIDTH);lineSVG.setAttribute("stroke","black");if(edgeType=="INDUCES"||edgeType=="REPRESSES"){lineSVG.setAttribute("stroke-dasharray",this.DASH_PARAMETERS)}this.svg.appendChild(lineSVG)};SVGExporter.prototype.findClippingPoints=function(sourceRectangle,targetRectangle){var sourceAABB={xMin:sourceRectangle.x-sourceRectangle.width/2,xMax:sourceRectangle.x+sourceRectangle.width/2,yMin:sourceRectangle.y-sourceRectangle.height/2,yMax:sourceRectangle.y+sourceRectangle.height/2};var targetAABB={xMin:targetRectangle.x-targetRectangle.width/2,xMax:targetRectangle.x+targetRectangle.width/2,yMin:targetRectangle.y-targetRectangle.height/2,yMax:targetRectangle.y+targetRectangle.height/2};var line1={x1:sourceRectangle.x,y1:sourceRectangle.y,x2:targetRectangle.x,y2:targetRectangle.y};var line2={x1:targetRectangle.x,y1:targetRectangle.y,x2:sourceRectangle.x,y2:sourceRectangle.y};var returnObj={sourceClipPoints:clipLine(line1,sourceAABB),targetClipPoints:clipLine(line2,targetAABB)};return returnObj};SVGExporter.prototype.createRect=function(node){var nodeRectangle=document.createElementNS(this.SVGNameSpace,"rect");var nodePosition=node.position();if(node.isParent()){nodeRectangle.setAttribute("x",nodePosition.x-node.width()/2-this.COMPOUND_MARGIN/2);nodeRectangle.setAttribute("y",nodePosition.y-node.height()/2-this.COMPOUND_MARGIN/2);nodeRectangle.setAttribute("width",node.width()+this.COMPOUND_MARGIN);nodeRectangle.setAttribute("height",node.height()+this.COMPOUND_MARGIN)}else{nodeRectangle.setAttribute("x",nodePosition.x-node.width()/2);nodeRectangle.setAttribute("y",nodePosition.y-node.height()/2);nodeRectangle.setAttribute("width",node.width());nodeRectangle.setAttribute("height",node.height())}nodeRectangle=this.createStyleForNodes(node,nodeRectangle);return nodeRectangle};SVGExporter.prototype.createText=function(node,genomicDataOffset){var verticalTextOffset=5;var nodePosition=node.position();var svgText=document.createElementNS(this.SVGNameSpace,"text");if(node.isParent()){verticalTextOffset=20;svgText.setAttribute("x",nodePosition.x);svgText.setAttribute("y",nodePosition.y+node.height()/2+verticalTextOffset)}else{svgText.setAttribute("x",nodePosition.x);svgText.setAttribute("y",nodePosition.y+verticalTextOffset+genomicDataOffset)}svgText.setAttribute("font-family","Arial");svgText.setAttribute("text-anchor","middle");svgText.setAttribute("font-size",this.NODE_FONT_SIZE);svgText.innerHTML=node.data().name;return svgText};SVGExporter.prototype.createStyleForNodes=function(node,nodeRectangle){var nodeType=node.data().type;var strokeWidth=this.NODE_STROKE_WIDTH;var strokeColor=this.NODE_STROKE_COLOR;var fillColor=this.NODE_FILL_COLOR;var opacity=this.NODE_OPACITY;var strokeOpacity=1;if(nodeType=="GENE"||nodeType=="COMPARTMENT"){nodeRectangle.setAttribute("rx",this.ROUNDING_FACTOR);nodeRectangle.setAttribute("ry",this.ROUNDING_FACTOR);if(nodeType=="COMPARTMENT")strokeWidth=this.COMPARTMENT_STROKE_WIDTH}if(nodeType=="PROCESS"){opacity=0;strokeOpacity=0}if(nodeType=="FAMILY"){fillColor=this.FAMILY_FILL_COLOR;strokeColor=this.FAMILY_STROKE_COLOR}var styleString="stroke-width:"+strokeWidth+";"+"stroke:"+strokeColor+";"+"fill-opacity:"+opacity+";"+"fill:"+fillColor+";"+"stroke-opacity:"+strokeOpacity+";";nodeRectangle.setAttribute("style",styleString);return nodeRectangle};function clipLine(line,rectangle){var INSIDE=0;var LEFT=1;var RIGHT=2;var BOTTOM=4;var TOP=8;function getOutCode(point,rectangle){var outcode=INSIDE;if(point.xrectangle.xMax)outcode=outcode|RIGHT;if(point.yrectangle.yMax)outcode=outcode|BOTTOM;return outcode}var outcode0=getOutCode({x:line.x1,y:line.y1},rectangle);var outcode1=getOutCode({x:line.x2,y:line.y2},rectangle);var slope=(line.y2-line.y1)/(line.x2-line.x1);var returnCoords={x:line.x1,y:line.y1,slope:slope};var accept=false;while(true){if(!(outcode0|outcode1)){accept=true;break}else if(outcode0&outcode1){break}else{var outCode=outcode0?outcode0:outcode1;if(outCode&TOP){returnCoords.x=line.x1+(rectangle.yMin-line.y1)/slope;returnCoords.y=rectangle.yMin}else if(outCode&BOTTOM){returnCoords.x=line.x1+(rectangle.yMax-line.y1)/slope;returnCoords.y=rectangle.yMax}else if(outCode&RIGHT){returnCoords.x=rectangle.xMax;returnCoords.y=line.y1+slope*(rectangle.xMax-line.x1)}else if(outCode&LEFT){returnCoords.x=rectangle.xMin;returnCoords.y=line.y1+slope*(rectangle.xMin-line.x1)}if(outCode==outcode0){outcode0=getOutCode({x:returnCoords.x,y:returnCoords.y},rectangle)}else{outcode1=getOutCode({x:returnCoords.x,y:returnCoords.y},rectangle)}}}return returnCoords}function dotProduct(v1,v2){var newX=v1.x*v2.x;var newY=v1.y*v2.y;return{x:newX,y:newY}}function unitVector(v){var inverseLength=1/Math.sqrt(v.x*v.x+v.y*v.y); diff --git a/public/index.html b/public/index.html index 7cb5d97f..e54e537e 100755 --- a/public/index.html +++ b/public/index.html @@ -15,8 +15,8 @@ - - + + @@ -655,7 +655,7 @@

Pathway Details

- - + + diff --git a/public/src/css/sass/base.scss b/public/src/css/sass/base.scss index cf911e36..acd716f9 100755 --- a/public/src/css/sass/base.scss +++ b/public/src/css/sass/base.scss @@ -14,6 +14,10 @@ @import "animate"; @import "notificationStyles"; +.gridModal{ + width: 300px !important; +} + body { font: 14px helvetica neue, helvetica, arial, sans-serif; diff --git a/public/src/js/NotificationFactory.js b/public/src/js/NotificationFactory.js index 4a3f9105..a715cea7 100644 --- a/public/src/js/NotificationFactory.js +++ b/public/src/js/NotificationFactory.js @@ -35,7 +35,7 @@ module.exports = (function ($) from: "bottom", align: "right" }, - delay: 0, + delay: 5000, offset: 20, spacing: 10, z_index: 1031,