@sjcrh/proteinpaint-client 2.63.0 → 2.63.2

package/dist/{recover-a08c8d01.js → recover-b1ec4fed.js}

@@ -1 +1 @@
-import{aB as t,M as e,aC as s,aD as r,q as i,E as o,aE as a,O as n,az as l,aF as p,x as c,aG as d,aH as m,aI as u}from"./app-f91922b4.js";import{F as f,g as h,a as g,f as j,T as b,N as y}from"./FilterRxComp-0e75dd8d.js";import{f as v}from"./FilterStateless-ad3df967.js";import{appInit as x}from"./app-bfce9bf5.js";import{r as w}from"./table-d6c411fd.js";import{g as T}from"./termsetting-9a7511e6.js";class C extends f{constructor(t){super(t);this.api={main:this.main.bind(this),getNormalRoot:()=>h(this.rawFilter),getPromise:t=>this.promises[t]};if(t.debug)this.api.Inner=this}async main(t,e={}){this.dom.controlsTip.hide();this.dom.treeTip.hide();const s="activeCohort"in e?e.activeCohort:this.activeCohort;const r=g(t,"filterUiRoot");if(r)delete r.tag;t.lst.push({tag:"filterUiRoot",type:"tvslst",join:"",lst:[]});t.join=t.lst.length>1?"and":"";const i=JSON.stringify(t);if(this.rawCopy==i&&JSON.stringify(this.activeCohort)==JSON.stringify(s))return;await super.main(i,e)}refresh(t){this.dom.controlsTip.hide();this.dom.treeTip.hide();const e=JSON.parse(JSON.stringify(this.rawFilter));const s=j(e,this.filter.$id);if(!s||this.rawFilter.$id===this.filter.$id){this.opts.callback(e)}else{const r=s.lst.findIndex((t=>t.$id==this.filter.$id));s.lst[r]=t;this.opts.callback(e)}const r=e.lst.findIndex((e=>e.$id===t.$id));e.lst.splice(r,1);this.main(e)}}const _=t(C);function k(t){const{holder:l,genome:p,mode:c,callback:d,vocabApi:m,titleText:u,minNumGenes:f}=t;let h=structuredClone(t.geneList||[]);const g=new e({padding:"0px",parent_menu:l.node(),test:"test"});l.selectAll("*").remove();const j=l.append("div").style("padding","5px");const b=structuredClone(h);const y=JSON.stringify(h.map((t=>t.gene)).sort());if(u){j.append("div").style("margin-bottom","10px").html(u)}const v={dom:{tdbBtns:{},holder:j,loadBtn:null,clearBtn:null,restoreBtn:null,geneHoldingDiv:null,statLegendDiv:null,submitBtn:null},params:[],statColor2label:null,destroy(){t.holder.remove()}};const x=j.append("div");const w=x.append("label");w.append("span").html("Search");const T=w.append("span");const C=s({tip:g,genome:p,row:T,geneOnly:true,callback:P,hideHelp:true,focusOff:true});const _=x.append("div").style("display","inline-flex").style("align-items","center").style("float","right").style("gap","5px");v.dom.geneHoldingDiv=j.append("div").append("div").style("display","flex").style("flex-wrap","wrap").style("gap","5px").style("min-height","20px").style("border","solid 1px #aaa").style("margin","10px 0px").style("padding","6px 2px").style("min-height","30px");v.dom.statLegendDiv=j.append("div");const k=j.append("div").style("margin-top","10px");const S=k.append("button").property("disabled",!(h===null||h===void 0?void 0:h.length)).text(`Submit`).on("click",(()=>{d({geneList:h})}));v.dom.submitBtn=S;function I(){var e,s,i,o,a,n;_.selectAll("*").remove();if(c=="expression"&&((s=(e=m.termdbConfig)===null||e===void 0?void 0:e.queries)===null||s===void 0?void 0:s.topVariablyExpressedGenes)){if(m.termdbConfig.queries.topVariablyExpressedGenes.arguments){for(const t of m.termdbConfig.queries.topVariablyExpressedGenes.arguments)E(t)}_.append("button").style("white-space","nowrap").text("Load top variably expressed genes").on("click",(t=>r(this,void 0,void 0,(function*(){t.target.disabled=true;const e={genome:m.state.vocab.genome,dslabel:m.state.vocab.dslabel,maxGenes:50};if(m.state.termfilter){if(m.state.termfilter.filter)e.filter=m.state.termfilter.filter;if(m.state.termfilter.filter0)e.filter0=m.state.termfilter.filter0}const s=yield m.getTopVariablyExpressedGenes(e);h=[];if(s.genes){for(const t of s.genes)h.push({gene:t})}B();t.target.disabled=false}))))}else if((o=(i=m.termdbConfig)===null||i===void 0?void 0:i.queries)===null||o===void 0?void 0:o.topMutatedGenes){if(m.termdbConfig.queries.topMutatedGenes.arguments){for(const t of m.termdbConfig.queries.topMutatedGenes.arguments)E(t)}v.dom.loadBtn=_.append("button").style("white-space","nowrap").html(`Load top mutated genes`).on("click",(()=>r(this,void 0,void 0,(function*(){v.dom.loadBtn.property("disabled",true);const t={filter0:m.state.termfilter.filter0};for(const{param:e,input:s}of v.params){const r=s.attr("id");t[r]=R({param:e,input:s})}const e=yield m.getTopMutatedGenes(t);h=[];h.push(...e.genes);B();v.dom.loadBtn.property("disabled",false)}))))}if((a=p===null||p===void 0?void 0:p.termdbs)===null||a===void 0?void 0:a.msigdb){for(const t in p.termdbs){const e=p.termdbs[t];v.dom.tdbBtns[t]=_.append("button").attr("name","msigdbBt").style("white-space","nowrap").html(`Load ${e.label} gene set &#9660;`).on("click",(e=>r(this,void 0,void 0,(function*(){g.clear().showunder(e.target);const s=yield import("./app-bfce9bf5.js");s.appInit({holder:g.d,state:{dslabel:t,genome:p.name,nav:{header_mode:"search_only"}},tree:{click_term:t=>{h=[];const e=t._geneset;if(e){for(const t of e)h.push({gene:t.symbol});B()}g.hide();S.node().focus()}}})}))))}}v.dom.clearBtn=_.append("button").property("disabled",!(h===null||h===void 0?void 0:h.length)).text("Clear").on("click",(()=>{h=[];B()}));if((n=t.geneList)===null||n===void 0?void 0:n.length){v.dom.restoreBtn=_.append("button").property("disabled",true).text("Restore").on("click",(()=>{h=b;B()}))}}function B(){var t;const e=h.some((t=>t.mutationStat));if(!e)h.sort(((t,e)=>{if(t.gene<e.gene)return-1;if(t.gene>e.gene)return 1;return 0}));v.dom.geneHoldingDiv.selectAll("*").remove();v.statColor2label=new Map;v.dom.geneHoldingDiv.selectAll("div").data(h||[]).enter().append("div").attr("title","click to delete").attr("class","sja_menuoption").attr("tabindex",0).style("position","relative").style("display","inline-block").style("padding","5px 16px 5px 9px").style("margin-left","5px").each(A).on("click",q).on("mouseover",(function(t){const e=i(t.target);e.append("div").style("margin-left","4px").classed("sjpp_deletebt",true).style("display","inline-block").style("position","absolute").style("right","0px").style("top","0px").style("transform","scale(0.6)").style("pointer-events","none").html(`<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="#000" class="bi bi-x-lg" viewBox="0 0 16 16">\n\t\t\t\t<path stroke='#f00' d="M2.146 2.854a.5.5 0 1 1 .708-.708L8 7.293l5.146-5.147a.5.5 0 0 1 .708.708L8.707 8l5.147 5.146a.5.5 0 0 1-.708.708L8 8.707l-5.146 5.147a.5.5 0 0 1-.708-.708L7.293 8 2.146 2.854Z"/>\n\t\t\t\t</svg>`)})).on("mouseout",(function(t){i(t.target).select(".sjpp_deletebt").remove()})).on("focus",(t=>{t.target.dispatchEvent(new PointerEvent("mouseover"))})).on("blur",(t=>{t.target.dispatchEvent(new PointerEvent("mouseout"))})).on("keyup",(t=>{if(t.key=="Enter")t.target.click()}));D();v.dom.clearBtn.property("disabled",!(h===null||h===void 0?void 0:h.length));const s=y!==JSON.stringify(h.map((t=>t.gene)).sort());(t=v.dom.restoreBtn)===null||t===void 0?void 0:t.property("disabled",!s);const r=f||0;v.dom.submitBtn.property("disabled",!s||(h===null||h===void 0?void 0:h.length)<r);if(s)S.node().focus()}function A(t){const e=i(this).style("border-radius","5px");if(t.mutationStat){e.html(`${t.gene}&nbsp;&nbsp;`);for(const s of t.mutationStat){let t,r;if("class"in s){if(!o[s.class])throw"invalid stat class";t=o[s.class].color;v.statColor2label.set(t,o[s.class].label)}else if("dt"in s){if(!a[s.dt])throw"invalid stat dt";t=a[s.dt];r="white";v.statColor2label.set(t,n[s.dt])}else{throw"stat missing dt/class"}e.insert("span").style("font-size",".7em").style("background-color",t).style("padding","1px 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import("./barchart.events-272fd122.js");case"../plots/barchart.js":return import("./barchart-e2af00a8.js");case"../plots/bars.renderer.js":return import("./bars.renderer-f0e5af5a.js");case"../plots/bars.settings.js":return import("./bars.settings-64bb4642.js");case"../plots/boxplot.js":return import("./boxplot-7de25274.js");case"../plots/brainImaging.js":return import("./brainImaging-007edaa3.js");case"../plots/controls.btns.js":return import("./controls.btns-bad9e4cf.js");case"../plots/controls.config.js":return import("./controls.config-e0f394cb.js");case"../plots/controls.divide.js":return import("./controls.divide-d8ac5a9b.js");case"../plots/controls.js":return import("./controls-8d4972c8.js");case"../plots/controls.overlay.js":return import("./controls.overlay-3ac8773d.js");case"../plots/controls.term1.js":return import("./controls.term1-008f4be4.js");case"../plots/cuminc.js":return import("./cuminc-72257faf.js");case"../plots/dataDownload.js":return import("./dataDownload-91da6dd6.js");case"../plots/dictionary.js":return import("./dictionary-48a38837.js");case"../plots/geneExpression.js":return import("./geneExpression-9ca2da4f.js");case"../plots/geneORA.js":return import("./geneORA-85850143.js");case"../plots/geneset.js":return import("./geneset-3b761b2c.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-f9b9bf42.js");case"../plots/genomeBrowser.js":return import("./genomeBrowser-2105a98f.js");case"../plots/hierCluster.config.js":return import("./hierCluster.config-3d124abf.js");case"../plots/hierCluster.interactivity.js":return import("./hierCluster.interactivity-3463cc0b.js").then((function(t){return t.i}));case"../plots/hierCluster.js":return import("./hierCluster-a7ff7f5a.js");case"../plots/hierCluster.renderers.js":return import("./hierCluster.renderers-668d0075.js").then((function(t){return t.r}));case"../plots/imagePlot.js":return import("./imagePlot-6d89200c.js");case"../plots/matrix.cells.js":return import("./matrix.cells-a5157233.js");case"../plots/matrix.cluster.js":return import("./matrix.cluster-acdfc6a7.js");case"../plots/matrix.config.js":return import("./matrix.config-cd01ebbd.js");case"../plots/matrix.controls.js":return import("./matrix.controls-86eb8d5c.js");case"../plots/matrix.data.js":return import("./matrix.data-e2d7ac16.js").then((function(t){return t.m}));case"../plots/matrix.dom.js":return import("./matrix.dom-e5f91cc0.js");case"../plots/matrix.groups.js":return import("./matrix.groups-f1969b5c.js").then((function(t){return t.m}));case"../plots/matrix.interactivity.js":return import("./matrix.interactivity-92bc8332.js");case"../plots/matrix.js":return import("./matrix-3d09a31f.js");case"../plots/matrix.layout.js":return import("./matrix.layout-29a8f334.js").then((function(t){return t.m}));case"../plots/matrix.legend.js":return import("./matrix.legend-8c28039e.js").then((function(t){return 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import("./profileRadarFacility-2c2db1dd.js");case"../plots/regression.inputs.js":return import("./regression.inputs-5718cf72.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-5718cf72.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-d587c1cf.js");case"../plots/regression.js":return import("./regression.inputs-5718cf72.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-748024be.js").then((function(t){return t.r}));case"../plots/sampleScatter.interactivity.js":return import("./sampleScatter.interactivity-e9c30652.js").then((function(t){return t.a}));case"../plots/sampleScatter.js":return import("./sampleScatter-031f47de.js").then((function(t){return t.a}));case"../plots/sampleScatter.renderer.js":return import("./sampleScatter-031f47de.js").then((function(t){return t.s}));case"../plots/sampleScatter.rendererThree.js":return import("./sampleScatter.rendererThree-3e6c032e.js").then((function(t){return t.c}));case"../plots/sampleView.js":return import("./sampleView-d6a91293.js");case"../plots/scatter.js":return import("./scatter-2e2c76f4.js");case"../plots/singleCellPlot.js":return import("./singleCellPlot-c7347a27.js");case"../plots/stattable.js":return import("./stattable-a7713026.js");case"../plots/summary.js":return import("./summary-592d8f81.js");case"../plots/survival.js":return import("./survival-450b6df4.js");case"../plots/table.js":return import("./table-bf604c50.js");case"../plots/variantBrowser.js":return import("./variantBrowser-05375469.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-534d6993.js");case"../plots/violin.js":return import("./violin-c1b78717.js");case"../plots/violin.renderer.js":return import("./violin.renderer-16540fb8.js");default:return new Promise((function(e,s){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(s.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}class I{constructor(t={}){this.type="charts";P(this)}async init(t){this.dom={holder:this.opts.holder,tip:new e({padding:"0px"})};this.makeButtons(t)}getState(t){const e=A(t);const s=JSON.parse(JSON.stringify(t.termdbConfig?.supportedChartTypes||{}));const r={vocab:t.vocab,activeCohort:t.activeCohort,termfilter:t.termfilter,supportedChartTypes:s[e]||["summary"],termdbConfig:t.termdbConfig};if(t?.termfilter?.filter){r.filter=h(t.termfilter.filter)}if(!r.supportedChartTypes.includes("dictionary")&&!r.termdbConfig.hiddenChartTypes?.includes("dictionary")){r.supportedChartTypes.push("dictionary")}return r}main(){this.dom.btns.style("display",(t=>this.state.supportedChartTypes.includes(t.chartType)?"":"none"))}}const B=l(I);function A(t){if(t?.termdbConfig?.selectCohort?.values){if(!Number.isInteger(t.activeCohort))throw"appState.activeCohort is not integer array 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s=e.map((t=>({term:structuredClone(t),q:{mode:y.continuous}})));if(s.length==1){t.config.chartType="summary";t.config.term=s[0];return}if(s.length==2){t.config.chartType="summary";t.config.term=s[0];t.config.term2=s[1];return}t.config.chartType="hierCluster";t.config.dataType=b.METABOLITE_INTENSITY;t.config.termgroups=[{name:"Metabolite Intensity Cluster",lst:s,type:"hierCluster"}]}}];for(const t in e?.termdbConfig.renamedChartTypes||[]){const r=s.find((e=>e.chartType===t));if(r){r.label=e.termdbConfig.renamedChartTypes[t]}}return s}function P(t){t.makeButtons=function(e){const s=D(t,e);t.dom.btns=t.dom.holder.selectAll("button").data(s).enter().append("button").style("margin","10px").style("padding","10px 15px").style("border-radius","20px").style("border-color","#ededed").html((t=>t.label)).on("click",(function(e,s){t.dom.tip.clear().showunder(this);s.clickTo(s)}))};t.showTree_select1term=async e=>{if(e.usecase.label){t.dom.tip.d.append("div").style("margin","3px 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c={index:0,name:l,label:l,lst:[],status:"new"};k({holder:o.append("div"),genome:r.opts.genome,geneList:s,mode:"expression",vocabApi:r.vocabApi,callback:async({geneList:t,groupName:e})=>{if(!c)throw`missing selectedGroup`;i.hide();const s={name:e||l,lst:[],type:"hierCluster"};const a=s.lst.filter((t=>t.term.type!="geneVariant"));const n=await Promise.all(t.map((async t=>{const e={gene:t.symbol||t.gene,name:t.symbol||t.gene,type:"geneExpression"};let r=s.lst.find((e=>e.term.name==t.symbol||e.term.name==t.gene));if(!r){r={term:e,q:{}}}return r})));if(n.length==1){const t=n[0];r.dispatch({type:"plot_create",config:{chartType:"summary",term:t}});return}if(n.length==2){const t=n[0];const e=n[1];r.dispatch({type:"plot_create",config:{chartType:"summary",term:t,term2:e}});return}s.lst=[...a,...n];if(!s.lst.length)tg.splice(c.index,1);o.selectAll("*").remove();r.dispatch({type:"plot_create",config:{chartType:"hierCluster",termgroups:[s],dataType:b.GENE_EXPRESSION}})}})};t.showTree_selectlst=async e=>{t.dom.tip.clear();if(e.usecase?.label){t.dom.tip.d.append("div").style("margin","3px 5px").style("padding","3px 5px").style("font-weight",600).html(e.usecase.label)}const s={type:"plot_create",id:R(),config:{chartType:e.chartType}};const r=await import("./app-bfce9bf5.js");t.dom.submenu=t.dom.tip.d.append("div");r.appInit({holder:t.dom.submenu,vocabApi:t.app.vocabApi,state:{activeCohort:t.state.activeCohort,nav:{header_mode:"search_only"},tree:{usecase:e.usecase}},tree:{submit_lst:r=>{const i=e.processSelection?e.processSelection(r):r;s.config[e.usecase.detail]=i;if(e.updateActionBySelectedTerms)e.updateActionBySelectedTerms(s,r);t.dom.tip.hide();t.app.dispatch(s)}}})};t.loadChartSpecificMenu=async e=>{t.dom.tip.clear();const s=await S(`../plots/${e.chartType}.js`);s.makeChartBtnMenu(t.dom.tip.d,t)};t.prepPlot=function(e){const s={type:"plot_prep",config:e.config,id:R()};t.app.dispatch(s)}}const q="_CHART_AUTOID_";let E=Date.now();function R(){return q+E++}const N=p(5);class O{constructor(t={}){this.type="groups";this.selectedGroupsIdx=new Set}async init(){this.dom={holder:this.opts.holder.append("div").style("margin","10px")};G(this);this.tip=new e({padding:"0px"})}getState(t){const e=A(t);const s={termfilter:t.termfilter,groups:V(t),termdbConfig:t.termdbConfig,customTerms:t.customTerms,supportedChartTypes:t.termdbConfig.supportedChartTypes[e],matrixplots:t.termdbConfig.matrixplots};return s}async main(){await L(this)}getMassFilter(){if(!this.state.termfilter.filter||this.state.termfilter.filter.lst.length==0){return{type:"tvslst",in:true,join:"",lst:[]}}const t=h(structuredClone(this.state.termfilter.filter));return t}async groups2samplelst(t){const e=[];const s=new Set,r=[];for(const i of t){const t=await this.app.vocabApi.getFilteredSampleCount(i.filter,"list");const o=[];for(const i of t){const t={sampleId:i.id};if("name"in i){t.sample=i.name}if(!s.has(i.id))o.push(t);else{for(const t of e){const e=t.items.findIndex((t=>t.sampleId===i.id));if(e!==-1)r.push(...t.items.splice(e,1))}}s.add(t.sampleId)}if(o.length)e.push({name:i.name,items:o,color:i.color})}if(r.length){const t=confirm('Overlap detected: 1 or more samples belong to >1 groups. 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e=t.dom.holder.append("div");t.dom.addNewGroupBtnHolder=e.append("span").style("margin-right","20px");t.dom.newTermSpan=e.append("span");t.dom.newTermSpan.append("span").style("padding-left","15px").text("Add variable:");t.dom.newTermNameInput=t.dom.newTermSpan.append("input").attr("type","text");t.dom.launchButton=t.dom.newTermSpan.append("span").attr("class","sja_menuoption").on("click",(()=>F(t)));t.dom.noGroupSelected=e.append("span").text("No groups selected").style("opacity",.5);t.dom.customTermDiv=t.dom.holder.append("div").style("margin","20px").style("border-left","solid 1px black").style("padding","10px");t.dom.holder.on("click",(t=>{if(z)z.hide()}))}async function L(t){if(!t.filterPrompt)t.filterPrompt=await _({holder:t.dom.addNewGroupBtnHolder,vocabApi:t.app.vocabApi,emptyLabel:"Add group",termdbConfig:t.state.termdbConfig,callback:e=>{X(t.app,e,t.state.groups)},debug:t.opts.debug});t.filterPrompt.main(t.getMassFilter());const e=structuredClone(t.state.groups);if(!e.length){t.updateLaunchButton();t.dom.filterTableDiv.style("display","none");t.displayCustomTerms();return}t.dom.filterTableDiv.style("display","").selectAll("*").remove();const s={div:t.dom.filterTableDiv,columns:[{label:"NAME",editCallback:async(e,s)=>{const r=s.value;const i=t.state.groups.findIndex((t=>t.name==r));if(i!=-1){alert(`Group named ${r} already exists`);L(t)}else await t.app.dispatch({type:"rename_group",index:e,newName:s.value})}},{label:"COLOR",editCallback:async(e,s)=>{await t.app.dispatch({type:"change_color_group",index:e,newColor:s.color})}},{label:"#SAMPLE"},{label:"FILTER"}],columnButtons:[{text:"Delete",callback:(s,r)=>{const i=e[r];t.app.vocabApi.deleteGroup(i.name)}}],rows:[]};for(const r of e){s.rows.push([{value:r.name},{color:r.color},{value:"n="+await t.app.vocabApi.getFilteredSampleCount(r.filter)},{}])}t.selectedGroupsIdx.clear();if(e.length==1){t.selectedGroupsIdx.add(0)}else{s.noButtonCallback=(e,s)=>{if(s.checked)t.selectedGroupsIdx.add(e);else t.selectedGroupsIdx.delete(e);t.updateLaunchButton()};s.selectedRows=[];for(let r=0;r<e.length;r++){s.selectedRows.push(r);t.selectedGroupsIdx.add(r)}}w(s);for(const[r,i]of s.rows.entries()){const s=e[r];v({holder:i[3].__td,vocabApi:t.app.vocabApi,termdbConfig:t.state.termdbConfig,callback:r=>{if(!r||r.lst.length==0){const t=e.findIndex((t=>t.name==s.name));e.splice(t,1)}else{s.filter=r}t.app.dispatch({type:"app_refresh",state:{groups:e}})}}).main(s.filter)}t.updateLaunchButton();t.displayCustomTerms()}async function F(t){const e=[];for(const s of t.selectedGroupsIdx){const r=t.state.groups[s];if(r)e.push(r)}if(e.length==0)throw"No groups, should not happen";const s=t.dom.newTermNameInput.property("value");const r=await 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import("./controls.btns-bad9e4cf.js");case"../plots/controls.config.js":return import("./controls.config-e0f394cb.js");case"../plots/controls.divide.js":return import("./controls.divide-d8ac5a9b.js");case"../plots/controls.js":return import("./controls-8d4972c8.js");case"../plots/controls.overlay.js":return import("./controls.overlay-3ac8773d.js");case"../plots/controls.term1.js":return import("./controls.term1-008f4be4.js");case"../plots/cuminc.js":return import("./cuminc-72257faf.js");case"../plots/dataDownload.js":return import("./dataDownload-91da6dd6.js");case"../plots/dictionary.js":return import("./dictionary-48a38837.js");case"../plots/geneExpression.js":return import("./geneExpression-9ca2da4f.js");case"../plots/geneORA.js":return import("./geneORA-85850143.js");case"../plots/geneset.js":return import("./geneset-3b761b2c.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-f9b9bf42.js");case"../plots/genomeBrowser.js":return 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import("./stattable-a7713026.js");case"../plots/summary.js":return import("./summary-592d8f81.js");case"../plots/survival.js":return import("./survival-450b6df4.js");case"../plots/table.js":return import("./table-bf604c50.js");case"../plots/variantBrowser.js":return import("./variantBrowser-05375469.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-534d6993.js");case"../plots/violin.js":return import("./violin-c1b78717.js");case"../plots/violin.renderer.js":return import("./violin.renderer-16540fb8.js");default:return new Promise((function(e,s){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(s.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}function et(t){switch(t){case"../plots/DEanalysis.js":return import("./DEanalysis-b86d0874.js");case"../plots/Disco.js":return import("./Disco-16cd51c0.js");case"../plots/DziViewer.js":return import("./DziViewer-5c2d68e7.js");case"../plots/barchart.data.js":return import("./FilterRxComp-0e75dd8d.js").then((function(t){return t.y}));case"../plots/barchart.events.js":return import("./barchart.events-272fd122.js");case"../plots/barchart.js":return import("./barchart-e2af00a8.js");case"../plots/bars.renderer.js":return import("./bars.renderer-f0e5af5a.js");case"../plots/bars.settings.js":return import("./bars.settings-64bb4642.js");case"../plots/boxplot.js":return import("./boxplot-7de25274.js");case"../plots/brainImaging.js":return import("./brainImaging-007edaa3.js");case"../plots/controls.btns.js":return import("./controls.btns-bad9e4cf.js");case"../plots/controls.config.js":return import("./controls.config-e0f394cb.js");case"../plots/controls.divide.js":return import("./controls.divide-d8ac5a9b.js");case"../plots/controls.js":return import("./controls-8d4972c8.js");case"../plots/controls.overlay.js":return import("./controls.overlay-3ac8773d.js");case"../plots/controls.term1.js":return import("./controls.term1-008f4be4.js");case"../plots/cuminc.js":return import("./cuminc-72257faf.js");case"../plots/dataDownload.js":return import("./dataDownload-91da6dd6.js");case"../plots/dictionary.js":return import("./dictionary-48a38837.js");case"../plots/geneExpression.js":return import("./geneExpression-9ca2da4f.js");case"../plots/geneORA.js":return import("./geneORA-85850143.js");case"../plots/geneset.js":return import("./geneset-3b761b2c.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-f9b9bf42.js");case"../plots/genomeBrowser.js":return import("./genomeBrowser-2105a98f.js");case"../plots/hierCluster.config.js":return import("./hierCluster.config-3d124abf.js");case"../plots/hierCluster.interactivity.js":return import("./hierCluster.interactivity-3463cc0b.js").then((function(t){return t.i}));case"../plots/hierCluster.js":return import("./hierCluster-a7ff7f5a.js");case"../plots/hierCluster.renderers.js":return import("./hierCluster.renderers-668d0075.js").then((function(t){return t.r}));case"../plots/imagePlot.js":return import("./imagePlot-6d89200c.js");case"../plots/matrix.cells.js":return import("./matrix.cells-a5157233.js");case"../plots/matrix.cluster.js":return import("./matrix.cluster-acdfc6a7.js");case"../plots/matrix.config.js":return import("./matrix.config-cd01ebbd.js");case"../plots/matrix.controls.js":return import("./matrix.controls-86eb8d5c.js");case"../plots/matrix.data.js":return import("./matrix.data-e2d7ac16.js").then((function(t){return t.m}));case"../plots/matrix.dom.js":return import("./matrix.dom-e5f91cc0.js");case"../plots/matrix.groups.js":return import("./matrix.groups-f1969b5c.js").then((function(t){return t.m}));case"../plots/matrix.interactivity.js":return import("./matrix.interactivity-92bc8332.js");case"../plots/matrix.js":return import("./matrix-3d09a31f.js");case"../plots/matrix.layout.js":return import("./matrix.layout-29a8f334.js").then((function(t){return t.m}));case"../plots/matrix.legend.js":return import("./matrix.legend-8c28039e.js").then((function(t){return t.m}));case"../plots/matrix.renderers.js":return import("./matrix.renderers-3b8dfd04.js");case"../plots/matrix.serieses.js":return import("./matrix.serieses-e079f04a.js").then((function(t){return t.m}));case"../plots/matrix.sort.js":return import("./matrix.sort-e1f83454.js");case"../plots/matrix.sorterUi.js":return import("./matrix.sorterUi-2025f39d.js");case"../plots/plot.app.js":return import("./plot.app-91a1d78d.js");case"../plots/plot.brainImaging.js":return import("./plot.brainImaging-d2c23bb7.js");case"../plots/plot.disco.js":return import("./plot.disco-70d493f4.js");case"../plots/plot.ssgq.js":return import("./plot.ssgq-9d364d41.js");case"../plots/profileBarchart.js":return import("./profileBarchart-c104f8e2.js");case"../plots/profilePlot.js":return import("./profilePlot-5ce5b6a0.js");case"../plots/profilePolar.js":return import("./profilePolar-610213d4.js");case"../plots/profileRadar.js":return import("./profileRadar-fddb18f7.js");case"../plots/profileRadarFacility.js":return import("./profileRadarFacility-2c2db1dd.js");case"../plots/regression.inputs.js":return import("./regression.inputs-5718cf72.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-5718cf72.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-d587c1cf.js");case"../plots/regression.js":return import("./regression.inputs-5718cf72.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-748024be.js").then((function(t){return t.r}));case"../plots/sampleScatter.interactivity.js":return import("./sampleScatter.interactivity-e9c30652.js").then((function(t){return t.a}));case"../plots/sampleScatter.js":return import("./sampleScatter-031f47de.js").then((function(t){return t.a}));case"../plots/sampleScatter.renderer.js":return import("./sampleScatter-031f47de.js").then((function(t){return t.s}));case"../plots/sampleScatter.rendererThree.js":return import("./sampleScatter.rendererThree-3e6c032e.js").then((function(t){return t.c}));case"../plots/sampleView.js":return import("./sampleView-d6a91293.js");case"../plots/scatter.js":return import("./scatter-2e2c76f4.js");case"../plots/singleCellPlot.js":return import("./singleCellPlot-c7347a27.js");case"../plots/stattable.js":return import("./stattable-a7713026.js");case"../plots/summary.js":return import("./summary-592d8f81.js");case"../plots/survival.js":return import("./survival-450b6df4.js");case"../plots/table.js":return import("./table-bf604c50.js");case"../plots/variantBrowser.js":return import("./variantBrowser-05375469.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-534d6993.js");case"../plots/violin.js":return import("./violin-c1b78717.js");case"../plots/violin.renderer.js":return import("./violin.renderer-16540fb8.js");default:return new Promise((function(e,s){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(s.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}function st(t){switch(t){case"../plots/DEanalysis.js":return import("./DEanalysis-b86d0874.js");case"../plots/Disco.js":return import("./Disco-16cd51c0.js");case"../plots/DziViewer.js":return import("./DziViewer-5c2d68e7.js");case"../plots/barchart.data.js":return import("./FilterRxComp-0e75dd8d.js").then((function(t){return t.y}));case"../plots/barchart.events.js":return import("./barchart.events-272fd122.js");case"../plots/barchart.js":return import("./barchart-e2af00a8.js");case"../plots/bars.renderer.js":return import("./bars.renderer-f0e5af5a.js");case"../plots/bars.settings.js":return import("./bars.settings-64bb4642.js");case"../plots/boxplot.js":return import("./boxplot-7de25274.js");case"../plots/brainImaging.js":return import("./brainImaging-007edaa3.js");case"../plots/controls.btns.js":return import("./controls.btns-bad9e4cf.js");case"../plots/controls.config.js":return import("./controls.config-e0f394cb.js");case"../plots/controls.divide.js":return import("./controls.divide-d8ac5a9b.js");case"../plots/controls.js":return import("./controls-8d4972c8.js");case"../plots/controls.overlay.js":return import("./controls.overlay-3ac8773d.js");case"../plots/controls.term1.js":return import("./controls.term1-008f4be4.js");case"../plots/cuminc.js":return import("./cuminc-72257faf.js");case"../plots/dataDownload.js":return import("./dataDownload-91da6dd6.js");case"../plots/dictionary.js":return import("./dictionary-48a38837.js");case"../plots/geneExpression.js":return import("./geneExpression-9ca2da4f.js");case"../plots/geneORA.js":return import("./geneORA-85850143.js");case"../plots/geneset.js":return import("./geneset-3b761b2c.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-f9b9bf42.js");case"../plots/genomeBrowser.js":return import("./genomeBrowser-2105a98f.js");case"../plots/hierCluster.config.js":return import("./hierCluster.config-3d124abf.js");case"../plots/hierCluster.interactivity.js":return import("./hierCluster.interactivity-3463cc0b.js").then((function(t){return t.i}));case"../plots/hierCluster.js":return import("./hierCluster-a7ff7f5a.js");case"../plots/hierCluster.renderers.js":return import("./hierCluster.renderers-668d0075.js").then((function(t){return t.r}));case"../plots/imagePlot.js":return import("./imagePlot-6d89200c.js");case"../plots/matrix.cells.js":return import("./matrix.cells-a5157233.js");case"../plots/matrix.cluster.js":return import("./matrix.cluster-acdfc6a7.js");case"../plots/matrix.config.js":return import("./matrix.config-cd01ebbd.js");case"../plots/matrix.controls.js":return import("./matrix.controls-86eb8d5c.js");case"../plots/matrix.data.js":return import("./matrix.data-e2d7ac16.js").then((function(t){return t.m}));case"../plots/matrix.dom.js":return import("./matrix.dom-e5f91cc0.js");case"../plots/matrix.groups.js":return import("./matrix.groups-f1969b5c.js").then((function(t){return t.m}));case"../plots/matrix.interactivity.js":return import("./matrix.interactivity-92bc8332.js");case"../plots/matrix.js":return import("./matrix-3d09a31f.js");case"../plots/matrix.layout.js":return import("./matrix.layout-29a8f334.js").then((function(t){return t.m}));case"../plots/matrix.legend.js":return import("./matrix.legend-8c28039e.js").then((function(t){return t.m}));case"../plots/matrix.renderers.js":return import("./matrix.renderers-3b8dfd04.js");case"../plots/matrix.serieses.js":return import("./matrix.serieses-e079f04a.js").then((function(t){return t.m}));case"../plots/matrix.sort.js":return import("./matrix.sort-e1f83454.js");case"../plots/matrix.sorterUi.js":return import("./matrix.sorterUi-2025f39d.js");case"../plots/plot.app.js":return import("./plot.app-91a1d78d.js");case"../plots/plot.brainImaging.js":return import("./plot.brainImaging-d2c23bb7.js");case"../plots/plot.disco.js":return import("./plot.disco-70d493f4.js");case"../plots/plot.ssgq.js":return import("./plot.ssgq-9d364d41.js");case"../plots/profileBarchart.js":return import("./profileBarchart-c104f8e2.js");case"../plots/profilePlot.js":return import("./profilePlot-5ce5b6a0.js");case"../plots/profilePolar.js":return import("./profilePolar-610213d4.js");case"../plots/profileRadar.js":return import("./profileRadar-fddb18f7.js");case"../plots/profileRadarFacility.js":return import("./profileRadarFacility-2c2db1dd.js");case"../plots/regression.inputs.js":return import("./regression.inputs-5718cf72.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-5718cf72.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-d587c1cf.js");case"../plots/regression.js":return import("./regression.inputs-5718cf72.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-748024be.js").then((function(t){return t.r}));case"../plots/sampleScatter.interactivity.js":return import("./sampleScatter.interactivity-e9c30652.js").then((function(t){return t.a}));case"../plots/sampleScatter.js":return import("./sampleScatter-031f47de.js").then((function(t){return t.a}));case"../plots/sampleScatter.renderer.js":return import("./sampleScatter-031f47de.js").then((function(t){return t.s}));case"../plots/sampleScatter.rendererThree.js":return import("./sampleScatter.rendererThree-3e6c032e.js").then((function(t){return t.c}));case"../plots/sampleView.js":return import("./sampleView-d6a91293.js");case"../plots/scatter.js":return import("./scatter-2e2c76f4.js");case"../plots/singleCellPlot.js":return import("./singleCellPlot-c7347a27.js");case"../plots/stattable.js":return import("./stattable-a7713026.js");case"../plots/summary.js":return import("./summary-592d8f81.js");case"../plots/survival.js":return import("./survival-450b6df4.js");case"../plots/table.js":return import("./table-bf604c50.js");case"../plots/variantBrowser.js":return import("./variantBrowser-05375469.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-534d6993.js");case"../plots/violin.js":return import("./violin-c1b78717.js");case"../plots/violin.renderer.js":return import("./violin.renderer-16540fb8.js");default:return new Promise((function(e,s){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(s.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}const rt="_MASS_AUTOID_"+Math.random().toString().slice(-6);let it=(+new Date).toString().slice(-8);function ot(){return rt+"_"+it++}const at=new Set(["with_tabs","hidden","search_only","hide_search","only_buttons","with_cohortHtmlSelect"]);const nt={nav:{header_mode:"with_tabs",activeTab:0},activeCohort:0,search:{isVisible:true},plots:[],termfilter:{filter:{type:"tvslst",in:true,join:"",lst:[]}},reuse:{customTermQ:{byId:{},byName:{}}},groups:[],customTerms:[],autoSave:true};class lt{constructor(t){this.type="store";this.defaultState=nt;this.prevGeneratedId=0}validateOpts(t){const e=t.state;if(e.vocab.dslabel){if(!e.vocab.genome)throw".state[.vocab].genome missing"}else{if(!Array.isArray(e.vocab.terms))throw"vocab.terms must be an array of objects"}}validateState(){if(!at.has(this.state.nav.header_mode))throw"invalid state.nav.header_mode"}async init(){try{this.state.termdbConfig=await this.app.vocabApi.getTermdbConfig();await this.setTermfilter();await this.rehydrateGroups();await this.app.vocabApi.main({termfilter:JSON.parse(JSON.stringify(this.state.termfilter)),termdbConfig:this.state.termdbConfig});for(const[t,e]of this.state.plots.entries()){const s=await st(`../plots/${e.chartType}.js`);const r=await s.getPlotConfig(e,this.app);this.state.plots[t]=r;if(!("id"in r))r.id=`_AUTOID_${it++}_${t}`;if(r.mayAdjustConfig)r.mayAdjustConfig(r)}}catch(t){throw t}}setId(t){t.$id=this.prevGeneratedId++;if(t.$lst){for(const e of t.$lst){this.setId(e)}}}async setTermfilter(){let t=g(this.state.termfilter.filter,"filterUiRoot");if(!t){this.state.termfilter.filter.tag="filterUiRoot";t=this.state.termfilter.filter}await Promise.all(pt(this.state.termfilter.filter,this.app.vocabApi));if(!this.state.termdbConfig.selectCohort){this.state.activeCohort=-1;if(this.state.activeTab===0)this.state.activeTab=1;if(this.state.nav.header_mode==="with_cohortHtmlSelect"){console.warn(`no termdbConfig.selectCohort to use for nav.header_mode = 'with_cohortHtmlSelect'`);this.state.nav.header_mode="search_only"}}else{let e=g(this.state.termfilter.filter,"cohortFilter");if(!e){e={tag:"cohortFilter",type:"tvs",tvs:{term:JSON.parse(JSON.stringify(this.state.termdbConfig.selectCohort.term)),values:this.state.activeCohort==-1?[]:this.state.termdbConfig.selectCohort.values[this.state.activeCohort].keys.map((t=>({key:t,label:t})))}};this.state.termfilter.filter={type:"tvslst",in:true,join:"and",lst:[e,t]}}else{const t=(t,e)=>t<e?-1:1;e.tvs.values.sort(((t,e)=>t.key<e.key?-1:1));const s=JSON.stringify(e.tvs.values.map((t=>t.key)).sort(t));const r=this.state.termdbConfig.selectCohort.values.findIndex((e=>s==JSON.stringify(e.keys.sort(t))));if(this.state.activeCohort!==-1&&this.state.activeCohort!==0&&r!==this.state.activeCohort){console.log("Warning: cohortFilter will override the state.activeCohort due to mismatch")}this.state.activeCohort=r}}}async rehydrateGroups(){const t=[];for(const e of this.state.groups){t.push(...pt(e.filter,this.app.vocabApi))}await Promise.all(t)}}function pt(t,e,s=[]){if(t.type=="tvslst"){for(const r of t.lst)pt(r,e,s)}else if(t.type=="tvs"){if(!t.tvs.term.name)s.push(e.getterm(t.tvs.term.id).then((e=>{t.tvs.term=e})))}else{throw`cannot rehydrate filter.type='${t.type}'`}return s}lt.prototype.actions={app_refresh(t={}){this.state=this.copyMerge(this.toJson(this.state),t.state||{});const e=new Set;if(t.subactions){for(const s of t.subactions){this.actions[s.type].call(this,s);if(s.type.startsWith("plot_"))e.add(s.id)}}for(const s in this.state.plots){if(s.mayAdjustConfig&&!e.has(s.id)){s.mayAdjustConfig(s,t.config)}}},tab_set(t){this.state.nav.activeTab=t.activeTab},cohort_set(t){this.state.activeCohort=t.activeCohort;const e=this.state.termdbConfig.selectCohort.values[t.activeCohort];const s=g(this.state.termfilter.filter,"cohortFilter");if(!s)throw`No item tagged with 'cohortFilter'`;s.tvs.values=e.keys.map((t=>({key:t,label:t})))},async plot_prep(t){const e={id:"id"in t?t.id:ot()};if(!t.config)throw".config{} missing for plot_prep";if(t.config.chartType&&Object.keys(t.config).length==1){const e=await et(`../plots/${t.config.chartType}.js`);const s=await e.getPlotConfig(t.config,this.app);t.config=Object.assign(s,t.config)}Object.assign(e,t.config);this.state.plots.push(e)},async plot_create(t){const e=await tt(`../plots/${t.config.chartType}.js`);const s=await e.getPlotConfig(t.config,this.app);if(!("id"in t))t.id=ot();s.id=t.id;if(s.mayAdjustConfig){s.mayAdjustConfig(s,t.config)}this.state.plots.push(s)},plot_edit(t){const e=this.state.plots.find((e=>e.id===t.id));if(!e)throw`missing plot id='${t.id}' in store.plot_edit()`;this.copyMerge(e,t.config,t.opts?t.opts:{});if(e.mayAdjustConfig){e.mayAdjustConfig(e,t.config)}ut(e,this.app.vocabApi);if(t.config&&"cutoff"in t.config){e.cutoff=t.config.cutoff}else{delete e.cutoff}},plot_delete(t){const e=this.state.plots.findIndex((e=>e.id===t.id));if(e!==-1)this.state.plots.splice(e,1)},plot_nestedEdits(t){const e=this.state.plots.find((e=>e.id===t.id));if(!e)throw`missing plot id='${t.id}' in store.plot_edit_nested`;for(const s of t.edits){const t=s.nestedKeys.pop();const r=s.nestedKeys.reduce(((t,e)=>t[e]),e);r[t]=s.value}ut(e,this.app.vocabApi)},async plot_splice(t){for(const e of t.subactions){await this.actions[e.type].call(this,e)}},filter_replace(t){if("filter0"in t){this.state.termfilter.filter0=t.filter0;return}const e=t.filter?t.filter:{type:"tvslst",join:"",in:1,lst:[]};if(!t.filter.tag){this.state.termfilter.filter=e}else{const s=g(this.state.termfilter.filter,t.filter.tag);if(!s)throw`cannot replace missing filter with tag '${t.filter.tag}'`;const r=j(this.state.termfilter.filter,s.$id);if(r==s){this.state.termfilter.filter=e}else{const t=r.lst.indexOf(s);r.lst[t]=e}}},cache_termq({termId:t,q:e}){if(!t)throw`missing termId for caching custom term.q`;if(!e?.reuseId)throw`missing or empty tw.q.reuseId as cache identifier for term='${t}'`;const s=this.state.reuse.customTermQ.byId;if(!s[t])s[t]={};s[t][e.reuseId]=e;for(const t of this.state.plots){if(!(t.chartType in dt))continue;const s=dt[t.chartType](t);for(const t of s){if(t?.q?.reuseId===e.reuseId)t.q=e}}},uncache_termq({term:t,q:e}){if(!t.id)throw`missing term.id for uncaching custom term.q`;if(!e.reuseId)throw`missing qname as uncache identifier for term.id='${t.id}'`;const s=this.state.reuse.customTermQ.byId[t.id];if(!s)throw`missing term.q cache for term.id='${t.id}`;if(!(e.reuseId in s))console.warn(`q.reuseId='${e.cacheid}' not cached for term.id='${t.id}'`);else{delete s[e.reuseId];for(const t of this.state.plots){if(!(t.chartType in dt))continue;const s=dt[t.chartType](t);for(const t of s){if(t.q.reuseId===e.reuseId){delete t.q.reuseId;delete t.q.name}}}}},add_customTerm(t){this.state.customTerms.push(t.obj)},delete_customTerm({name:t}){const e=this.state.customTerms.findIndex((e=>e.name==t));if(e!=-1)this.state.customTerms.splice(e,1)},add_group(t){if(this.state.nav.header_mode!="hidden"){const e=t.obj;const s=`Group ${this.state.groups.length+1}`;const r=Z([e]);const i={name:s,filter:Y(r),plotId:e.plotId};this.state.groups.push(i);this.state.nav.activeTab=1}else if("plotId"in t.obj){const e=this.state.plots.find((e=>e.id==t.obj.plotId));if(e.groups){t.obj.index=e.groups.length;t.obj.name=`Group ${e.groups.length+1}`;e.groups.push(t.obj)}}},rename_group(t){const e=t.index;const s=t.newName;if(this.state.nav.header_mode!="hidden"){this.state.groups[e].name=s}else{for(const t of this.state.plots){if(t?.groups){t.groups[e].name=s}}}},change_color_group(t){const e=t.index;const s=t.newColor;if(this.state.nav.header_mode!="hidden"){this.state.groups[e].color=s}else{for(const t of this.state.plots){if(t?.groups){t.groups[e].color=s}}}},delete_group({name:t}){if(this.state.nav.header_mode!="hidden"){const e=this.state.groups.findIndex((e=>e.name==t));if(e!=-1)this.state.groups.splice(e,1)}else{for(const e of this.state.plots){if(e?.groups){const s=e.groups.findIndex((e=>e.name==t));if(s!=-1)e.groups.splice(s,1)}}}}};const ct=t=>[t.term0,t.term,t.term2].filter((t=>!!t));const dt={summary:ct,survival:ct,cuminc:ct,regression:t=>[t.outcome,...t.independent].filter((t=>!!t)),matrix:t=>t.termgroups.reduce(((t,e)=>{t.push(...e.lst);return t}),[])};const mt=d(lt);function ut(t,e){if(!("id"in t))throw"plot error: plot.id missing";try{if(t.chartType=="regression"){ht(t,e)}else if(t.chartType=="matrix"||t.chartType=="hierCluster"){if(!t.termgroups)throw`plot error: missing the config.termgroups for '${t.chartType}'`;if(!Array.isArray(t.termgroups))`plot error: config.termgroups must be an array '${t.chartType}'`;if(!t.samplegroups)throw`plot error: missing the config.samplegroups for '${t.chartType}'`;if(!Array.isArray(t.samplegroups))`plot error: config.samplegroups must be an array '${t.chartType}'`}else if(t.chartType=="dataDownload"){if(!t.terms)throw`plot error: missing the config.terms for '${t.chartType}'`;if(!Array.isArray(t.terms))`plot error: config.terms must be an array '${t.chartType}'`;for(const s of t.terms){gt(s,e)}}else if(t.chartType=="sampleScatter"){if(!t.name)throw`plot error: missing the plot name for '${t.chartType}'`;if(!t.colorTW)`plot error: missing the plot color term wrapper for '${t.chartType}'`;if(!t.file)`plot error: missing the plot coordinates file for '${t.chartType}'`}else if(t.chartType=="genomeBrowser"){}else if(t.chartType=="Disco"){}else if(t.chartType=="profileBarchart"){}else if(t.chartType=="profilePolar"||t.chartType=="polar"){}else if(t.chartType=="DEanalysis"){}else if(t.chartType=="geneORA"){}else if(t.chartType=="sampleView"){}else if(t.chartType=="profileRadar"||t.chartType=="profileRadarFacility"){}else if(t.chartType=="singleCellPlot"){}else if(t.chartType=="brainImaging"){}else{ft(t,e)}}catch(t){throw t}}function ft(t,e){try{if(t.term)gt(t.chartType=="regression"?t.outcome:t.term,e)}catch(t){throw"plot.term error: "+t}if(t.term2){try{gt(t.term2,e)}catch(t){throw"plot.term2 error: "+t}if(t.term.term.type=="condition"&&t.term.term.id==t.term2.term.id){if(t.term.q.bar_by_grade&&t.term2.q.bar_by_grade)throw"plot error: term2 is the same CHC, but both cannot be using bar_by_grade";if(t.term.q.bar_by_children&&t.term2.q.bar_by_children)throw"plot error: term2 is the same CHC, but both cannot be using bar_by_children"}}if(t.term0){try{gt(t.term0,e)}catch(t){throw"plot.term0 error: "+t}}}function ht(t,e){if(!t.outcome)throw"plot error: plot.outcome{} not an object";try{gt(t.chartType=="regression"?t.outcome:t.term,e)}catch(t){throw"plot.outcome error: "+t}if(t.independent){for(const s of t.independent){gt(s,e)}}}function gt(t,e){if(!t.term)throw".term{} missing";if(!e.graphable(t.term))throw".term is not graphable (not a valid type)";if(!t.term.name)throw".term.name missing";if(!t.q)throw".q{} missing";switch(t.term.type){case"integer":case"float":case"survival":break;case"categorical":if(t.q.groupsetting&&!t.q.groupsetting.disabled){if(!t.term.values)throw".values{} missing when groupsetting is allowed"}break;case"condition":if(!t.term.values)throw".values{} missing";if(!t.q.bar_by_grade&&!t.q.bar_by_children)throw"neither q.bar_by_grade or q.bar_by_children is set to true";if(!t.q.value_by_max_grade&&!t.q.value_by_most_recent&&!t.q.value_by_computable_grade)throw"neither q.value_by_max_grade or q.value_by_most_recent or q.value_by_computable_grade is true";break;case"snplst":case"snplocus":case"geneVariant":break;case"samplelst":break;case b.GENE_EXPRESSION:break;case b.METABOLITE_INTENSITY:break;default:if(t.term.isgenotype){console.log('to add in type:"genotype"');break}throw`unknown term type='${t.term.type}'`}}class jt{constructor(t={}){this.type="recover";this.initialHolderDisplay=t.holder.style("display");this.dom={holder:t.holder,btnDiv:t.holder.append("div").style("position","sticky").style("top","12px").style("right","20px").style("margin",t.margin?t.margin:"10px").style("text-align","right")};this.hasStatePreMain=true;this.reactsTo=t.reactsTo||(()=>true);this.getState=t.getState||(t=>t);this.debouncedTrack=()=>{this.trackPending=true;this.trackState();this.render()};this.wait="wait"in t?t.wait:800;this.maxHistoryLen=t.maxHistoryLen||10}preApiFreeze(t){t.replaceLastState=t=>{if(this.isRecovering)return;this.state=this.getState(t);if(!this.trackPending)this.history[this.currIndex]=this.state}}init(){this.app.register(this.api);this.currIndex=-1;this.history=[];this.isActive=!isNaN(this.maxHistoryLen)&&+this.maxHistoryLen>0;if(this.isActive){yt(this);this.initUi()}this.eventTypes=["postInit","postRender"]}async main(){if(!this.isActive)return;if(this.opts.hide?.(this.state)){this.dom.holder.style("display","none");return}this.dom.holder.style("display",this.initialHolderDisplay||"");if(!this.timedTrack){this.trackState();this.trackPending=true;this.timedTrack=setTimeout((()=>{}),this.wait);return}clearTimeout(this.timedTrack);this.trackPending=true;this.timedTrack=setTimeout(this.debouncedTrack,this.wait)}trackState(){if(this.isRecovering){this.isRecovering=false;return}if(this.state._scope_=="none")return;this.isRecovering=false;const t=this.opts.adjustTrackedState?this.opts.adjustTrackedState(this.state):this.state;if(!t){console.error("no state to track");return}if(!Object.isFrozen(t))m(t);if(this.currIndex==-1)this.origState=t;if(this.currIndex<this.history.length-1){this.history.splice(this.currIndex,this.history.length-(this.currIndex+1))}if(u(t,this.history[this.history.length-1]))return;this.history.push(t);this.currIndex+=1;if(this.history.length>this.maxHistoryLen){this.history.splice(1,1);this.currIndex+=-1}this.trackPending=false}goto(t){if(t<0&&this.currIndex+t>-1)this.currIndex+=t;else if(t>0&&this.currIndex+t<this.history.length)this.currIndex+=t;else return;this.isRecovering=true;const e=this.history[this.currIndex];this.render();if(this.opts.plot_id){const t=structuredClone(e);this.app.dispatch({type:"plot_edit",id:this.opts.plot_id,config:t.config,_scope_:t._scope_})}else{this.app.dispatch({type:"app_refresh",state:e})}}reset(){this.currIndex=0;this.isRecovering=true;const t=this.origState;if(this.opts.plot_id){const e=t.plots.find((t=>t.id===this.opts.plot_id));this.app.dispatch({type:"plot_edit",id:this.opts.plot_id,config:structuredClone(e)})}else this.app.dispatch({type:"app_refresh",state:t})}}const bt=l(jt);function yt(t){t.initUi=function(){t.dom.undoBtn=t.dom.btnDiv.append("button").attr("title","undo the previous action").property("disabled",true).style("margin","0 0 0 4px").style("border","1px solid #ccc").style("vertical-align","middle").html(t.opts.undoHtml||`<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="#000" class="bi bi-arrow-counterclockwise" viewBox="0 0 16 16" style='vertical-align: middle'>\n\t\t\t  <path stroke='#000' stroke-width='0.25' fill-rule="evenodd" d="M8 3a5 5 0 1 1-4.546 2.914.5.5 0 0 0-.908-.417A6 6 0 1 0 8 2v1z"/>\n\t\t\t  <path d="M8 4.466V.534a.25.25 0 0 0-.41-.192L5.23 2.308a.25.25 0 0 0 0 .384l2.36 1.966A.25.25 0 0 0 8 4.466z"/>\n\t\t\t</svg>`).on("click",(()=>t.goto(-1)));t.dom.redoBtn=t.dom.btnDiv.append("button").attr("title","redo a subsequent action").property("disabled",true).style("margin",t.opts.resetHtml?"0":"0 4px 0 0").style("border","1px solid #ccc").style("vertical-align","middle").html(t.opts.redoHtml||`<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="#000" class="bi bi-arrow-clockwise" viewBox="0 0 16 16" style='vertical-align: middle'>\n\t\t\t  <path stroke='#000' stroke-width='0.25' fill-rule="evenodd" d="M8 3a5 5 0 1 0 4.546 2.914.5.5 0 0 1 .908-.417A6 6 0 1 1 8 2v1z"/>\n\t\t\t  <path d="M8 4.466V.534a.25.25 0 0 1 .41-.192l2.36 1.966c.12.1.12.284 0 .384L8.41 4.658A.25.25 0 0 1 8 4.466z"/>\n\t\t\t</svg>`).on("click",(()=>t.goto(1)));if(t.opts.resetHtml)t.dom.resetBtn=t.dom.btnDiv.append("button").attr("title","Restore the initial rendered state").property("disabled",true).style("margin","0 4px 0 0").style("border","1px solid #ccc").style("vertical-align","middle").html(t.opts.resetHtml).on("click",(()=>t.reset()))};t.render=function(){if(t.dom.undoBtn)t.dom.undoBtn.property("disabled",t.currIndex<1||t.history.length===1);if(t.dom.redoBtn)t.dom.redoBtn.property("disabled",t.history.length<2||t.currIndex>=t.history.length-1);if(t.dom.resetBtn)t.dom.resetBtn.property("disabled",t.currIndex===0)}}export{Y as a,Z as b,B as c,W as d,Q as e,J as f,$ as g,X as h,A as i,V as j,k,K as l,U as o,bt as r,mt as s};
+import{aB as t,M as e,aC as s,aD as r,q as i,E as o,aE as a,O as n,az as l,aF as p,x as c,aG as m,aH as d,aI as u}from"./app-71453429.js";import{F as h,g as f,a as g,f as j,T as b,N as y}from"./FilterRxComp-fc769f34.js";import{f as v}from"./FilterStateless-8f30f856.js";import{appInit as x}from"./app-fb676934.js";import{r as w}from"./table-1dae543a.js";import{g as T}from"./termsetting-636d2271.js";class C extends h{constructor(t){super(t);this.api={main:this.main.bind(this),getNormalRoot:()=>f(this.rawFilter),getPromise:t=>this.promises[t]};if(t.debug)this.api.Inner=this}async main(t,e={}){this.dom.controlsTip.hide();this.dom.treeTip.hide();const s="activeCohort"in e?e.activeCohort:this.activeCohort;const r=g(t,"filterUiRoot");if(r)delete r.tag;t.lst.push({tag:"filterUiRoot",type:"tvslst",join:"",lst:[]});t.join=t.lst.length>1?"and":"";const i=JSON.stringify(t);if(this.rawCopy==i&&JSON.stringify(this.activeCohort)==JSON.stringify(s))return;await super.main(i,e)}refresh(t){this.dom.controlsTip.hide();this.dom.treeTip.hide();const e=JSON.parse(JSON.stringify(this.rawFilter));const s=j(e,this.filter.$id);if(!s||this.rawFilter.$id===this.filter.$id){this.opts.callback(e)}else{const r=s.lst.findIndex((t=>t.$id==this.filter.$id));s.lst[r]=t;this.opts.callback(e)}const r=e.lst.findIndex((e=>e.$id===t.$id));e.lst.splice(r,1);this.main(e)}}const _=t(C);function k(t){const{holder:l,genome:p,mode:c,callback:m,vocabApi:d,titleText:u,minNumGenes:h}=t;let f=structuredClone(t.geneList||[]);const g=new e({padding:"0px",parent_menu:l.node(),test:"test"});l.selectAll("*").remove();const j=l.append("div").style("padding","5px");const b=structuredClone(f);const y=JSON.stringify(f.map((t=>t.gene)).sort());if(u){j.append("div").style("margin-bottom","10px").html(u)}const v={dom:{tdbBtns:{},holder:j,loadBtn:null,clearBtn:null,restoreBtn:null,geneHoldingDiv:null,statLegendDiv:null,submitBtn:null},params:[],statColor2label:null,destroy(){t.holder.remove()}};const x=j.append("div");const w=x.append("label");w.append("span").html("Search");const T=w.append("span");const C=s({tip:g,genome:p,row:T,geneOnly:true,callback:P,hideHelp:true,focusOff:true});const _=x.append("div").style("display","inline-flex").style("align-items","center").style("float","right").style("gap","5px");v.dom.geneHoldingDiv=j.append("div").append("div").style("display","flex").style("flex-wrap","wrap").style("gap","5px").style("min-height","20px").style("border","solid 1px #aaa").style("margin","10px 0px").style("padding","6px 2px").style("min-height","30px");v.dom.statLegendDiv=j.append("div");const k=j.append("div").style("margin-top","10px");const S=k.append("button").property("disabled",!(f===null||f===void 0?void 0:f.length)).text(`Submit`).on("click",(()=>{m({geneList:f})}));v.dom.submitBtn=S;function I(){var e,s,i,o,a,n;_.selectAll("*").remove();if(c=="expression"&&((s=(e=d.termdbConfig)===null||e===void 0?void 0:e.queries)===null||s===void 0?void 0:s.topVariablyExpressedGenes)){if(d.termdbConfig.queries.topVariablyExpressedGenes.arguments){for(const t of d.termdbConfig.queries.topVariablyExpressedGenes.arguments)E(t)}_.append("button").style("white-space","nowrap").text("Load top variably expressed genes").on("click",(t=>r(this,void 0,void 0,(function*(){t.target.disabled=true;const e={genome:d.state.vocab.genome,dslabel:d.state.vocab.dslabel,maxGenes:50};if(d.state.termfilter){if(d.state.termfilter.filter)e.filter=d.state.termfilter.filter;if(d.state.termfilter.filter0)e.filter0=d.state.termfilter.filter0}const s=yield d.getTopVariablyExpressedGenes(e);f=[];if(s.genes){for(const t of s.genes)f.push({gene:t})}B();t.target.disabled=false}))))}else if((o=(i=d.termdbConfig)===null||i===void 0?void 0:i.queries)===null||o===void 0?void 0:o.topMutatedGenes){if(d.termdbConfig.queries.topMutatedGenes.arguments){for(const t of d.termdbConfig.queries.topMutatedGenes.arguments)E(t)}v.dom.loadBtn=_.append("button").style("white-space","nowrap").html(`Load top mutated genes`).on("click",(()=>r(this,void 0,void 0,(function*(){v.dom.loadBtn.property("disabled",true);const t={filter0:d.state.termfilter.filter0};for(const{param:e,input:s}of v.params){const r=s.attr("id");t[r]=R({param:e,input:s})}const e=yield d.getTopMutatedGenes(t);f=[];f.push(...e.genes);B();v.dom.loadBtn.property("disabled",false)}))))}if((a=p===null||p===void 0?void 0:p.termdbs)===null||a===void 0?void 0:a.msigdb){for(const t in p.termdbs){const e=p.termdbs[t];v.dom.tdbBtns[t]=_.append("button").attr("name","msigdbBt").style("white-space","nowrap").html(`Load ${e.label} gene set &#9660;`).on("click",(e=>r(this,void 0,void 0,(function*(){g.clear().showunder(e.target);const s=yield import("./app-fb676934.js");s.appInit({holder:g.d,state:{dslabel:t,genome:p.name,nav:{header_mode:"search_only"}},tree:{click_term:t=>{f=[];const e=t._geneset;if(e){for(const t of e)f.push({gene:t.symbol});B()}g.hide();S.node().focus()}}})}))))}}v.dom.clearBtn=_.append("button").property("disabled",!(f===null||f===void 0?void 0:f.length)).text("Clear").on("click",(()=>{f=[];B()}));if((n=t.geneList)===null||n===void 0?void 0:n.length){v.dom.restoreBtn=_.append("button").property("disabled",true).text("Restore").on("click",(()=>{f=b;B()}))}}function B(){var t;const e=f.some((t=>t.mutationStat));if(!e)f.sort(((t,e)=>{if(t.gene<e.gene)return-1;if(t.gene>e.gene)return 1;return 0}));v.dom.geneHoldingDiv.selectAll("*").remove();v.statColor2label=new Map;v.dom.geneHoldingDiv.selectAll("div").data(f||[]).enter().append("div").attr("title","click to delete").attr("class","sja_menuoption").attr("tabindex",0).style("position","relative").style("display","inline-block").style("padding","5px 16px 5px 9px").style("margin-left","5px").each(A).on("click",q).on("mouseover",(function(t){const e=i(t.target);e.append("div").style("margin-left","4px").classed("sjpp_deletebt",true).style("display","inline-block").style("position","absolute").style("right","0px").style("top","0px").style("transform","scale(0.6)").style("pointer-events","none").html(`<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="#000" class="bi bi-x-lg" viewBox="0 0 16 16">\n\t\t\t\t<path stroke='#f00' d="M2.146 2.854a.5.5 0 1 1 .708-.708L8 7.293l5.146-5.147a.5.5 0 0 1 .708.708L8.707 8l5.147 5.146a.5.5 0 0 1-.708.708L8 8.707l-5.146 5.147a.5.5 0 0 1-.708-.708L7.293 8 2.146 2.854Z"/>\n\t\t\t\t</svg>`)})).on("mouseout",(function(t){i(t.target).select(".sjpp_deletebt").remove()})).on("focus",(t=>{t.target.dispatchEvent(new PointerEvent("mouseover"))})).on("blur",(t=>{t.target.dispatchEvent(new PointerEvent("mouseout"))})).on("keyup",(t=>{if(t.key=="Enter")t.target.click()}));D();v.dom.clearBtn.property("disabled",!(f===null||f===void 0?void 0:f.length));const s=y!==JSON.stringify(f.map((t=>t.gene)).sort());(t=v.dom.restoreBtn)===null||t===void 0?void 0:t.property("disabled",!s);const r=h||0;v.dom.submitBtn.property("disabled",!s||(f===null||f===void 0?void 0:f.length)<r);if(s)S.node().focus()}function A(t){const e=i(this).style("border-radius","5px");if(t.mutationStat){e.html(`${t.gene}&nbsp;&nbsp;`);for(const s of t.mutationStat){let t,r;if("class"in s){if(!o[s.class])throw"invalid stat class";t=o[s.class].color;v.statColor2label.set(t,o[s.class].label)}else if("dt"in s){if(!a[s.dt])throw"invalid stat dt";t=a[s.dt];r="white";v.statColor2label.set(t,n[s.dt])}else{throw"stat missing dt/class"}e.insert("span").style("font-size",".7em").style("background-color",t).style("padding","1px 2px").style("color",r||"black").text(s.count)}}else{e.insert("div").style("display","inline-block").html(t.gene)}}function D(){if(!v.statColor2label||v.statColor2label.size==0){v.dom.statLegendDiv.style("display","none");return}v.dom.statLegendDiv.style("display","block").selectAll("*").remove();for(const[t,e]of v.statColor2label){v.dom.statLegendDiv.append("div").style("display","inline-block").style("width","12px").style("height","12px").style("background-color",t);v.dom.statLegendDiv.append("span").html(` ${e} &nbsp;&nbsp;`)}}function P(){const t=C.geneSymbol;for(const e of f){if(e.gene==t){window.alert(`The gene ${t} has already been added`);return}}f.push({gene:t});B()}function q(t,e){const s=f.findIndex((t=>t.gene===e.gene));if(s!=-1){f.splice(s,1);B()}}function E(t){let e;if(t.type=="boolean"){e=_.append("input").attr("type","checkbox").attr("id",t.id);if(t.value)e.property("checked",t.value);_.append("label").html(t.label).attr("for",t.id)}else if(t.type=="string"&&t.value){e=_.append("input").attr("type","checkbox").attr("id",t.id);e.property("checked",true);_.append("label").html(t.label).attr("for",t.id)}else if(t.type=="number"){e=_.append("input").attr("type","number").style("width","40px").attr("id",t.id);if(t.value)e.attr("value",t.value);_.append("span").html(t.label)}v.params.push({param:t,input:e})}function R({param:t,input:e}){const s=e.node().value;if(e.attr("type")=="number")return Number(s);if(e.attr("type")=="checkbox"){if(t.type=="string")return e.node().checked?t.value:"";if(t.type=="boolean")return e.node().checked?1:0}}I();B();return v}function S(t){switch(t){case"../plots/DEanalysis.js":return import("./DEanalysis-567989ff.js");case"../plots/Disco.js":return import("./Disco-5d1404ce.js");case"../plots/DziViewer.js":return import("./DziViewer-3f466d90.js");case"../plots/barchart.data.js":return import("./FilterRxComp-fc769f34.js").then((function(t){return t.y}));case"../plots/barchart.events.js":return import("./barchart.events-e24facf7.js");case"../plots/barchart.js":return import("./barchart-ef4874c8.js");case"../plots/bars.renderer.js":return import("./bars.renderer-c46d3f44.js");case"../plots/bars.settings.js":return import("./bars.settings-64bb4642.js");case"../plots/boxplot.js":return import("./boxplot-a2e1ace0.js");case"../plots/brainImaging.js":return import("./brainImaging-21701238.js");case"../plots/controls.btns.js":return import("./controls.btns-ad7b28a2.js");case"../plots/controls.config.js":return import("./controls.config-6cf816fb.js");case"../plots/controls.divide.js":return import("./controls.divide-3c0d52d7.js");case"../plots/controls.js":return import("./controls-0467d2ec.js");case"../plots/controls.overlay.js":return import("./controls.overlay-3a55c2ec.js");case"../plots/controls.term1.js":return import("./controls.term1-59f4cd60.js");case"../plots/cuminc.js":return import("./cuminc-8d21132b.js");case"../plots/dataDownload.js":return import("./dataDownload-bfa92dad.js");case"../plots/dictionary.js":return import("./dictionary-89e860ee.js");case"../plots/geneExpression.js":return import("./geneExpression-9047481a.js");case"../plots/geneORA.js":return import("./geneORA-ffb2497e.js");case"../plots/geneset.js":return import("./geneset-3522bcda.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-bef8bf99.js");case"../plots/genomeBrowser.js":return import("./genomeBrowser-9b72eb22.js");case"../plots/hierCluster.config.js":return import("./hierCluster.config-f8686a30.js");case"../plots/hierCluster.interactivity.js":return import("./hierCluster.interactivity-3b5f1e81.js").then((function(t){return t.i}));case"../plots/hierCluster.js":return import("./hierCluster-3b14b2b3.js");case"../plots/hierCluster.renderers.js":return import("./hierCluster.renderers-9f9a7cad.js").then((function(t){return t.r}));case"../plots/imagePlot.js":return import("./imagePlot-095b9a92.js");case"../plots/matrix.cells.js":return import("./matrix.cells-3620eb3a.js");case"../plots/matrix.cluster.js":return import("./matrix.cluster-15b8a865.js");case"../plots/matrix.config.js":return import("./matrix.config-8247bea5.js");case"../plots/matrix.controls.js":return import("./matrix.controls-dea65894.js");case"../plots/matrix.data.js":return import("./matrix.data-121a1a8c.js").then((function(t){return t.m}));case"../plots/matrix.dom.js":return import("./matrix.dom-83c5fa39.js");case"../plots/matrix.groups.js":return import("./matrix.groups-2e1202ef.js").then((function(t){return t.m}));case"../plots/matrix.interactivity.js":return import("./matrix.interactivity-2b076155.js");case"../plots/matrix.js":return import("./matrix-3fae58f8.js");case"../plots/matrix.layout.js":return import("./matrix.layout-8dc54c05.js").then((function(t){return t.m}));case"../plots/matrix.legend.js":return import("./matrix.legend-e0078739.js").then((function(t){return t.m}));case"../plots/matrix.renderers.js":return import("./matrix.renderers-0c8eddc9.js");case"../plots/matrix.serieses.js":return import("./matrix.serieses-2898da6b.js").then((function(t){return t.m}));case"../plots/matrix.sort.js":return import("./matrix.sort-249d4a35.js");case"../plots/matrix.sorterUi.js":return import("./matrix.sorterUi-d26208c8.js");case"../plots/plot.app.js":return import("./plot.app-c841507a.js");case"../plots/plot.brainImaging.js":return import("./plot.brainImaging-325ebded.js");case"../plots/plot.disco.js":return import("./plot.disco-621d1b8e.js");case"../plots/plot.ssgq.js":return import("./plot.ssgq-1949c207.js");case"../plots/profileBarchart.js":return import("./profileBarchart-11755d7c.js");case"../plots/profilePlot.js":return import("./profilePlot-8ee3034a.js");case"../plots/profilePolar.js":return import("./profilePolar-9fe70c32.js");case"../plots/profileRadar.js":return import("./profileRadar-0e744181.js");case"../plots/profileRadarFacility.js":return import("./profileRadarFacility-102544c5.js");case"../plots/regression.inputs.js":return import("./regression.inputs-ad548745.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-ad548745.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-1618447a.js");case"../plots/regression.js":return import("./regression.inputs-ad548745.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-25008028.js").then((function(t){return t.r}));case"../plots/sampleScatter.interactivity.js":return import("./sampleScatter.interactivity-cfa3451d.js").then((function(t){return t.a}));case"../plots/sampleScatter.js":return import("./sampleScatter-47dd82cb.js").then((function(t){return t.a}));case"../plots/sampleScatter.renderer.js":return import("./sampleScatter-47dd82cb.js").then((function(t){return t.s}));case"../plots/sampleScatter.rendererThree.js":return import("./sampleScatter.rendererThree-c5321d24.js").then((function(t){return t.c}));case"../plots/sampleView.js":return import("./sampleView-30b97c7d.js");case"../plots/scatter.js":return import("./scatter-8a337eeb.js");case"../plots/singleCellPlot.js":return import("./singleCellPlot-360eaec6.js");case"../plots/stattable.js":return import("./stattable-886f7dad.js");case"../plots/summary.js":return import("./summary-ee2045a5.js");case"../plots/survival.js":return import("./survival-d7bd3c6b.js");case"../plots/table.js":return import("./table-b4a61573.js");case"../plots/variantBrowser.js":return import("./variantBrowser-910b4bcd.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-bcf0ccc2.js");case"../plots/violin.js":return import("./violin-a41b2e2b.js");case"../plots/violin.renderer.js":return import("./violin.renderer-149310eb.js");default:return new Promise((function(e,s){(typeof 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t.c}));case"../plots/sampleView.js":return import("./sampleView-30b97c7d.js");case"../plots/scatter.js":return import("./scatter-8a337eeb.js");case"../plots/singleCellPlot.js":return import("./singleCellPlot-360eaec6.js");case"../plots/stattable.js":return import("./stattable-886f7dad.js");case"../plots/summary.js":return import("./summary-ee2045a5.js");case"../plots/survival.js":return import("./survival-d7bd3c6b.js");case"../plots/table.js":return import("./table-b4a61573.js");case"../plots/variantBrowser.js":return import("./variantBrowser-910b4bcd.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-bcf0ccc2.js");case"../plots/violin.js":return import("./violin-a41b2e2b.js");case"../plots/violin.renderer.js":return import("./violin.renderer-149310eb.js");default:return new Promise((function(e,s){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(s.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}const rt="_MASS_AUTOID_"+Math.random().toString().slice(-6);let it=(+new Date).toString().slice(-8);function ot(){return rt+"_"+it++}const at=new Set(["with_tabs","hidden","search_only","hide_search","only_buttons","with_cohortHtmlSelect"]);const nt={nav:{header_mode:"with_tabs",activeTab:0},activeCohort:0,search:{isVisible:true},plots:[],termfilter:{filter:{type:"tvslst",in:true,join:"",lst:[]}},reuse:{customTermQ:{byId:{},byName:{}}},groups:[],customTerms:[],autoSave:true};class lt{constructor(t){this.type="store";this.defaultState=nt;this.prevGeneratedId=0}validateOpts(t){const e=t.state;if(e.vocab.dslabel){if(!e.vocab.genome)throw".state[.vocab].genome missing"}else{if(!Array.isArray(e.vocab.terms))throw"vocab.terms must be an array of objects"}}validateState(){if(!at.has(this.state.nav.header_mode))throw"invalid state.nav.header_mode"}async init(){try{this.state.termdbConfig=await this.app.vocabApi.getTermdbConfig();await this.setTermfilter();await this.rehydrateGroups();await this.app.vocabApi.main({termfilter:JSON.parse(JSON.stringify(this.state.termfilter)),termdbConfig:this.state.termdbConfig});for(const[t,e]of this.state.plots.entries()){const s=await st(`../plots/${e.chartType}.js`);const r=await s.getPlotConfig(e,this.app);this.state.plots[t]=r;if(!("id"in r))r.id=`_AUTOID_${it++}_${t}`;if(r.mayAdjustConfig)r.mayAdjustConfig(r)}}catch(t){throw t}}setId(t){t.$id=this.prevGeneratedId++;if(t.$lst){for(const e of t.$lst){this.setId(e)}}}async setTermfilter(){let t=g(this.state.termfilter.filter,"filterUiRoot");if(!t){this.state.termfilter.filter.tag="filterUiRoot";t=this.state.termfilter.filter}await Promise.all(pt(this.state.termfilter.filter,this.app.vocabApi));if(!this.state.termdbConfig.selectCohort){this.state.activeCohort=-1;if(this.state.activeTab===0)this.state.activeTab=1;if(this.state.nav.header_mode==="with_cohortHtmlSelect"){console.warn(`no termdbConfig.selectCohort to use for nav.header_mode = 'with_cohortHtmlSelect'`);this.state.nav.header_mode="search_only"}}else{let e=g(this.state.termfilter.filter,"cohortFilter");if(!e){e={tag:"cohortFilter",type:"tvs",tvs:{term:JSON.parse(JSON.stringify(this.state.termdbConfig.selectCohort.term)),values:this.state.activeCohort==-1?[]:this.state.termdbConfig.selectCohort.values[this.state.activeCohort].keys.map((t=>({key:t,label:t})))}};this.state.termfilter.filter={type:"tvslst",in:true,join:"and",lst:[e,t]}}else{const t=(t,e)=>t<e?-1:1;e.tvs.values.sort(((t,e)=>t.key<e.key?-1:1));const s=JSON.stringify(e.tvs.values.map((t=>t.key)).sort(t));const r=this.state.termdbConfig.selectCohort.values.findIndex((e=>s==JSON.stringify(e.keys.sort(t))));if(this.state.activeCohort!==-1&&this.state.activeCohort!==0&&r!==this.state.activeCohort){console.log("Warning: cohortFilter will override the state.activeCohort due to mismatch")}this.state.activeCohort=r}}}async rehydrateGroups(){const t=[];for(const e of this.state.groups){t.push(...pt(e.filter,this.app.vocabApi))}await Promise.all(t)}}function pt(t,e,s=[]){if(t.type=="tvslst"){for(const r of t.lst)pt(r,e,s)}else if(t.type=="tvs"){if(!t.tvs.term.name)s.push(e.getterm(t.tvs.term.id).then((e=>{t.tvs.term=e})))}else{throw`cannot rehydrate filter.type='${t.type}'`}return s}lt.prototype.actions={app_refresh(t={}){this.state=this.copyMerge(this.toJson(this.state),t.state||{});const e=new Set;if(t.subactions){for(const s of t.subactions){this.actions[s.type].call(this,s);if(s.type.startsWith("plot_"))e.add(s.id)}}for(const s in this.state.plots){if(s.mayAdjustConfig&&!e.has(s.id)){s.mayAdjustConfig(s,t.config)}}},tab_set(t){this.state.nav.activeTab=t.activeTab},cohort_set(t){this.state.activeCohort=t.activeCohort;const e=this.state.termdbConfig.selectCohort.values[t.activeCohort];const s=g(this.state.termfilter.filter,"cohortFilter");if(!s)throw`No item tagged with 'cohortFilter'`;s.tvs.values=e.keys.map((t=>({key:t,label:t})))},async plot_prep(t){const e={id:"id"in t?t.id:ot()};if(!t.config)throw".config{} missing for plot_prep";if(t.config.chartType&&Object.keys(t.config).length==1){const e=await et(`../plots/${t.config.chartType}.js`);const s=await e.getPlotConfig(t.config,this.app);t.config=Object.assign(s,t.config)}Object.assign(e,t.config);this.state.plots.push(e)},async plot_create(t){const e=await tt(`../plots/${t.config.chartType}.js`);const s=await e.getPlotConfig(t.config,this.app);if(!("id"in t))t.id=ot();s.id=t.id;if(s.mayAdjustConfig){s.mayAdjustConfig(s,t.config)}this.state.plots.push(s)},plot_edit(t){const e=this.state.plots.find((e=>e.id===t.id));if(!e)throw`missing plot id='${t.id}' in store.plot_edit()`;this.copyMerge(e,t.config,t.opts?t.opts:{});if(e.mayAdjustConfig){e.mayAdjustConfig(e,t.config)}ut(e,this.app.vocabApi);if(t.config&&"cutoff"in t.config){e.cutoff=t.config.cutoff}else{delete e.cutoff}},plot_delete(t){const e=this.state.plots.findIndex((e=>e.id===t.id));if(e!==-1)this.state.plots.splice(e,1)},plot_nestedEdits(t){const e=this.state.plots.find((e=>e.id===t.id));if(!e)throw`missing plot id='${t.id}' in store.plot_edit_nested`;for(const s of t.edits){const t=s.nestedKeys.pop();const r=s.nestedKeys.reduce(((t,e)=>t[e]),e);r[t]=s.value}ut(e,this.app.vocabApi)},async plot_splice(t){for(const e of t.subactions){await this.actions[e.type].call(this,e)}},filter_replace(t){if("filter0"in t){this.state.termfilter.filter0=t.filter0;return}const e=t.filter?t.filter:{type:"tvslst",join:"",in:1,lst:[]};if(!t.filter.tag){this.state.termfilter.filter=e}else{const s=g(this.state.termfilter.filter,t.filter.tag);if(!s)throw`cannot replace missing filter with tag '${t.filter.tag}'`;const r=j(this.state.termfilter.filter,s.$id);if(r==s){this.state.termfilter.filter=e}else{const t=r.lst.indexOf(s);r.lst[t]=e}}},cache_termq({termId:t,q:e}){if(!t)throw`missing termId for caching custom term.q`;if(!e?.reuseId)throw`missing or empty tw.q.reuseId as cache identifier for term='${t}'`;const s=this.state.reuse.customTermQ.byId;if(!s[t])s[t]={};s[t][e.reuseId]=e;for(const t of this.state.plots){if(!(t.chartType in mt))continue;const s=mt[t.chartType](t);for(const t of s){if(t?.q?.reuseId===e.reuseId)t.q=e}}},uncache_termq({term:t,q:e}){if(!t.id)throw`missing term.id for uncaching custom term.q`;if(!e.reuseId)throw`missing qname as uncache identifier for term.id='${t.id}'`;const s=this.state.reuse.customTermQ.byId[t.id];if(!s)throw`missing term.q cache for term.id='${t.id}`;if(!(e.reuseId in s))console.warn(`q.reuseId='${e.cacheid}' not cached for term.id='${t.id}'`);else{delete s[e.reuseId];for(const t of this.state.plots){if(!(t.chartType in mt))continue;const s=mt[t.chartType](t);for(const t of s){if(t.q.reuseId===e.reuseId){delete t.q.reuseId;delete t.q.name}}}}},add_customTerm(t){this.state.customTerms.push(t.obj)},delete_customTerm({name:t}){const e=this.state.customTerms.findIndex((e=>e.name==t));if(e!=-1)this.state.customTerms.splice(e,1)},add_group(t){if(this.state.nav.header_mode!="hidden"){const e=t.obj;const s=`Group ${this.state.groups.length+1}`;const r=Z([e]);const i={name:s,filter:Y(r),plotId:e.plotId};this.state.groups.push(i);this.state.nav.activeTab=1}else if("plotId"in t.obj){const e=this.state.plots.find((e=>e.id==t.obj.plotId));if(e.groups){t.obj.index=e.groups.length;t.obj.name=`Group ${e.groups.length+1}`;e.groups.push(t.obj)}}},rename_group(t){const e=t.index;const s=t.newName;if(this.state.nav.header_mode!="hidden"){this.state.groups[e].name=s}else{for(const t of this.state.plots){if(t?.groups){t.groups[e].name=s}}}},change_color_group(t){const e=t.index;const s=t.newColor;if(this.state.nav.header_mode!="hidden"){this.state.groups[e].color=s}else{for(const t of this.state.plots){if(t?.groups){t.groups[e].color=s}}}},delete_group({name:t}){if(this.state.nav.header_mode!="hidden"){const e=this.state.groups.findIndex((e=>e.name==t));if(e!=-1)this.state.groups.splice(e,1)}else{for(const e of this.state.plots){if(e?.groups){const s=e.groups.findIndex((e=>e.name==t));if(s!=-1)e.groups.splice(s,1)}}}}};const ct=t=>[t.term0,t.term,t.term2].filter((t=>!!t));const mt={summary:ct,survival:ct,cuminc:ct,regression:t=>[t.outcome,...t.independent].filter((t=>!!t)),matrix:t=>t.termgroups.reduce(((t,e)=>{t.push(...e.lst);return t}),[])};const dt=m(lt);function ut(t,e){if(!("id"in t))throw"plot error: plot.id missing";try{if(t.chartType=="regression"){ft(t,e)}else if(t.chartType=="matrix"||t.chartType=="hierCluster"){if(!t.termgroups)throw`plot error: missing the config.termgroups for '${t.chartType}'`;if(!Array.isArray(t.termgroups))`plot error: config.termgroups must be an array '${t.chartType}'`;if(!t.samplegroups)throw`plot error: missing the config.samplegroups for '${t.chartType}'`;if(!Array.isArray(t.samplegroups))`plot error: config.samplegroups must be an array '${t.chartType}'`}else if(t.chartType=="dataDownload"){if(!t.terms)throw`plot error: missing the config.terms for '${t.chartType}'`;if(!Array.isArray(t.terms))`plot error: config.terms must be an array '${t.chartType}'`;for(const s of t.terms){gt(s,e)}}else if(t.chartType=="sampleScatter"){if(!t.name)throw`plot error: missing the plot name for '${t.chartType}'`;if(!t.colorTW)`plot error: missing the plot color term wrapper for '${t.chartType}'`;if(!t.file)`plot error: missing the plot coordinates file for '${t.chartType}'`}else if(t.chartType=="genomeBrowser"){}else if(t.chartType=="Disco"){}else if(t.chartType=="profileBarchart"){}else if(t.chartType=="profilePolar"||t.chartType=="polar"){}else if(t.chartType=="DEanalysis"){}else if(t.chartType=="geneORA"){}else if(t.chartType=="sampleView"){}else if(t.chartType=="profileRadar"||t.chartType=="profileRadarFacility"){}else if(t.chartType=="singleCellPlot"){}else if(t.chartType=="brainImaging"){}else{ht(t,e)}}catch(t){throw t}}function ht(t,e){try{if(t.term)gt(t.chartType=="regression"?t.outcome:t.term,e)}catch(t){throw"plot.term error: "+t}if(t.term2){try{gt(t.term2,e)}catch(t){throw"plot.term2 error: "+t}if(t.term.term.type=="condition"&&t.term.term.id==t.term2.term.id){if(t.term.q.bar_by_grade&&t.term2.q.bar_by_grade)throw"plot error: term2 is the same CHC, but both cannot be using bar_by_grade";if(t.term.q.bar_by_children&&t.term2.q.bar_by_children)throw"plot error: term2 is the same CHC, but both cannot be using bar_by_children"}}if(t.term0){try{gt(t.term0,e)}catch(t){throw"plot.term0 error: "+t}}}function ft(t,e){if(!t.outcome)throw"plot error: plot.outcome{} not an object";try{gt(t.chartType=="regression"?t.outcome:t.term,e)}catch(t){throw"plot.outcome error: "+t}if(t.independent){for(const s of t.independent){gt(s,e)}}}function gt(t,e){if(!t.term)throw".term{} missing";if(!e.graphable(t.term))throw".term is not graphable (not a valid type)";if(!t.term.name)throw".term.name missing";if(!t.q)throw".q{} missing";switch(t.term.type){case"integer":case"float":case"survival":break;case"categorical":if(t.q.groupsetting&&!t.q.groupsetting.disabled){if(!t.term.values)throw".values{} missing when groupsetting is allowed"}break;case"condition":if(!t.term.values)throw".values{} missing";if(!t.q.bar_by_grade&&!t.q.bar_by_children)throw"neither q.bar_by_grade or q.bar_by_children is set to true";if(!t.q.value_by_max_grade&&!t.q.value_by_most_recent&&!t.q.value_by_computable_grade)throw"neither q.value_by_max_grade or q.value_by_most_recent or q.value_by_computable_grade is true";break;case"snplst":case"snplocus":case"geneVariant":break;case"samplelst":break;case b.GENE_EXPRESSION:break;case b.METABOLITE_INTENSITY:break;default:if(t.term.isgenotype){console.log('to add in type:"genotype"');break}throw`unknown term type='${t.term.type}'`}}class jt{constructor(t={}){this.type="recover";this.initialHolderDisplay=t.holder.style("display");this.dom={holder:t.holder,btnDiv:t.holder.append("div").style("position","sticky").style("top","12px").style("right","20px").style("margin",t.margin?t.margin:"10px").style("text-align","right")};this.hasStatePreMain=true;this.reactsTo=t.reactsTo||(()=>true);this.getState=t.getState||(t=>t);this.debouncedTrack=()=>{this.trackPending=true;this.trackState();this.render()};this.wait="wait"in t?t.wait:800;this.maxHistoryLen=t.maxHistoryLen||10}preApiFreeze(t){t.replaceLastState=t=>{if(this.isRecovering)return;this.state=this.getState(t);if(!this.trackPending)this.history[this.currIndex]=this.state}}init(){this.app.register(this.api);this.currIndex=-1;this.history=[];this.isActive=!isNaN(this.maxHistoryLen)&&+this.maxHistoryLen>0;if(this.isActive){yt(this);this.initUi()}this.eventTypes=["postInit","postRender"]}async main(){if(!this.isActive)return;if(this.opts.hide?.(this.state)){this.dom.holder.style("display","none");return}this.dom.holder.style("display",this.initialHolderDisplay||"");if(!this.timedTrack){this.trackState();this.trackPending=true;this.timedTrack=setTimeout((()=>{}),this.wait);return}clearTimeout(this.timedTrack);this.trackPending=true;this.timedTrack=setTimeout(this.debouncedTrack,this.wait)}trackState(){if(this.isRecovering){this.isRecovering=false;return}if(this.state._scope_=="none")return;this.isRecovering=false;const t=this.opts.adjustTrackedState?this.opts.adjustTrackedState(this.state):this.state;if(!t){console.error("no state to track");return}if(!Object.isFrozen(t))d(t);if(this.currIndex==-1)this.origState=t;if(this.currIndex<this.history.length-1){this.history.splice(this.currIndex,this.history.length-(this.currIndex+1))}if(u(t,this.history[this.history.length-1]))return;this.history.push(t);this.currIndex+=1;if(this.history.length>this.maxHistoryLen){this.history.splice(1,1);this.currIndex+=-1}this.trackPending=false}goto(t){if(t<0&&this.currIndex+t>-1)this.currIndex+=t;else if(t>0&&this.currIndex+t<this.history.length)this.currIndex+=t;else return;this.isRecovering=true;const e=this.history[this.currIndex];this.render();if(this.opts.plot_id){const t=structuredClone(e);this.app.dispatch({type:"plot_edit",id:this.opts.plot_id,config:t.config,_scope_:t._scope_})}else{this.app.dispatch({type:"app_refresh",state:e})}}reset(){this.currIndex=0;this.isRecovering=true;const t=this.origState;if(this.opts.plot_id){const e=t.plots.find((t=>t.id===this.opts.plot_id));this.app.dispatch({type:"plot_edit",id:this.opts.plot_id,config:structuredClone(e)})}else this.app.dispatch({type:"app_refresh",state:t})}}const bt=l(jt);function yt(t){t.initUi=function(){t.dom.undoBtn=t.dom.btnDiv.append("button").attr("title","undo the previous action").property("disabled",true).style("margin","0 0 0 4px").style("border","1px solid #ccc").style("vertical-align","middle").html(t.opts.undoHtml||`<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="#000" class="bi bi-arrow-counterclockwise" viewBox="0 0 16 16" style='vertical-align: middle'>\n\t\t\t  <path stroke='#000' stroke-width='0.25' fill-rule="evenodd" d="M8 3a5 5 0 1 1-4.546 2.914.5.5 0 0 0-.908-.417A6 6 0 1 0 8 2v1z"/>\n\t\t\t  <path d="M8 4.466V.534a.25.25 0 0 0-.41-.192L5.23 2.308a.25.25 0 0 0 0 .384l2.36 1.966A.25.25 0 0 0 8 4.466z"/>\n\t\t\t</svg>`).on("click",(()=>t.goto(-1)));t.dom.redoBtn=t.dom.btnDiv.append("button").attr("title","redo a subsequent action").property("disabled",true).style("margin",t.opts.resetHtml?"0":"0 4px 0 0").style("border","1px solid #ccc").style("vertical-align","middle").html(t.opts.redoHtml||`<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="#000" class="bi bi-arrow-clockwise" viewBox="0 0 16 16" style='vertical-align: middle'>\n\t\t\t  <path stroke='#000' stroke-width='0.25' fill-rule="evenodd" d="M8 3a5 5 0 1 0 4.546 2.914.5.5 0 0 1 .908-.417A6 6 0 1 1 8 2v1z"/>\n\t\t\t  <path d="M8 4.466V.534a.25.25 0 0 1 .41-.192l2.36 1.966c.12.1.12.284 0 .384L8.41 4.658A.25.25 0 0 1 8 4.466z"/>\n\t\t\t</svg>`).on("click",(()=>t.goto(1)));if(t.opts.resetHtml)t.dom.resetBtn=t.dom.btnDiv.append("button").attr("title","Restore the initial rendered state").property("disabled",true).style("margin","0 4px 0 0").style("border","1px solid #ccc").style("vertical-align","middle").html(t.opts.resetHtml).on("click",(()=>t.reset()))};t.render=function(){if(t.dom.undoBtn)t.dom.undoBtn.property("disabled",t.currIndex<1||t.history.length===1);if(t.dom.redoBtn)t.dom.redoBtn.property("disabled",t.history.length<2||t.currIndex>=t.history.length-1);if(t.dom.resetBtn)t.dom.resetBtn.property("disabled",t.currIndex===0)}}export{Y as a,Z as b,B as c,W as d,Q as e,J as f,$ as g,X as h,A as i,V as j,k,K as l,U as o,bt as r,dt as s};

package/dist/{regression.inputs-5718cf72.js → regression.inputs-ad548745.js}

@@ -1 +1 @@
-import{f as t,t as e}from"./termsetting-9a7511e6.js";import{az as i,aS as s,ac as n,M as o,q as r}from"./app-f91922b4.js";import{d as a,u as c}from"./FilterRxComp-0e75dd8d.js";import{InputValuesTable as p}from"./regression.inputs.values.table-d587c1cf.js";import{mayRunSnplstTask as d}from"./snplst.sampleSum-e47d05f0.js";import{R as l}from"./regression.results-748024be.js";class m{constructor(t){this.type="regression";this.genomeObj=t.app.opts.genome}async init(t){this.dom={header:this.opts.header,errordiv:this.opts.holder.append("div"),inputs:this.opts.holder.append("div").style("margin","20px 10px"),results:this.opts.holder.append("div").style("margin-left","40px")};const e=t.plots.find((t=>t.id===this.id));this.inputs=new O({app:this.app,parent:this,id:this.id,holder:this.dom.inputs,regressionType:e.regressionType});this.results=new l({app:this.app,parent:this,id:this.id,holder:this.dom.results,regressionType:e.regressionType})}getState(t,e){const i=t.plots.find((t=>t.id===this.id));if(!i){throw`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`}if(!i.regressionType)throw"regressionType is required";return{vocab:t.vocab,formIsComplete:i.outcome&&i.independent.length,activeCohort:t.activeCohort,termfilter:t.termfilter,config:i,allowedTermTypes:t.termdbConfig.allowedTermTypes,minTimeSinceDx:t.termdbConfig.minTimeSinceDx}}async main(){try{this.config=JSON.parse(JSON.stringify(this.state.config));this.mayUpdateSandboxHeader();this.getFilter();await this.inputs.main();await this.results.main();this.inputs.resetSubmitButton()}catch(t){if(this.inputs.hasError){this.results.main()}n(this.dom.errordiv,"Error: "+(t.error||t));if(t.stack)console.log(t.stack)}}mayUpdateSandboxHeader(){if(!this.dom.header)return;const t=this.config.outcome;this.dom.header.html((t?t.term.name:"")+'<span style="opacity:.6;font-size:.7em;margin-left:10px;">'+this.config.regressionType.toUpperCase()+" REGRESSION</span>")}getFilter(){const t=[];if(this.state.termfilter?.filter)t.push(this.state.termfilter.filter);const e=[this.config.outcome,...this.config.independent];const i=e.filter((t=>t?.q.restrictAncestry));if(i.length){if(i.length>1){const t=new Set(i.map((t=>t.q.restrictAncestry.name)));if(t.size>1)throw"samples cannot be restricted to more than 1 ancestry"}const e=i[0];t.push({type:"tvs",tvs:e.q.restrictAncestry.tvs});this.inputs.dom.submitMsg.style("display","block").text(`restricting analysis to samples of ${e.q.restrictAncestry.name}`)}else{this.inputs.dom.submitMsg.style("display","none")}this.filter={type:"tvslst",join:"and",lst:t}}}const u=i(m);const f=u;let h=1;async function g(e,i){if(!e.outcome){e.outcome={}}{const s=i.opts.state.plots.find((t=>t.chartType=="regression"));if(!s)throw"regression plot missing in state";await t(e.outcome,i.vocabApi,y(s.regressionType,"outcome"))}const n="id"in e?e.id:`_REGRESSION_${h++}`;const o={id:n};o.outcome=e.outcome;if(e.independent){if(!Array.isArray(e.independent))throw".independent[] is not array";for(const s of e.independent){const e=!s.q?.mode?{numeric:{mode:"continuous"}}:undefined;await t(s,i.vocabApi,e)}o.independent=e.independent;delete e.independent}else{o.independent=[]}return s(o,e)}function y(t,e=""){const i={};i["numeric"]=t=="logistic"&&e=="outcome"?{mode:"binary"}:{mode:"discrete"};i["categorical"]=t=="logistic"&&e=="outcome"?{mode:"binary"}:{mode:"discrete"};if(e=="outcome"){if(t=="cox"){i.condition={mode:"cox"}}if(t=="logistic"){i.condition={mode:"binary"}}}return i}function b(t,e){const i=[{label:"Linear",type:"linear"},{label:"Logistic",type:"logistic"},{label:"Cox",type:"cox"}];for(const{label:s,type:n}of i){t.append("div").attr("class","sja_menuoption sja_sharp_border").text(s).on("click",(()=>{e.dom.tip.hide();e.prepPlot({config:{chartType:"regression",regressionType:n,independent:[]}})}))}}var v=Object.freeze({__proto__:null,regressionInit:u,componentInit:f,getPlotConfig:g,get_defaultQ4fillTW:y,makeChartBtnMenu:b});class x{constructor(t){this.opts=t;this.section=t.section;this.term=t.term;this.parent=t.parent}async init(t){const i=t.append("div");const s=i.append("span").style("display","inline-block");const n=i.append("span").style("margin-left","20px");this.dom={holder:t,termRow:i,pillDiv:s,interactionDiv:n,err_div:t.append("div").style("display","none").style("padding","5px").style("background-color","rgba(255,100,100,0.2)"),infoDiv:t.append("div"),tip:new o};try{const{app:t,config:i,state:s,disable_terms:n}=this.parent;const o={placeholder:this.section.selectPrompt,placeholderIcon:this.section.placeholderIcon,holder:this.dom.pillDiv,vocabApi:t.vocabApi,noTermPromptOptions:this.opts.noTermPromptOptions,activeCohort:s.activeCohort,debug:t.opts.debug,menuOptions:this.section.configKey=="outcome"?"{edit,reuse,replace}":"{edit,reuse,remove}",usecase:{target:"regression",detail:this.section.configKey,regressionType:i.regressionType},disable_terms:n,abbrCutoff:50,genomeObj:this.parent.parent.genomeObj,defaultQ4fillTW:y(i.regressionType,this.section.configKey),callback:t=>{this.parent.editConfig(this,t)}};this.furbishTsConstructorArg(o);this.pill=await e(o);if(this.section.configKey=="outcome"){this.setQ=S(i.regressionType)}this.valuesTable=new p({holder:this.dom.infoDiv,input:this,callback:t=>{this.parent.editConfig(this,t)}})}catch(t){this.displayError([t])}}furbishTsConstructorArg(t){const e=this.parent.config.regressionType;if(this.section.configKey=="outcome"){if(e=="logistic"){t.numericEditMenuVersion=["binary"];return}if(e=="linear"){t.numericEditMenuVersion=["continuous"];return}if(e=="cox"){return}throw"unknown regressionType"}if(this.section.configKey=="independent"){t.numericEditMenuVersion=["continuous","discrete","spline"];return}throw"unknown section.configKey: "+this.section.configKey}displayError(t){this.hasError=true;this.dom.err_div.selectAll("*").remove();this.dom.err_div.style("display","block").selectAll("div").data(Array.isArray(t)?t:[t]).enter().append("div").text((t=>t));this.parent.handleError();console.error(t)}async main(){const t=this.term;if(t){delete t.error}this.dom.err_div.style("display","none").text("");this.hasError=false;const e=[];try{if(t&&this.setQ){const{app:e,state:i}=this.parent;await this.setQ[t.term.type](t,e.vocabApi,this.parent.parent.filter,i)}try{await this.updateTerm()}catch(t){e.push(t)}await this.pill.main(this.getPillArgs());this.renderInteractionPrompt();await this.valuesTable.main();const i=t&&t.error||this.pill.error;if(i)e.push(i);if(e.length)throw e}catch(e){this.displayError(e)}}async updateTerm(){const t=this.term;if(!t)return;if(!t.q)throw".term.q missing on this input";if(!t.q.mode&&a(t.term.type)){if(t.term.type=="categorical"||t.term.type=="condition"||t.term.type=="survival")t.q.mode="discrete";else t.q.mode="continuous"}const e=t.term.type=="snplst"||t.term.type=="snplocus"?{cacheid:t.q.cacheid}:{term1_q:t.q};const i=await this.parent.app.vocabApi.getCategories(t.term,this.parent.parent.filter,e);if(!i)throw`no data for term.id='${t.term.id}'`;if(i.error)throw i.error;d(t,i);this.termStatus={topInfoStatus:[],bottomSummaryStatus:undefined,sampleCounts:undefined,excludeCounts:undefined,allowToSelectRefGrp:false};if(t.q.numOfSampleWithAnyValidGT){const e=t.term.snps.reduce(((t,e)=>t+(e.invalid?1:0)),0);this.termStatus.topInfoStatus.push(`${t.q.numOfSampleWithAnyValidGT} samples with valid genotypes`+(e>0?` ${e} invalid SNP${e>1?"s":""}.`:""))}if("geneticModel"in t.q){this.termStatus.topInfoStatus.push("Genetic model: "+(t.q.geneticModel==0?"Additive":t.q.geneticModel==1?"Dominant":t.q.geneticModel==2?"Recessive":"By genotype"))}if(t.q.restrictAncestry){this.termStatus.topInfoStatus.push("Analyzing "+t.q.restrictAncestry.name);if(t.q.restrictAncestry.PCcount){this.termStatus.topInfoStatus.push(`Adjusting for top ${t.q.restrictAncestry.PCcount} ancestry principal components`)}}if(t.term.reachedVariantLimit){this.termStatus.topInfoStatus.push(`<span class=sja_mcdot style="background:#aaa;font-size:1em">\n\t\t\t\t&nbsp;&#9888; Restricted to first ${t.term.snps.length}\n\t\t\t\tvariants of this region.&nbsp;</span> Try zooming in.`)}this.orderedLabels=i.orderedLabels;if(i.lst){this.summarizeSample(t,i.lst);if(t.term.type=="float"||t.term.type=="integer"){if(t.q.mode!="continuous"&&t.q.mode!="spline"){this.termStatus.allowToSelectRefGrp=true}if(t.q.scale&&t.q.scale!=1)this.termStatus.topInfoStatus.push(`Scale: Per ${t.q.scale}`);if(t.q.mode=="discrete"){this.termStatus.topInfoStatus.push(`Discrete variable with ${this.termStatus.sampleCounts.length} bins`)}if(t.q.mode=="spline"){this.termStatus.topInfoStatus.push(`Cubic spline variable with ${t.q.knots.length} knots: ${t.q.knots.map((t=>Number(t.value))).sort(((t,e)=>t-e)).join(", ")}`)}}else if(t.term.type=="categorical"){this.termStatus.allowToSelectRefGrp=true}else if(t.term.type=="condition"){if(this.section.configKey=="outcome"&&this.parent.opts.regressionType=="logistic"){this.termStatus.allowToSelectRefGrp=true}if(this.section.configKey=="outcome"&&this.parent.opts.regressionType=="cox"){if(!["age","time"].includes(t.q.timeScale))throw"invalid q.timeScale";const e=this.parent.app.vocabApi.termdbConfig;this.termStatus.topInfoStatus.push(`Time axis: ${t.q.timeScale=="time"?e.timeUnit:"age"}`);this.termStatus.topInfoStatus.push(`<span style="padding-left: 10px;">-start: ${t.q.timeScale=="time"?" ":"age at "}entry into the cohort (i.e., ${e.cohortStartTimeMsg})</span>`);this.termStatus.topInfoStatus.push(`<span style="padding-left: 10px;">-end: ${t.q.timeScale=="time"?" ":"age at "}event or censoring/death</span>`);const i=Object.keys(t.term.values).map(Number);const s=Math.max(...i);this.termStatus.topInfoStatus.push(`<div style="padding-top: 8px;">Event: first occurrence of grade ${t.q.breaks[0]===s?t.q.breaks[0]:`${t.q.breaks[0]}-${s}</div>`}`)}}this.maySet_refGrp(t)}}summarizeSample(t,e){const i=new Set;if(t.term.values){for(const e in t.term.values){if(t.term.values[e].uncomputable)i.add(t.term.values[e].label)}}if(t.q.mode=="cox"){const t=e.find((t=>t.key==-1));if(t)i.add(t.label)}const s=this.termStatus.sampleCounts=e.filter((t=>!i.has(t.label)));const n=this.termStatus.excludeCounts=e.filter((t=>i.has(t.label)));const o={included:0,excluded:0,total:0};s.forEach((t=>o.included+=t.samplecount));n.forEach((t=>o.excluded+=t.samplecount));o.total=o.included+o.excluded;if(t.term.type=="condition"&&o.total){o.excluded=o.total-o.included}this.termStatus.bottomSummaryStatus=`${o.included} samples included`+(o.excluded?`. ${o.excluded} samples excluded:`:"");if(t&&t.q.mode!=="continuous"&&s.length<2)throw`there should be two or more discrete values with samples for variable='${t.term.name}'`}maySet_refGrp(t){if(this.section.configKey=="outcome"&&this.parent.config.regressionType=="cox"){return}if(t.q.mode=="continuous"){t.refGrp="NA";return}const e=this.termStatus.sampleCounts;if(!("refGrp"in t)||!e.find((e=>e.key==t.refGrp))){const i=this.orderedLabels;if(i&&i.length)e.sort(((t,e)=>i.indexOf(t.key)-i.indexOf(e.key)));else e.sort(((t,e)=>t.samplecount<e.samplecount?1:-1));t.refGrp=e[0].key}}getPillArgs(){const t=this.section;const{config:e,state:i,disable_terms:s}=this.parent;const n=Object.assign({activeCohort:i.activeCohort,disable_terms:s,usecase:{target:"regression",detail:t.configKey,regressionType:e.regressionType}},this.term);n.filter=this.parent.parent.filter;return n}remove(){this.dom.termRow.transition().duration(500).style("opacity",0).remove();for(const t in this.dom){delete this.dom[t]}}renderInteractionPrompt(){this.dom.interactionDiv.style("display","none");if(!this.term)return;if(this.section.configKey!="independent")return;if(this.term.q.mode=="spline")return;{let t=0;for(const e of this.section.inputLst){if(e.term&&e.term.q.mode!="spline"){t++}}if(t<2)return}const t=this.term.interactions.length;this.dom.interactionDiv.style("display","inline").html(t==0?"Add interactions":`${t} interaction${t>1?"s":""}`).style("padding","5px").style("background-color",t==0?null:"#ececec").style("border-radius",t==0?null:"6px").style("color",t==0?"rgb(153, 153, 153)":"#000").style("font-size",t==0?"0.8em":"").style("cursor","pointer").on("click",(()=>this.renderInteractionOptions()))}renderInteractionOptions(){const t=this;t.dom.tip.clear().showunder(t.dom.interactionDiv.node());t.dom.tip.d.append("div").style("padding","5px").style("font-size","0.8em").style("color","rgb(153, 153, 153)").html(`Selected variables will each form pairwise interaction with ${this.term.term.name}`);t.dom.tip.d.append("div").selectAll("div").data(t.parent.config.independent.filter((e=>e&&e.term.id!==t.term.term.id&&e.q.mode!="spline"))).enter().append("div").style("margin","5px").each((function(e){const i=r(this).append("label");i.append("input").attr("type","checkbox").property("checked",t.term.interactions.includes(e.term.id));i.append("span").text(" "+e.term.name)}));t.dom.tip.d.append("button").text("Apply").style("margin","5px").on("click",(()=>{t.dom.tip.hide();t.term.interactions=[];t.dom.tip.d.selectAll("input").each((function(e){if(r(this).property("checked"))t.term.interactions.push(e.term.id)}));for(const e of t.parent.config.independent){const i=e.interactions.indexOf(t.term.term.id);if(t.term.interactions.includes(e.term.id)){if(i==-1)e.interactions.push(t.term.term.id)}else if(i!=-1){e.interactions.splice(i,1)}}t.parent.editConfig(t,t.term)}))}}function S(t){return{integer:t=="logistic"?w:_,float:t=="logistic"?w:_,geneExpression:t=="logistic"?w:_,categorical:q,condition:T,survival:T}}async function w(t,e,i,s){if(t.q.mode=="binary"&&t.q.lst&&t.q.lst.length==2){t.q.mode="binary";return}const n=await e.getPercentile(t.term.id,[50],i);if(n.error||!n.values.length||!Number.isFinite(n.values[0]))throw"cannot get median value: "+(n.error||"no data");const o=t.term.type=="integer"?Math.round(n.values[0]):Number(n.values[0].toFixed(2));t.q={mode:"binary",type:"custom-bin",lst:[{startunbounded:true,stopinclusive:true,stop:o},{stopunbounded:true,startinclusive:false,start:o}]};t.q.lst.forEach((e=>{e.label=c(e,t.q)}));t.refGrp=t.q.lst[0].label}function T(t,e,i,s){if(s.config.regressionType=="logistic"){if(!t.refGrp)t.refGrp=t.q.groups[0].name}if(s.config.regressionType=="cox"){if(!t.q.timeScale)t.q.timeScale="time"}}async function q(t,e,i,s){const{term:n,q:o}=t;if(o.mode=="binary"){if(o.type=="values"&&Object.keys(n.values).length==2)return;if(o.type=="predefined-groupset"){const t=o.groupsetting.predefined_groupset_idx;const e=n.groupsetting;if(e[t]&&Object.keys(e[t]).length==2)return}if(o.type=="custom-groupset"){const t=o.groupsetting.customset;if(t.groups.length==2)return}}const r={term1_q:o};const a=await e.getCategories(n,i,r);if(a.error)throw"cannot get categories: "+a.error;const c=new Map;const p=[];let d=false;const l=n.type=="condition"&&n.groupsetting.lst.length;if(n.groupsetting&&n.groupsetting.inuse){for(const t of n.groupsetting.lst[0].groups){if(t.type=="filter"&&t.filter4activeCohort){d=true}}}for(const t of a.lst){c.set(t.key,t.samplecount);if(n.values&&n.values[t.key]&&n.values[t.key].uncomputable)continue;p.push(t.key)}if(p.length<2&&!d&&!l){o.type="values";t.error="less than 2 categories/grades - cannot create separate groups";return}if(p.length==2&&!d&&!l){o.type="values";return}const m=n.groupsetting;const u=o.groupsetting;u.inuse=true;u.activeCohort=e.state.activeCohort;if(u.customset&&u.customset.groups&&u.customset.groups.length==2&&k(u.customset,c)){o.type="custom-groupset";return}if(m&&m.lst){if(u.predefined_groupset_idx>=0&&m.lst[u.predefined_groupset_idx]&&m.lst[u.predefined_groupset_idx].groups.length==2&&k(m.lst[u.predefined_groupset_idx],c)){o.type="predefined-groupset";return}const t=m.lst.findIndex((t=>t.groups.length==2));if(t!=-1&&k(m.lst[t],c)){u.predefined_groupset_idx=t;o.type="predefined-groupset";return}}const f={activeCohort:s.activeCohort,groups:[{name:"Group 1",type:"values",values:[]},{name:"Group 2",type:"values",values:[]}]};const h=Math.round(p.length/2);for(const[t,e]of p.entries()){if(t<h)f.groups[0].values.push({key:e});else f.groups[1].values.push({key:e})}u.customset=f;o.type="custom-groupset"}function _(t){if(!t.q.type){console.log("may not happen: why is input.term.q not yet set for numeric term at this point")}t.q.mode="continuous"}function k(t,e){for(const i of t.groups){let t=0;if(i.type=="values"){for(const s of i.values)t+=e.get(s.key)||0;if(t==0)return false}}return true}var A=Object.freeze({__proto__:null,InputTerm:x});const C=[{termtype:"snplst",html:"A list of variants"},{termtype:"snplocus",html:"Variants in a locus"},{termtype:"prs",text:"Polygenic risk score"}];class O{constructor(t){this.opts=t;this.app=t.app;this.parent=t.parent;E(this);I(this);this.createSectionConfigs();this.initUI()}createSectionConfigs(){this.outcome={heading:"Outcome variable",selectPrompt:this.opts.regressionType=="linear"?"Select continuous outcome variable":"Select outcome variable",placeholderIcon:"",configKey:"outcome",limit:1,usecase:{target:"regression",regressionType:this.opts.regressionType,detail:"outcome"},inputLst:[],dom:{}};this.independent={heading:"Independent variable(s)",selectPrompt:"Add independent variable",placeholderIcon:"",configKey:"independent",limit:10,usecase:{target:"regression",regressionType:this.opts.regressionType,detail:"independent"},inputLst:[],dom:{}};this.sections=[this.outcome,this.independent]}async main(){try{this.config=this.parent.config;this.state=this.parent.state;this.hasError=false;this.setDisableTerms();const t=[];for(const e of this.sections){await this.renderSection(e);for(const i of e.inputLst){i.dom.holder.style("border-left",i.term?"1px solid #bbb":"");t.push(i.main())}}await Promise.all(t);for(const t of this.sections){for(const e of t.inputLst){if(e.term&&e.term.error||e.hasError){this.hasError=true}}}}catch(t){this.hasError=true;throw t}}setDisableTerms(){this.disable_terms=[];if(this.config.outcome&&this.config.outcome.term)this.disable_terms.push(this.config.outcome.term);if(this.config.independent){for(const t of this.config.independent){this.disable_terms.push(t.term)}}}handleError(){this.hasError=true;this.dom.submitBtn.property("disabled",true)}getNoTermPromptOptions(t){if(t.configKey!="independent")return;const e=[];for(const i of C){if(!this.state.allowedTermTypes.includes(i.termtype)){continue}if(t.inputLst.find((t=>t.term&&t.term.term.type==i.termtype))){continue}e.push(i)}if(e.length){e.unshift({isDictionary:true,text:"Dictionary variable"})}return e}}function I(t){t.initUI=()=>{const e=t.opts.holder.append("div").style("display","block");t.dom={div:t.opts.holder,controls:e,body:e.append("div"),foot:e.append("div").style("margin","0px 20px").style("display","flex").style("align-items","center").style("gap","20px")};t.dom.submitBtn=t.dom.foot.append("div").append("button").style("display","none").style("padding","5px 15px").style("border-radius","15px").style("cursor","pointer").text("Run analysis").on("click",t.submit);t.dom.submitMsg=t.dom.foot.append("div").style("display","none").style("color","#cc0000").style("font-style","italic").style("font-size","0.8em");for(const e of t.sections){const i=t.dom.body.append("div");t.addSection(e,i)}};t.addSection=function(t,e){e.style("display","none").style("margin","3px 5px").style("padding","3px 5px");t.dom={holder:e,headingDiv:e.append("div").style("margin","3px 5px 20px 5px").style("font-size","17px").style("color","#bbb").text(t.heading),inputsDiv:e.append("div")}};t.renderSection=function(n){n.dom.holder.style("display",n.configKey=="outcome"||t.config.outcome?"block":"none");e(n);const o=n.dom.inputsDiv.selectAll(":scope > div").data(n.inputLst,(t=>t.term&&t.term.term.id));o.exit().each(s);o.enter().append("div").each(i)};function e(e){const i=t.config[e.configKey];const s=Array.isArray(i)?i:i?[i]:[];for(const n of s){if(e.configKey=="independent"){if(!n.interactions)n.interactions=[];for(const t of n.interactions){const e=i.find((e=>e.term.id==t));if(!e)throw"interacting partner not found in independents: "+t;if(!e.interactions)e.interactions=[];if(!e.interactions.includes(n.term.id))e.interactions.push(n.term.id)}}const s=e.inputLst.find((t=>t.term&&t.term.term.id==n.term.id));if(!s){e.inputLst.push(new x({section:e,term:n,parent:t}))}else{s.term=n}}$(e,t)}async function i(t){await t.init(r(this).style("width","fit-content").style("margin","0px 15px 35px 25px").style("padding","0px 5px"))}function s(t){t.remove();for(const e in t.dom){delete t.dom[e]}const e=r(this);e.transition().duration(500).style("opacity",0).remove()}t.resetSubmitButton=()=>{t.dom.submitBtn.text("Run analysis").style("display",t.config.outcome&&t.config.independent.length?"block":"none").property("disabled",t.hasError)}}function E(t){t.editConfig=async(e,i)=>{if(!i){const t=e.section.inputLst.findIndex((t=>t===e));if(t==-1)throw`deleting an unknown input`;e.section.inputLst.splice(t,1);if(e.term){for(const t of e.section.inputLst){if(!t.term||!t.term.interactions)continue;const i=t.term.interactions.indexOf(e.term.term.id);if(i!=-1)t.term.interactions.splice(i,1)}}}else{const t=e.term;if(t&&i.term.id===t.term.id){for(const e in t){if(!(e in i))i[e]=t[e]}}e.term=i;if(i.q.mode=="spline"&&i.interactions){for(const t of e.section.inputLst){if(!t.term||!t.term.interactions)continue;const i=t.term.interactions.indexOf(e.term.term.id);if(i!=-1)t.term.interactions.splice(i,1)}i.interactions=[]}}const s=[];for(const t of e.section.inputLst){if(t.term)s.push(t.term)}const n=e.section.configKey;const o=Array.isArray(t.config[n])?s:s[0];t.app.dispatch({type:"plot_edit",id:t.parent.id,chartType:"regression",config:{hasUnsubmittedEdits:true,[n]:JSON.parse(JSON.stringify(o))}})};t.submit=()=>{t.dom.submitBtn.property("disabled",true);if(t.hasError){alert("Please fix the input variable errors (highlighted in red background).");return}const e=JSON.parse(JSON.stringify(t.config));e.hasUnsubmittedEdits=false;t.app.dispatch({type:"plot_edit",id:t.parent.id,chartType:"regression",config:e})}}function $(t,e){if(t.inputLst.length>=t.limit){return}const i=t.inputLst.find((t=>!t.term));if(i){const s=e.getNoTermPromptOptions(t);if(s){i.pill.main({noTermPromptOptions:s})}return}t.inputLst.push(new x({section:t,parent:e,noTermPromptOptions:e.getNoTermPromptOptions(t)}))}var P=Object.freeze({__proto__:null,RegressionInputs:O});export{A as a,P as b,v as r};
+import{f as t,t as e}from"./termsetting-636d2271.js";import{az as i,aS as s,ac as n,M as o,q as r}from"./app-71453429.js";import{d as a,u as c}from"./FilterRxComp-fc769f34.js";import{InputValuesTable as p}from"./regression.inputs.values.table-1618447a.js";import{mayRunSnplstTask as l}from"./snplst.sampleSum-e47d05f0.js";import{R as d}from"./regression.results-25008028.js";class m{constructor(t){this.type="regression";this.genomeObj=t.app.opts.genome}async init(t){this.dom={header:this.opts.header,errordiv:this.opts.holder.append("div"),inputs:this.opts.holder.append("div").style("margin","20px 10px"),results:this.opts.holder.append("div").style("margin-left","40px")};const e=t.plots.find((t=>t.id===this.id));this.inputs=new O({app:this.app,parent:this,id:this.id,holder:this.dom.inputs,regressionType:e.regressionType});this.results=new d({app:this.app,parent:this,id:this.id,holder:this.dom.results,regressionType:e.regressionType})}getState(t,e){const i=t.plots.find((t=>t.id===this.id));if(!i){throw`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`}if(!i.regressionType)throw"regressionType is required";return{vocab:t.vocab,formIsComplete:i.outcome&&i.independent.length,activeCohort:t.activeCohort,termfilter:t.termfilter,config:i,allowedTermTypes:t.termdbConfig.allowedTermTypes,minTimeSinceDx:t.termdbConfig.minTimeSinceDx}}async main(){try{this.config=JSON.parse(JSON.stringify(this.state.config));this.mayUpdateSandboxHeader();this.getFilter();await this.inputs.main();await this.results.main();this.inputs.resetSubmitButton()}catch(t){if(this.inputs.hasError){this.results.main()}n(this.dom.errordiv,"Error: "+(t.error||t));if(t.stack)console.log(t.stack)}}mayUpdateSandboxHeader(){if(!this.dom.header)return;const t=this.config.outcome;this.dom.header.html((t?t.term.name:"")+'<span style="opacity:.6;font-size:.7em;margin-left:10px;">'+this.config.regressionType.toUpperCase()+" REGRESSION</span>")}getFilter(){const t=[];if(this.state.termfilter?.filter)t.push(this.state.termfilter.filter);const e=[this.config.outcome,...this.config.independent];const i=e.filter((t=>t?.q.restrictAncestry));if(i.length){if(i.length>1){const t=new Set(i.map((t=>t.q.restrictAncestry.name)));if(t.size>1)throw"samples cannot be restricted to more than 1 ancestry"}const e=i[0];t.push({type:"tvs",tvs:e.q.restrictAncestry.tvs});this.inputs.dom.submitMsg.style("display","block").text(`restricting analysis to samples of ${e.q.restrictAncestry.name}`)}else{this.inputs.dom.submitMsg.style("display","none")}this.filter={type:"tvslst",join:"and",lst:t}}}const u=i(m);const f=u;let h=1;async function g(e,i){if(!e.outcome){e.outcome={}}{const s=i.opts.state.plots.find((t=>t.chartType=="regression"));if(!s)throw"regression plot missing in state";await t(e.outcome,i.vocabApi,y(s.regressionType,"outcome"))}const n="id"in e?e.id:`_REGRESSION_${h++}`;const o={id:n};o.outcome=e.outcome;if(e.independent){if(!Array.isArray(e.independent))throw".independent[] is not array";for(const s of e.independent){const e=!s.q?.mode?{numeric:{mode:"continuous"}}:undefined;await t(s,i.vocabApi,e)}o.independent=e.independent;delete e.independent}else{o.independent=[]}return s(o,e)}function y(t,e=""){const i={};i["numeric"]=t=="logistic"&&e=="outcome"?{mode:"binary"}:{mode:"discrete"};i["categorical"]=t=="logistic"&&e=="outcome"?{mode:"binary"}:{mode:"discrete"};if(e=="outcome"){if(t=="cox"){i.condition={mode:"cox"}}if(t=="logistic"){i.condition={mode:"binary"}}}return i}function b(t,e){const i=[{label:"Linear",type:"linear"},{label:"Logistic",type:"logistic"},{label:"Cox",type:"cox"}];for(const{label:s,type:n}of i){t.append("div").attr("class","sja_menuoption sja_sharp_border").text(s).on("click",(()=>{e.dom.tip.hide();e.prepPlot({config:{chartType:"regression",regressionType:n,independent:[]}})}))}}var v=Object.freeze({__proto__:null,regressionInit:u,componentInit:f,getPlotConfig:g,get_defaultQ4fillTW:y,makeChartBtnMenu:b});class x{constructor(t){this.opts=t;this.section=t.section;this.term=t.term;this.parent=t.parent}async init(t){const i=t.append("div");const s=i.append("span").style("display","inline-block");const n=i.append("span").style("margin-left","20px");this.dom={holder:t,termRow:i,pillDiv:s,interactionDiv:n,err_div:t.append("div").style("display","none").style("padding","5px").style("background-color","rgba(255,100,100,0.2)"),infoDiv:t.append("div"),tip:new o};try{const{app:t,config:i,state:s,disable_terms:n}=this.parent;const o={placeholder:this.section.selectPrompt,placeholderIcon:this.section.placeholderIcon,holder:this.dom.pillDiv,vocabApi:t.vocabApi,noTermPromptOptions:this.opts.noTermPromptOptions,activeCohort:s.activeCohort,debug:t.opts.debug,menuOptions:this.section.configKey=="outcome"?"{edit,reuse,replace}":"{edit,reuse,remove}",usecase:{target:"regression",detail:this.section.configKey,regressionType:i.regressionType},disable_terms:n,abbrCutoff:50,genomeObj:this.parent.parent.genomeObj,defaultQ4fillTW:y(i.regressionType,this.section.configKey),callback:t=>{this.parent.editConfig(this,t)}};this.furbishTsConstructorArg(o);this.pill=await e(o);if(this.section.configKey=="outcome"){this.setQ=S(i.regressionType)}this.valuesTable=new p({holder:this.dom.infoDiv,input:this,callback:t=>{this.parent.editConfig(this,t)}})}catch(t){this.displayError([t])}}furbishTsConstructorArg(t){const e=this.parent.config.regressionType;if(this.section.configKey=="outcome"){if(e=="logistic"){t.numericEditMenuVersion=["binary"];return}if(e=="linear"){t.numericEditMenuVersion=["continuous"];return}if(e=="cox"){return}throw"unknown regressionType"}if(this.section.configKey=="independent"){t.numericEditMenuVersion=["continuous","discrete","spline"];return}throw"unknown section.configKey: "+this.section.configKey}displayError(t){this.hasError=true;this.dom.err_div.selectAll("*").remove();this.dom.err_div.style("display","block").selectAll("div").data(Array.isArray(t)?t:[t]).enter().append("div").text((t=>t));this.parent.handleError();console.error(t)}async main(){const t=this.term;if(t){delete t.error}this.dom.err_div.style("display","none").text("");this.hasError=false;const e=[];try{if(t&&this.setQ){const{app:e,state:i}=this.parent;await this.setQ[t.term.type](t,e.vocabApi,this.parent.parent.filter,i)}try{await this.updateTerm()}catch(t){e.push(t)}await this.pill.main(this.getPillArgs());this.renderInteractionPrompt();await this.valuesTable.main();const i=t&&t.error||this.pill.error;if(i)e.push(i);if(e.length)throw e}catch(e){this.displayError(e)}}async updateTerm(){const t=this.term;if(!t)return;if(!t.q)throw".term.q missing on this input";if(!t.q.mode&&a(t.term.type)){if(t.term.type=="categorical"||t.term.type=="condition"||t.term.type=="survival")t.q.mode="discrete";else t.q.mode="continuous"}const e=t.term.type=="snplst"||t.term.type=="snplocus"?{cacheid:t.q.cacheid}:{term1_q:t.q};const i=await this.parent.app.vocabApi.getCategories(t.term,this.parent.parent.filter,e);if(!i)throw`no data for term.id='${t.term.id}'`;if(i.error)throw i.error;l(t,i);this.termStatus={topInfoStatus:[],bottomSummaryStatus:undefined,sampleCounts:undefined,excludeCounts:undefined,allowToSelectRefGrp:false};if(t.q.numOfSampleWithAnyValidGT){const e=t.term.snps.reduce(((t,e)=>t+(e.invalid?1:0)),0);this.termStatus.topInfoStatus.push(`${t.q.numOfSampleWithAnyValidGT} samples with valid genotypes`+(e>0?` ${e} invalid SNP${e>1?"s":""}.`:""))}if("geneticModel"in t.q){this.termStatus.topInfoStatus.push("Genetic model: "+(t.q.geneticModel==0?"Additive":t.q.geneticModel==1?"Dominant":t.q.geneticModel==2?"Recessive":"By genotype"))}if(t.q.restrictAncestry){this.termStatus.topInfoStatus.push("Analyzing "+t.q.restrictAncestry.name);if(t.q.restrictAncestry.PCcount){this.termStatus.topInfoStatus.push(`Adjusting for top ${t.q.restrictAncestry.PCcount} ancestry principal components`)}}if(t.term.reachedVariantLimit){this.termStatus.topInfoStatus.push(`<span class=sja_mcdot style="background:#aaa;font-size:1em">\n\t\t\t\t&nbsp;&#9888; Restricted to first ${t.term.snps.length}\n\t\t\t\tvariants of this region.&nbsp;</span> Try zooming in.`)}this.orderedLabels=i.orderedLabels;if(i.lst){this.summarizeSample(t,i.lst);if(t.term.type=="float"||t.term.type=="integer"){if(t.q.mode!="continuous"&&t.q.mode!="spline"){this.termStatus.allowToSelectRefGrp=true}if(t.q.scale&&t.q.scale!=1)this.termStatus.topInfoStatus.push(`Scale: Per ${t.q.scale}`);if(t.q.mode=="discrete"){this.termStatus.topInfoStatus.push(`Discrete variable with ${this.termStatus.sampleCounts.length} bins`)}if(t.q.mode=="spline"){this.termStatus.topInfoStatus.push(`Cubic spline variable with ${t.q.knots.length} knots: ${t.q.knots.map((t=>Number(t.value))).sort(((t,e)=>t-e)).join(", ")}`)}}else if(t.term.type=="categorical"){this.termStatus.allowToSelectRefGrp=true}else if(t.term.type=="condition"){if(this.section.configKey=="outcome"&&this.parent.opts.regressionType=="logistic"){this.termStatus.allowToSelectRefGrp=true}if(this.section.configKey=="outcome"&&this.parent.opts.regressionType=="cox"){if(!["age","time"].includes(t.q.timeScale))throw"invalid q.timeScale";const e=this.parent.app.vocabApi.termdbConfig;this.termStatus.topInfoStatus.push(`Time axis: ${t.q.timeScale=="time"?e.timeUnit:"age"}`);this.termStatus.topInfoStatus.push(`<span style="padding-left: 10px;">-start: ${t.q.timeScale=="time"?" ":"age at "}entry into the cohort (i.e., ${e.cohortStartTimeMsg})</span>`);this.termStatus.topInfoStatus.push(`<span style="padding-left: 10px;">-end: ${t.q.timeScale=="time"?" ":"age at "}event or censoring/death</span>`);const i=Object.keys(t.term.values).map(Number);const s=Math.max(...i);this.termStatus.topInfoStatus.push(`<div style="padding-top: 8px;">Event: first occurrence of grade ${t.q.breaks[0]===s?t.q.breaks[0]:`${t.q.breaks[0]}-${s}</div>`}`)}}this.maySet_refGrp(t)}}summarizeSample(t,e){const i=new Set;if(t.term.values){for(const e in t.term.values){if(t.term.values[e].uncomputable)i.add(t.term.values[e].label)}}if(t.q.mode=="cox"){const t=e.find((t=>t.key==-1));if(t)i.add(t.label)}const s=this.termStatus.sampleCounts=e.filter((t=>!i.has(t.label)));const n=this.termStatus.excludeCounts=e.filter((t=>i.has(t.label)));const o={included:0,excluded:0,total:0};s.forEach((t=>o.included+=t.samplecount));n.forEach((t=>o.excluded+=t.samplecount));o.total=o.included+o.excluded;if(t.term.type=="condition"&&o.total){o.excluded=o.total-o.included}this.termStatus.bottomSummaryStatus=`${o.included} samples included`+(o.excluded?`. ${o.excluded} samples excluded:`:"");if(t&&t.q.mode!=="continuous"&&s.length<2)throw`there should be two or more discrete values with samples for variable='${t.term.name}'`}maySet_refGrp(t){if(this.section.configKey=="outcome"&&this.parent.config.regressionType=="cox"){return}if(t.q.mode=="continuous"){t.refGrp="NA";return}const e=this.termStatus.sampleCounts;if(!("refGrp"in t)||!e.find((e=>e.key==t.refGrp))){const i=this.orderedLabels;if(i&&i.length)e.sort(((t,e)=>i.indexOf(t.key)-i.indexOf(e.key)));else e.sort(((t,e)=>t.samplecount<e.samplecount?1:-1));t.refGrp=e[0].key}}getPillArgs(){const t=this.section;const{config:e,state:i,disable_terms:s}=this.parent;const n=Object.assign({activeCohort:i.activeCohort,disable_terms:s,usecase:{target:"regression",detail:t.configKey,regressionType:e.regressionType}},this.term);n.filter=this.parent.parent.filter;return n}remove(){this.dom.termRow.transition().duration(500).style("opacity",0).remove();for(const t in this.dom){delete this.dom[t]}}renderInteractionPrompt(){this.dom.interactionDiv.style("display","none");if(!this.term)return;if(this.section.configKey!="independent")return;if(this.term.q.mode=="spline")return;{let t=0;for(const e of this.section.inputLst){if(e.term&&e.term.q.mode!="spline"){t++}}if(t<2)return}const t=this.term.interactions.length;this.dom.interactionDiv.style("display","inline").html(t==0?"Add interactions":`${t} interaction${t>1?"s":""}`).style("padding","5px").style("background-color",t==0?null:"#ececec").style("border-radius",t==0?null:"6px").style("color",t==0?"rgb(153, 153, 153)":"#000").style("font-size",t==0?"0.8em":"").style("cursor","pointer").on("click",(()=>this.renderInteractionOptions()))}renderInteractionOptions(){const t=this;t.dom.tip.clear().showunder(t.dom.interactionDiv.node());t.dom.tip.d.append("div").style("padding","5px").style("font-size","0.8em").style("color","rgb(153, 153, 153)").html(`Selected variables will each form pairwise interaction with ${this.term.term.name}`);t.dom.tip.d.append("div").selectAll("div").data(t.parent.config.independent.filter((e=>e&&e.term.id!==t.term.term.id&&e.q.mode!="spline"))).enter().append("div").style("margin","5px").each((function(e){const i=r(this).append("label");i.append("input").attr("type","checkbox").property("checked",t.term.interactions.includes(e.term.id));i.append("span").text(" "+e.term.name)}));t.dom.tip.d.append("button").text("Apply").style("margin","5px").on("click",(()=>{t.dom.tip.hide();t.term.interactions=[];t.dom.tip.d.selectAll("input").each((function(e){if(r(this).property("checked"))t.term.interactions.push(e.term.id)}));for(const e of t.parent.config.independent){const i=e.interactions.indexOf(t.term.term.id);if(t.term.interactions.includes(e.term.id)){if(i==-1)e.interactions.push(t.term.term.id)}else if(i!=-1){e.interactions.splice(i,1)}}t.parent.editConfig(t,t.term)}))}}function S(t){return{integer:t=="logistic"?w:_,float:t=="logistic"?w:_,geneExpression:t=="logistic"?w:_,categorical:q,condition:T,survival:T}}async function w(t,e,i,s){if(t.q.mode=="binary"&&t.q.lst&&t.q.lst.length==2){t.q.mode="binary";return}const n=await e.getPercentile(t.term.id,[50],i);if(n.error||!n.values.length||!Number.isFinite(n.values[0]))throw"cannot get median value: "+(n.error||"no data");const o=t.term.type=="integer"?Math.round(n.values[0]):Number(n.values[0].toFixed(2));t.q={mode:"binary",type:"custom-bin",lst:[{startunbounded:true,stopinclusive:true,stop:o},{stopunbounded:true,startinclusive:false,start:o}]};t.q.lst.forEach((e=>{e.label=c(e,t.q)}));t.refGrp=t.q.lst[0].label}function T(t,e,i,s){if(s.config.regressionType=="logistic"){if(!t.refGrp)t.refGrp=t.q.groups[0].name}if(s.config.regressionType=="cox"){if(!t.q.timeScale)t.q.timeScale="time"}}async function q(t,e,i,s){const{term:n,q:o}=t;if(o.mode=="binary"){if(o.type=="values"&&Object.keys(n.values).length==2)return;if(o.type=="predefined-groupset"){const t=o.groupsetting.predefined_groupset_idx;const e=n.groupsetting;if(e[t]&&Object.keys(e[t]).length==2)return}if(o.type=="custom-groupset"){const t=o.groupsetting.customset;if(t.groups.length==2)return}}const r={term1_q:o};const a=await e.getCategories(n,i,r);if(a.error)throw"cannot get categories: "+a.error;const c=new Map;const p=[];let l=false;const d=n.type=="condition"&&n.groupsetting.lst.length;if(n.groupsetting&&n.groupsetting.inuse){for(const t of n.groupsetting.lst[0].groups){if(t.type=="filter"&&t.filter4activeCohort){l=true}}}for(const t of a.lst){c.set(t.key,t.samplecount);if(n.values&&n.values[t.key]&&n.values[t.key].uncomputable)continue;p.push(t.key)}if(p.length<2&&!l&&!d){o.type="values";t.error="less than 2 categories/grades - cannot create separate groups";return}if(p.length==2&&!l&&!d){o.type="values";return}const m=n.groupsetting;const u=o.groupsetting;u.inuse=true;u.activeCohort=e.state.activeCohort;if(u.customset&&u.customset.groups&&u.customset.groups.length==2&&k(u.customset,c)){o.type="custom-groupset";return}if(m&&m.lst){if(u.predefined_groupset_idx>=0&&m.lst[u.predefined_groupset_idx]&&m.lst[u.predefined_groupset_idx].groups.length==2&&k(m.lst[u.predefined_groupset_idx],c)){o.type="predefined-groupset";return}const t=m.lst.findIndex((t=>t.groups.length==2));if(t!=-1&&k(m.lst[t],c)){u.predefined_groupset_idx=t;o.type="predefined-groupset";return}}const f={activeCohort:s.activeCohort,groups:[{name:"Group 1",type:"values",values:[]},{name:"Group 2",type:"values",values:[]}]};const h=Math.round(p.length/2);for(const[t,e]of p.entries()){if(t<h)f.groups[0].values.push({key:e});else f.groups[1].values.push({key:e})}u.customset=f;o.type="custom-groupset"}function _(t){if(!t.q.type){console.log("may not happen: why is input.term.q not yet set for numeric term at this point")}t.q.mode="continuous"}function k(t,e){for(const i of t.groups){let t=0;if(i.type=="values"){for(const s of i.values)t+=e.get(s.key)||0;if(t==0)return false}}return true}var A=Object.freeze({__proto__:null,InputTerm:x});const C=[{termtype:"snplst",html:"A list of variants"},{termtype:"snplocus",html:"Variants in a locus"},{termtype:"prs",text:"Polygenic risk score"}];class O{constructor(t){this.opts=t;this.app=t.app;this.parent=t.parent;E(this);I(this);this.createSectionConfigs();this.initUI()}createSectionConfigs(){this.outcome={heading:"Outcome variable",selectPrompt:this.opts.regressionType=="linear"?"Select continuous outcome variable":"Select outcome variable",placeholderIcon:"",configKey:"outcome",limit:1,usecase:{target:"regression",regressionType:this.opts.regressionType,detail:"outcome"},inputLst:[],dom:{}};this.independent={heading:"Independent variable(s)",selectPrompt:"Add independent variable",placeholderIcon:"",configKey:"independent",limit:10,usecase:{target:"regression",regressionType:this.opts.regressionType,detail:"independent"},inputLst:[],dom:{}};this.sections=[this.outcome,this.independent]}async main(){try{this.config=this.parent.config;this.state=this.parent.state;this.hasError=false;this.setDisableTerms();const t=[];for(const e of this.sections){await this.renderSection(e);for(const i of e.inputLst){i.dom.holder.style("border-left",i.term?"1px solid #bbb":"");t.push(i.main())}}await Promise.all(t);for(const t of this.sections){for(const e of t.inputLst){if(e.term&&e.term.error||e.hasError){this.hasError=true}}}}catch(t){this.hasError=true;throw t}}setDisableTerms(){this.disable_terms=[];if(this.config.outcome&&this.config.outcome.term)this.disable_terms.push(this.config.outcome.term);if(this.config.independent){for(const t of this.config.independent){this.disable_terms.push(t.term)}}}handleError(){this.hasError=true;this.dom.submitBtn.property("disabled",true)}getNoTermPromptOptions(t){if(t.configKey!="independent")return;const e=[];for(const i of C){if(!this.state.allowedTermTypes.includes(i.termtype)){continue}if(t.inputLst.find((t=>t.term&&t.term.term.type==i.termtype))){continue}e.push(i)}if(e.length){e.unshift({isDictionary:true,text:"Dictionary variable"})}return e}}function I(t){t.initUI=()=>{const e=t.opts.holder.append("div").style("display","block");t.dom={div:t.opts.holder,controls:e,body:e.append("div"),foot:e.append("div").style("margin","0px 20px").style("display","flex").style("align-items","center").style("gap","20px")};t.dom.submitBtn=t.dom.foot.append("div").append("button").style("display","none").style("padding","5px 15px").style("border-radius","15px").style("cursor","pointer").text("Run analysis").on("click",t.submit);t.dom.submitMsg=t.dom.foot.append("div").style("display","none").style("color","#cc0000").style("font-style","italic").style("font-size","0.8em");for(const e of t.sections){const i=t.dom.body.append("div");t.addSection(e,i)}};t.addSection=function(t,e){e.style("display","none").style("margin","3px 5px").style("padding","3px 5px");t.dom={holder:e,headingDiv:e.append("div").style("margin","3px 5px 20px 5px").style("font-size","17px").style("color","#bbb").text(t.heading),inputsDiv:e.append("div")}};t.renderSection=function(n){n.dom.holder.style("display",n.configKey=="outcome"||t.config.outcome?"block":"none");e(n);const o=n.dom.inputsDiv.selectAll(":scope > div").data(n.inputLst,(t=>t.term&&t.term.term.id));o.exit().each(s);o.enter().append("div").each(i)};function e(e){const i=t.config[e.configKey];const s=Array.isArray(i)?i:i?[i]:[];for(const n of s){if(e.configKey=="independent"){if(!n.interactions)n.interactions=[];for(const t of n.interactions){const e=i.find((e=>e.term.id==t));if(!e)throw"interacting partner not found in independents: "+t;if(!e.interactions)e.interactions=[];if(!e.interactions.includes(n.term.id))e.interactions.push(n.term.id)}}const s=e.inputLst.find((t=>t.term&&t.term.term.id==n.term.id));if(!s){e.inputLst.push(new x({section:e,term:n,parent:t}))}else{s.term=n}}$(e,t)}async function i(t){await t.init(r(this).style("width","fit-content").style("margin","0px 15px 35px 25px").style("padding","0px 5px"))}function s(t){t.remove();for(const e in t.dom){delete t.dom[e]}const e=r(this);e.transition().duration(500).style("opacity",0).remove()}t.resetSubmitButton=()=>{t.dom.submitBtn.text("Run analysis").style("display",t.config.outcome&&t.config.independent.length?"block":"none").property("disabled",t.hasError)}}function E(t){t.editConfig=async(e,i)=>{if(!i){const t=e.section.inputLst.findIndex((t=>t===e));if(t==-1)throw`deleting an unknown input`;e.section.inputLst.splice(t,1);if(e.term){for(const t of e.section.inputLst){if(!t.term||!t.term.interactions)continue;const i=t.term.interactions.indexOf(e.term.term.id);if(i!=-1)t.term.interactions.splice(i,1)}}}else{const t=e.term;if(t&&i.term.id===t.term.id){for(const e in t){if(!(e in i))i[e]=t[e]}}e.term=i;if(i.q.mode=="spline"&&i.interactions){for(const t of e.section.inputLst){if(!t.term||!t.term.interactions)continue;const i=t.term.interactions.indexOf(e.term.term.id);if(i!=-1)t.term.interactions.splice(i,1)}i.interactions=[]}}const s=[];for(const t of e.section.inputLst){if(t.term)s.push(t.term)}const n=e.section.configKey;const o=Array.isArray(t.config[n])?s:s[0];t.app.dispatch({type:"plot_edit",id:t.parent.id,chartType:"regression",config:{hasUnsubmittedEdits:true,[n]:JSON.parse(JSON.stringify(o))}})};t.submit=()=>{t.dom.submitBtn.property("disabled",true);if(t.hasError){alert("Please fix the input variable errors (highlighted in red background).");return}const e=JSON.parse(JSON.stringify(t.config));e.hasUnsubmittedEdits=false;t.app.dispatch({type:"plot_edit",id:t.parent.id,chartType:"regression",config:e})}}function $(t,e){if(t.inputLst.length>=t.limit){return}const i=t.inputLst.find((t=>!t.term));if(i){const s=e.getNoTermPromptOptions(t);if(s){i.pill.main({noTermPromptOptions:s})}return}t.inputLst.push(new x({section:t,parent:e,noTermPromptOptions:e.getNoTermPromptOptions(t)}))}var P=Object.freeze({__proto__:null,RegressionInputs:O});export{A as a,P as b,v as r};

package/dist/{regression.inputs.values.table-d587c1cf.js → regression.inputs.values.table-1618447a.js}

@@ -1 +1 @@
-import{getDefaultViolinSettings as t}from"./violin-c1b78717.js";import{appInit as e}from"./plot.app-91a1d78d.js";import{q as o}from"./app-f91922b4.js";import"./controls-8d4972c8.js";import"./controls.btns-bad9e4cf.js";import"./controls.config-e0f394cb.js";import"./controls.overlay-3ac8773d.js";import"./termsetting-9a7511e6.js";import"path";import"./FilterRxComp-0e75dd8d.js";import"./table-d6c411fd.js";import"./controls.term1-008f4be4.js";import"./controls.divide-d8ac5a9b.js";import"./violin.renderer-16540fb8.js";import"./brush-db0ed33a.js";import"./pointer-c7475677.js";import"./nodrag-777a34a5.js";import"./axis-6cb4f314.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";import"./log-4d74231e.js";import"./html.legend-3e428f9e.js";import"./violin.interactivity-534d6993.js";import"./niceNumLabels-8fdc6507.js";import"./recover-a08c8d01.js";import"./FilterStateless-ad3df967.js";import"./app-bfce9bf5.js";import"./termInfo-96285f4a.js";const l="#fff6dc";class i{constructor(t){this.opts=t;this.input=t.input;s(this);this.setDOM(t.holder)}main(){try{const t=this.input.term;if(!t||!this.input.termStatus){this.dom.holder.style("display","none");this.dom.loading_div.style("display","none");return}else if(t){this.dom.holder.style("display","block");this.dom.loading_div.style("display","block");this.updateValueCount();this.dom.loading_div.style("display","none");this.render();return}}catch(t){this.dom.loading_div.style("display","none");throw t}}updateValueCount(){const t=this.input;try{if(t.pill&&t.pill.validateQ){t.pill.validateQ({term:t.term.term,q:t.term.q,sampleCounts:t.termStatus.sampleCounts})}}catch(e){t.term.error=e}}}function s(i){i.setDOM=t=>{i.dom={holder:t.style("margin","10px").style("font-size",".8em").style("text-align","left").style("color","#999"),loading_div:t.append("div").text("Loading..").style("display","none"),top_info_div:t.append("div").style("padding-bottom","5px"),violin_div:t.append("div").style("color","black").style("padding-top","5px"),table_div:t.append("table").style("margin","5px 0px 15px 0px").style("border-collapse","collapse").style("color","black"),bottom_info_div:t.append("div"),excluded_div:t.append("table").style("display","none").style("margin","5px 10px").style("border-collapse","collapse")}};i.render=async()=>{const t=i.input;s(t);await n(t);p(t);d(t)};function s(t){if(t.termStatus.topInfoStatus?.length){i.dom.top_info_div.style("display","block").html(t.termStatus.topInfoStatus.join("<br>"))}else{i.dom.top_info_div.style("display","none")}}async function n(o){if(o.term.q.mode=="continuous"||o.term.q.mode=="spline"){i.dom.violin_div.style("display","block");i.dom.table_div.style("display","none");if(i.plotAppApi){const t={type:"app_refresh",state:{termfilter:{filter:i.input.parent.parent.filter}},subactions:[{type:"plot_edit",id:i.violinApi.id,config:{term:o.term}}]};i.plotAppApi.dispatch(t)}else{const l={holder:i.dom.violin_div,vocabApi:i.input.parent.app.vocabApi,state:{vocab:{genome:i.input.parent.app.vocabApi.genome,dslabel:i.input.parent.app.vocabApi.dslabel},termfilter:{filter:i.input.parent.parent.filter},plots:[{chartType:"violin",term:o.term,settings:{violin:t(null,{svgw:350,axisHeight:25,rightMargin:10,datasymbol:"rug",radius:3,plotThickness:100})}}]},violin:{mode:"minimal"}};i.plotAppApi=await e(l);const s=i.plotAppApi.getState().plots[0].id;i.violinApi=i.plotAppApi.getComponents(`plots.${s}`)}}else{i.dom.violin_div.style("display","none");const t=o.termStatus.sampleCounts;if(!t||!t.length){i.dom.table_div.style("display","none");return}i.dom.table_div.style("display","block");const e=i.input.orderedLabels;const l=e&&e.length?(t,o)=>e.indexOf(t.label)-e.indexOf(o.label):(t,e)=>e.samplecount-t.samplecount;const s=t.sort(l);const n=Math.max(...s.map((t=>t.samplecount)),0);s.forEach((t=>t.bar_width_frac=Number((1-(n-t.samplecount)/n).toFixed(4))));i.dom.table_div.selectAll("tr").remove();const p=i.dom.table_div.selectAll("tr").data(s,(t=>t.key));p.enter().append("tr").each(a)}}function p(t){if(t.termStatus.bottomSummaryStatus){i.dom.bottom_info_div.style("display","block").html(t.termStatus.bottomSummaryStatus)}else{i.dom.bottom_info_div.style("display","none")}}function d(t){const e=t.termStatus.excludeCounts;if(!e||!e.length){i.dom.excluded_div.style("display","none");return}i.dom.excluded_div.style("display","block").selectAll("tr").remove();const o=i.dom.excluded_div.selectAll("tr").data(e,(t=>t.key));o.enter().append("tr").each(a);i.dom.excluded_div.selectAll("td").style("color","#999")}function a(t){const e=o(this);const l=this.parentNode.__data__;l.term;const i=150;e.style("text-align","left").style("cursor",l.termStatus.allowToSelectRefGrp?"pointer":"default");const s="1px 10px 1px 0px";e.append("td").style("padding",s).style("text-align","left").style("color","black").text(t.samplecount!==undefined?"n="+t.samplecount:"");e.append("td").style("padding",s).style("text-align","left").style("color","black").text(t.label);const n=e.append("td").style("padding",s);const p=i*t.bar_width_frac;n.append("div").style("margin",s).style("width",p+"px").style("height","15px").style("background-color","#ddd");r({input:l,item:t,tr:e,rendered:false})}function r({input:t,item:e,tr:s,rendered:n}){if(!e.bar_width_frac)return;const p=t.term;const d=t.termStatus.allowToSelectRefGrp;let a;if(n){s.style("background","white");a=o(s.node().lastChild).select("div").style("display",e.key===p.refGrp&&d?"inline-block":"none").style("border",e.key===p.refGrp&&d?"1px solid #bbb":"")}else if(t.term.q.mode!="cutoff"){const t=s.append("td").style("padding","1px 5px").style("text-align","left");a=t.append("div").style("display",e.key===p.refGrp&&d?"inline-block":"none").style("padding","2px 10px").style("border",e.key===p.refGrp&&d?"1px solid #bbb":"").style("border-radius","10px").style("color","#999").style("font-size",".7em").text("REFERENCE");if(d){s.on("mouseover",(()=>{if(p.refGrp!==e.key){s.style("background",l);a.style("display","inline-block").style("border","").text("Set as reference")}else s.style("background","white")})).on("mouseout",(()=>{s.style("background","white");if(p.refGrp!==e.key)a.style("display","none")})).on("click",(()=>{p.refGrp=e.key;a.style("border","1px solid #bbb").text("REFERENCE");i.opts.callback(p)}))}}}}export{i as InputValuesTable};
+import{getDefaultViolinSettings as t}from"./violin-a41b2e2b.js";import{appInit as e}from"./plot.app-c841507a.js";import{q as o}from"./app-71453429.js";import"./controls-0467d2ec.js";import"./controls.btns-ad7b28a2.js";import"./controls.config-6cf816fb.js";import"./controls.overlay-3a55c2ec.js";import"./termsetting-636d2271.js";import"path";import"./FilterRxComp-fc769f34.js";import"./table-1dae543a.js";import"./controls.term1-59f4cd60.js";import"./controls.divide-3c0d52d7.js";import"./violin.renderer-149310eb.js";import"./brush-bb4566a3.js";import"./pointer-c7475677.js";import"./nodrag-bed2488c.js";import"./axis-6cb4f314.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";import"./log-ca1e2a74.js";import"./html.legend-ef8066dd.js";import"./violin.interactivity-bcf0ccc2.js";import"./niceNumLabels-ddb76164.js";import"./recover-b1ec4fed.js";import"./FilterStateless-8f30f856.js";import"./app-fb676934.js";import"./termInfo-4c759483.js";const l="#fff6dc";class i{constructor(t){this.opts=t;this.input=t.input;s(this);this.setDOM(t.holder)}main(){try{const t=this.input.term;if(!t||!this.input.termStatus){this.dom.holder.style("display","none");this.dom.loading_div.style("display","none");return}else if(t){this.dom.holder.style("display","block");this.dom.loading_div.style("display","block");this.updateValueCount();this.dom.loading_div.style("display","none");this.render();return}}catch(t){this.dom.loading_div.style("display","none");throw t}}updateValueCount(){const t=this.input;try{if(t.pill&&t.pill.validateQ){t.pill.validateQ({term:t.term.term,q:t.term.q,sampleCounts:t.termStatus.sampleCounts})}}catch(e){t.term.error=e}}}function s(i){i.setDOM=t=>{i.dom={holder:t.style("margin","10px").style("font-size",".8em").style("text-align","left").style("color","#999"),loading_div:t.append("div").text("Loading..").style("display","none"),top_info_div:t.append("div").style("padding-bottom","5px"),violin_div:t.append("div").style("color","black").style("padding-top","5px"),table_div:t.append("table").style("margin","5px 0px 15px 0px").style("border-collapse","collapse").style("color","black"),bottom_info_div:t.append("div"),excluded_div:t.append("table").style("display","none").style("margin","5px 10px").style("border-collapse","collapse")}};i.render=async()=>{const t=i.input;s(t);await n(t);p(t);d(t)};function s(t){if(t.termStatus.topInfoStatus?.length){i.dom.top_info_div.style("display","block").html(t.termStatus.topInfoStatus.join("<br>"))}else{i.dom.top_info_div.style("display","none")}}async function n(o){if(o.term.q.mode=="continuous"||o.term.q.mode=="spline"){i.dom.violin_div.style("display","block");i.dom.table_div.style("display","none");if(i.plotAppApi){const t={type:"app_refresh",state:{termfilter:{filter:i.input.parent.parent.filter}},subactions:[{type:"plot_edit",id:i.violinApi.id,config:{term:o.term}}]};i.plotAppApi.dispatch(t)}else{const l={holder:i.dom.violin_div,vocabApi:i.input.parent.app.vocabApi,state:{vocab:{genome:i.input.parent.app.vocabApi.genome,dslabel:i.input.parent.app.vocabApi.dslabel},termfilter:{filter:i.input.parent.parent.filter},plots:[{chartType:"violin",term:o.term,settings:{violin:t(null,{svgw:350,axisHeight:25,rightMargin:10,datasymbol:"rug",radius:3,plotThickness:100})}}]},violin:{mode:"minimal"}};i.plotAppApi=await e(l);const s=i.plotAppApi.getState().plots[0].id;i.violinApi=i.plotAppApi.getComponents(`plots.${s}`)}}else{i.dom.violin_div.style("display","none");const t=o.termStatus.sampleCounts;if(!t||!t.length){i.dom.table_div.style("display","none");return}i.dom.table_div.style("display","block");const e=i.input.orderedLabels;const l=e&&e.length?(t,o)=>e.indexOf(t.label)-e.indexOf(o.label):(t,e)=>e.samplecount-t.samplecount;const s=t.sort(l);const n=Math.max(...s.map((t=>t.samplecount)),0);s.forEach((t=>t.bar_width_frac=Number((1-(n-t.samplecount)/n).toFixed(4))));i.dom.table_div.selectAll("tr").remove();const p=i.dom.table_div.selectAll("tr").data(s,(t=>t.key));p.enter().append("tr").each(r)}}function p(t){if(t.termStatus.bottomSummaryStatus){i.dom.bottom_info_div.style("display","block").html(t.termStatus.bottomSummaryStatus)}else{i.dom.bottom_info_div.style("display","none")}}function d(t){const e=t.termStatus.excludeCounts;if(!e||!e.length){i.dom.excluded_div.style("display","none");return}i.dom.excluded_div.style("display","block").selectAll("tr").remove();const o=i.dom.excluded_div.selectAll("tr").data(e,(t=>t.key));o.enter().append("tr").each(r);i.dom.excluded_div.selectAll("td").style("color","#999")}function r(t){const e=o(this);const l=this.parentNode.__data__;l.term;const i=150;e.style("text-align","left").style("cursor",l.termStatus.allowToSelectRefGrp?"pointer":"default");const s="1px 10px 1px 0px";e.append("td").style("padding",s).style("text-align","left").style("color","black").text(t.samplecount!==undefined?"n="+t.samplecount:"");e.append("td").style("padding",s).style("text-align","left").style("color","black").text(t.label);const n=e.append("td").style("padding",s);const p=i*t.bar_width_frac;n.append("div").style("margin",s).style("width",p+"px").style("height","15px").style("background-color","#ddd");a({input:l,item:t,tr:e,rendered:false})}function a({input:t,item:e,tr:s,rendered:n}){if(!e.bar_width_frac)return;const p=t.term;const d=t.termStatus.allowToSelectRefGrp;let r;if(n){s.style("background","white");r=o(s.node().lastChild).select("div").style("display",e.key===p.refGrp&&d?"inline-block":"none").style("border",e.key===p.refGrp&&d?"1px solid #bbb":"")}else if(t.term.q.mode!="cutoff"){const t=s.append("td").style("padding","1px 5px").style("text-align","left");r=t.append("div").style("display",e.key===p.refGrp&&d?"inline-block":"none").style("padding","2px 10px").style("border",e.key===p.refGrp&&d?"1px solid #bbb":"").style("border-radius","10px").style("color","#999").style("font-size",".7em").text("REFERENCE");if(d){s.on("mouseover",(()=>{if(p.refGrp!==e.key){s.style("background",l);r.style("display","inline-block").style("border","").text("Set as reference")}else s.style("background","white")})).on("mouseout",(()=>{s.style("background","white");if(p.refGrp!==e.key)r.style("display","none")})).on("click",(()=>{p.refGrp=e.key;r.style("border","1px solid #bbb").text("REFERENCE");i.opts.callback(p)}))}}}}export{i as InputValuesTable};