@sjcrh/proteinpaint-client 2.77.0 → 2.78.0

package/dist/termdb.bins-06fd21c1.js

@@ -0,0 +1 @@
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package/dist/termsetting-c12f1c69.js

@@ -0,0 +1 @@
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i==="undefined")i=this.partial;this.debug("match",t,this.pattern);if(this.comment)return false;if(this.empty)return t==="";if(t==="/"&&i)return true;var n=this.options;if(X.sep!=="/"){t=t.split(X.sep).join("/")}t=t.split(re);this.debug(this.pattern,"split",t);var r=this.set;this.debug(this.pattern,"set",r);var s;var o;for(o=t.length-1;o>=0;o--){s=t[o];if(s)break}for(o=0;o<r.length;o++){var a=r[o];var l=t;if(n.matchBase&&a.length===1){l=[s]}var d=this.matchOne(l,a,i);if(d){if(n.flipNegate)return true;return!this.negate}}if(n.flipNegate)return false;return this.negate};le.prototype.matchOne=function(e,t,i){var n=this.options;this.debug("matchOne",{this:this,file:e,pattern:t});this.debug("matchOne",e.length,t.length);for(var r=0,s=0,o=e.length,a=t.length;r<o&&s<a;r++,s++){this.debug("matchOne loop");var l=t[s];var d=e[r];this.debug(t,l,d);if(l===false)return false;if(l===z){this.debug("GLOBSTAR",[t,l,d]);var p=r;var u=s+1;if(u===a){this.debug("** at the end");for(;r<o;r++){if(e[r]==="."||e[r]===".."||!n.dot&&e[r].charAt(0)===".")return false}return true}while(p<o){var c=e[p];this.debug("\nglobstar while",e,p,t,u,c);if(this.matchOne(e.slice(p),t.slice(u),i)){this.debug("globstar found match!",p,o,c);return true}else{if(c==="."||c===".."||!n.dot&&c.charAt(0)==="."){this.debug("dot detected!",e,p,t,u);break}this.debug("globstar swallow a segment, and continue");p++}}if(i){this.debug("\n>>> no match, partial?",e,p,t,u);if(p===o)return true}return false}var f;if(typeof l==="string"){f=d===l;this.debug("string match",l,d,f)}else{f=d.match(l);this.debug("pattern match",l,d,f)}if(!f)return false}if(r===o&&s===a){return true}else if(r===o){return i}else if(s===a){return r===o-1&&e[r]===""}throw new Error("wtf?")};function ge(e){return e.replace(/\\(.)/g,"$1")}function ve(e){return e.replace(/[-[\]{}()*+?.,\\^$|#\s]/g,"\\$&")}class be{constructor(e,t){var i;this.isAtomic=true;this.type=e.type;this.isAtomic=true;if(e.$id)this.$id=e.$id;if(e.sortSamples)this.sortSamples=e.sortSamples;if(e.minNumSamples)this.minNumSamples=e.minNumSamples;if(e.valueFilter)this.valueFilter=e.valueFilter;if((i=t.addons)===null||i===void 0?void 0:i[this.type]){Object.defineProperties(this,t.addons[this.type])}}static setHiddenValues(e,t){if(e.hiddenValues)return;e.hiddenValues={};if(t.values){for(const i in t.values){if(t.values[i].uncomputable)e.hiddenValues[i]=1}}}render(e){console.log(e);throw`should implement this method in subclass code, as needed`}}var we,qe,Te,xe,Ee,Se;class Ne extends be{constructor(e,t){super(e,t);this.term=e.term}static fill(e,t={}){var i;if(!e.term)throw`missing tw.term, must already be filled in`;if(e.term.type!="categorical")throw`incorrect term.type='${(i=e.term)===null||i===void 0?void 0:i.type}', expecting 'categorical'`;if(t.defaultQ!=null){t.defaultQ.isAtomic=true;o(e.q,t.defaultQ)}if(!e.q.mode)e.q.mode="discrete";if(!e.q)e.q={type:"values",isAtomic:true};if(!e.type)e.type=!e.q.type||e.q.type=="values"?"CatTWValues":e.q.type=="predefined-groupset"?"CatTWPredefinedGS":e.q.type=="custom-groupset"?"CatTWCustomGS":undefined;switch(e.type){case"CatTWValues":return _e.fill(e);case"CatTWPredefinedGS":return Ae.fill(e);case"CatTWCustomGS":return Ie.fill(e);default:throw`tw.type='${e.type} (q.mode:q.type=${e.q.mode}:${e.q.type}' is not supported by CategoricalBase.fill()`}}}class _e extends Ne{constructor(t,i={}){super(t,i);we.set(this,void 0);qe.set(this,void 0);this.q=t.q;e(this,we,t,"f");e(this,qe,i,"f")}getTw(){return t(this,we,"f")}static fill(e){if(!e.type)e.type="CatTWValues";else if(e.type!="CatTWValues")throw`expecting tw.type='CatTWValues', got '${e.type}'`;if(e.term.type!="categorical")throw`expecting tw.term.type='categorical', got '${e.term.type}'`;const{term:t,q:i}=e;if(!i.type)i.type="values";else if(i.type!="values")throw`expecting tw.q.type='values', got ${e.q.type}`;if(!t.values)t.values={};if(i.mode=="binary"){if(Object.keys(e.term.values).length!=2)throw"term.values must have exactly two keys"}vt(i,t);return e}}we=new WeakMap,qe=new WeakMap;class Ae extends Ne{constructor(i,n={}){super(i,n);Te.set(this,void 0);xe.set(this,void 0);this.q=i.q;e(this,Te,i,"f");Object.defineProperty(this,"groupset",{value:this.term.groupsetting[t(this,Te,"f").q.predefined_groupset_idx]});e(this,xe,n,"f")}getTw(){return t(this,Te,"f")}static fill(e){var t,i;if(!e.type)e.type="CatTWPredefinedGS";else if(e.type!="CatTWPredefinedGS")throw`expecting tw.type='CatTWPredefinedGS', got '${e.type}'`;if(e.term.type!="categorical")throw`expecting tw.term.type='categorical', got '${e.term.type}'`;if(e.q.type!="predefined-groupset")throw`expecting tw.q.type='predefined-groupset', got '${e.q.type}'`;const{term:n,q:r}=e;const s=r.predefined_groupset_idx;if(s!==undefined&&!Number.isInteger(s))throw`missing or invalid tw.q.predefined_groupset_idx='${s}'`;r.predefined_groupset_idx=s||0;const o=e.term.groupsetting;if(!o)throw"no term.groupsetting";if(!((t=o.lst)===null||t===void 0?void 0:t.length))throw"term.groupsetting.lst is empty";const a=(i=o.lst)===null||i===void 0?void 0:i[r.predefined_groupset_idx];if(!a)throw`no groupset entry for groupsetting.lst?.[predefined_groupset_idx=${s}]`;if(r.mode=="binary"){if(a.groups.length!=2)throw"there must be exactly two groups"}vt(r,n);return e}}Te=new WeakMap,xe=new WeakMap;class Ie extends Ne{constructor(t,i={}){super(t,i);Ee.set(this,void 0);Se.set(this,void 0);this.q=t.q;Object.defineProperty(this,"groupset",{value:this.q.customset});e(this,Ee,t,"f");e(this,Se,i,"f")}getTw(){return t(this,Ee,"f")}static fill(e){if(!e.type)e.type="CatTWCustomGS";else if(e.type!="CatTWCustomGS")throw`expecting tw.type='CatTWCustomGS', got '${e.type}'`;if(e.term.type!="categorical")throw`expecting tw.term.type='categorical', got '${e.term.type}'`;if(e.q.type!="custom-groupset")throw`expecting tw.q.type='custom-groupset', got '${e.q.type}'`;const{term:t,q:i}=e;if(!i.customset)throw`missing tw.q.customset`;if(i.mode=="binary"){if(i.customset.groups.length!=2)throw"there must be exactly two groups"}vt(i,t);return e}}Ee=new WeakMap,Se=new WeakMap;function Ce(e,t){const i=Number(e);if(Number.isInteger(i))return i;if(Math.abs(i)<1)return Number(i.toPrecision(t));return Number(i.toFixed(t))}function Oe(e){const t=je(e);let i=Math.abs(e)>1?2:t>0?t+1:2;return Ce(e,i)}function je(e){const t=e.toString();const i=t.indexOf(".");if(i===-1||i===t.length-1){return 0}let n=0;for(let e=i+1;e<t.length;e++){if(t[e]==="0"){n++}else if(t[e]>="1"&&t[e]<="9"){break}}return n}var ke,Pe,$e,Me,Le,Re,We,Be;class Ge extends be{constructor(e,t){super(e,t);this.term=e.term}static fill(e,t={}){return i(this,void 0,void 0,(function*(){if(!e.term)throw`missing tw.term, must already be filled in`;if(!Ge.termTypes.has(e.term.type))throw`non-numeric term.type='${e.term.type}'`;if(t.defaultQ){t.defaultQ.isAtomic=true;e.q.isAtomic=true;if(t.defaultQ.preferredBins=="median"){if(!t.defaultQ.type)t.defaultQ.type="custom-bin";else if(t.defaultQ.type!="custom-bin")throw".type must be custom-bin when .preferredBins=median"}o(e.q,t.defaultQ)}if(!e.q.mode)e.q.mode="discrete";if(!e.q.type){if(e.q.mode=="binary")e.q.type="custom-bin";else if(e.q.mode=="discrete")He(e)}e.type=e.q.type=="regular-bin"?"NumTWRegularBin":e.q.type=="custom-bin"||e.q.mode=="binary"?"NumTWCustomBin":e.q.mode=="continuous"?"NumTWCont":e.q.mode=="spline"?"NumTWSpline":e.type;switch(e.type){case"NumTWRegularBin":return yield Ve.fill(e);case"NumTWCustomBin":return yield De.fill(e,t);case"NumTWCont":return yield Qe.fill(e);case"NumTWSpline":return yield Ye.fill(e);default:throw`tw.type='${e.type} (q.mode:q.type=${e.q.mode}:${e.q.type}' is not supported by NumericBase.fill()`}}))}}Ge.termTypes=new Set(["integer","float","geneExpression","metaboliteIntensity"]);class Ve extends Ge{constructor(t,i={}){super(t,i);ke.set(this,void 0);Pe.set(this,void 0);this.q=t.q;e(this,ke,t,"f");e(this,Pe,i,"f")}getTw(){return t(this,ke,"f")}static fill(e){var t;return i(this,void 0,void 0,(function*(){if(!e.type)e.type="NumTWRegularBin";else if(e.type!="NumTWRegularBin")throw`expecting tw.type='NumTWRegularBin', got '${e.type}'`;if(!e.q.mode)e.q.mode="discrete";else if(e.q.mode!="discrete"&&e.q.mode!="binary"&&e.q.mode!="continuous")throw`expecting tw.q.mode='discrete'|'binary'|'continous', got '${e.q.mode}'`;if(e.q.type&&e.q.type!="regular-bin")throw`expecting tw.q.type='regular-bin', got '${e.q.type}'`;if(!e.q.first_bin||!a(e.q.bin_size))He(e);if(!a(e.q.bin_size))throw`tw.q.bin_size=${e.q.bin_size} is not numeric`;if(!e.q.first_bin)throw`missing tw.q.first_bin`;if(!a((t=e.q.first_bin)===null||t===void 0?void 0:t.stop))throw`tw.q.first_bin.stop is not numeric`;be.setHiddenValues(e.q,e.term);return e}))}}ke=new WeakMap,Pe=new WeakMap;class De extends Ge{constructor(t,i={}){super(t,i);$e.set(this,void 0);Me.set(this,void 0);this.q=t.q;e(this,$e,t,"f");e(this,Me,i,"f")}getTw(){return t(this,$e,"f")}static fill(e,t={}){return i(this,void 0,void 0,(function*(){if(!e.type)e.type="NumTWCustomBin";else if(e.type!="NumTWCustomBin")throw`expecting tw.type='NumTWCustomBin', got '${e.type}'`;if(!e.q.mode)e.q.mode="discrete";else if(e.q.mode!="discrete"&&e.q.mode!="binary"&&e.q.mode!="continuous")throw`expecting tw.q.mode='discrete'|binary|continuous', got '${e.q.mode}'`;if(e.q.mode=="binary"&&!e.q.preferredBins)e.q.preferredBins="median";if(e.q.preferredBins=="median"){const i=yield t.vocabApi.getPercentile(e.term.id,[50]);if(!i.values)throw".values[] missing from vocab.getPercentile()";const n=Oe(i.values[0]);if(!a(n))throw"median value not a number";e.q.type="custom-bin";e.q.lst=[{startunbounded:true,stop:n,stopinclusive:false,label:"<"+n},{start:n,startinclusive:true,stopunbounded:true,label:"≥"+n}];delete e.q.preferredBins}else if(e.q.type!="custom-bin")throw`expecting tw.q.type='custom-bin', got '${e.q.type}'`;if(!Array.isArray(e.q.lst))He(e);if(!e.q.lst||!e.q.lst.length)throw`missing or empty q.lst[] for custom-bin`;if(e.q.mode=="binary"&&e.q.lst.length!=2)throw`numeric q.mode='binary' requires exactly 2 bins`;be.setHiddenValues(e.q,e.term);e.type="NumTWCustomBin";return e}))}}$e=new WeakMap,Me=new WeakMap;class Qe extends Ge{constructor(t,i={}){super(t,i);Le.set(this,void 0);Re.set(this,void 0);this.q=t.q;e(this,Le,t,"f");e(this,Re,i,"f")}getTw(){return t(this,Le,"f")}static fill(e){return i(this,void 0,void 0,(function*(){if(!e.type)e.type="NumTWCont";else if(e.type!="NumTWCont")throw`expecting tw.type='NumTWCont', got '${e.type}'`;if(e.q.mode!="continuous")throw`tw.q.mode='${e.q.mode}', expecting 'continuous'`;be.setHiddenValues(e.q,e.term);e.type="NumTWCont";return e}))}}Le=new WeakMap,Re=new WeakMap;class Ye extends Ge{constructor(t,i={}){super(t,i);We.set(this,void 0);Be.set(this,void 0);this.q=t.q;e(this,We,t,"f");e(this,Be,i,"f")}static fill(e){return i(this,void 0,void 0,(function*(){if(!e.type)e.type="NumTWSpline";else if(e.type!="NumTWSpline")throw`expecting tw.type='NumTWSpline', got '${e.type}'`;if(e.q.mode!="spline")throw`tw.q.mode='${e.q.mode}', expecting 'spline'`;if(!e.q.knots)throw`missing tw.q.knots`;if(!e.q.knots.length)throw`empty tw.q.knots[]`;be.setHiddenValues(e.q,e.term);e.type="NumTWSpline";return e}))}}We=new WeakMap,Be=new WeakMap;const Ue=new Set(["default","less","median"]);function He(e){if(!e.term.bins)throw`missing tw.term.bins`;const t=e.q.preferredBins||"default";if(!Ue.has(t))throw`invalid preferredBins='${t}'`;if(t!="median"){if(!Object.keys(e.term.bins).includes(t));const i=e.term.bins[t];if(e.q.type&&e.q.type!=i.type)throw`mismatched tw.q.type and term.bins[preferredBins].type`;const n=Object.keys(e.q);for(const[t,r]of Object.entries(i)){if(!n.includes(t))e.q[t]=r}delete e.q.preferredBins}}class Fe{constructor(e){this.opts=e}static init(e,t={}){switch(e.type){case"CatTWValues":return new _e(e,t);case"CatTWPredefinedGS":return new Ae(e,t);case"CatTWCustomGS":return new Ie(e,t);case"NumTWRegularBin":return new Ve(e,t);case"NumTWCustomBin":return new De(e,t);case"NumTWCont":return new Qe(e,t);default:throw`unable to init(tw)`}}static initRaw(e,t={}){return i(this,void 0,void 0,(function*(){const i=yield Fe.fill(e,t);return Fe.init(i,t)}))}static fill(e,t={}){var n,r;return i(this,void 0,void 0,(function*(){yield Fe.preprocess(e,t===null||t===void 0?void 0:t.vocabApi);const i=e.term.type=="float"||e.term.type=="integer"?"numeric":e.term.type;t.defaultQ=((n=t.defaultQByTsHandler)===null||n===void 0?void 0:n[i])||null;switch(e.term.type){case"categorical":{return yield Ne.fill(e,t)}case"integer":case"float":return yield Ge.fill(e,t);default:throw`unrecognized tw.term?.type='${(r=e.term)===null||r===void 0?void 0:r.type}'`}}))}static preprocess(e,t){return i(this,void 0,void 0,(function*(){const i=Object.keys(e);if(!i.length)throw`empty tw object`;if(e.id&&!e.term){yield ct([e],t);delete e.id}if(!e.q)e.q={};e.q.isAtomic=true;Fe.reshapeLegacyTw(e)}))}static reshapeLegacyTw(e){if(Object.keys(e.q).includes("groupsetting")){if(!e.q.groupsetting.inuse){e.q.type="values"}else if(e.q.type=="predefined-groupset"){e.q.predefined_groupset_idx=e.q.groupsetting.predefined_groupset_idx}else if(e.q.type=="custom-groupset"){e.q.customset=e.q.groupsetting.customset}else{throw"invalid q.type"}delete e.q["groupsetting"]}}}function Xe(e){switch(e){case"./handlers/categorical.ts":return import("./categorical-f67752ed.js");case"./handlers/condition.ts":return import("./condition-dcc70001.js");case"./handlers/density.ts":return import("./density-e023c28f.js");case"./handlers/geneExpression.ts":return import("./geneExpression-e4a5a2cd.js");case"./handlers/geneVariant.ts":return import("./geneVariant-447d6af9.js");case"./handlers/groupsetting.ts":return import("./groupsetting-697a1503.js");case"./handlers/metaboliteIntensity.ts":return import("./metaboliteIntensity-f407ad0c.js");case"./handlers/numeric.binary.ts":return import("./numeric.binary-da92d665.js");case"./handlers/numeric.continuous.ts":return import("./numeric.continuous-92d1dea8.js");case"./handlers/numeric.discrete.ts":return import("./numeric.discrete-cd8f09b1.js");case"./handlers/numeric.spline.ts":return import("./numeric.spline-9a9987b6.js");case"./handlers/numeric.toggle.ts":return import("./numeric.toggle-8f68f077.js");case"./handlers/numeric.ts":return import("./numeric-eb1d29b3.js");case"./handlers/samplelst.ts":return import("./samplelst-27115b0e.js");case"./handlers/singleCellCellType.ts":return import("./singleCellCellType-b4061c59.js");case"./handlers/singleCellGeneExpression.ts":return import("./singleCellGeneExpression-547149f2.js");case"./handlers/snp.ts":return import("./snp-6bbefa83.js");case"./handlers/snplocus.ts":return import("./snplocus-84450f3d.js");case"./handlers/snplst.sampleSum.ts":return import("./snplst.sampleSum-e47d05f0.js");case"./handlers/snplst.ts":return import("./snplst-6865d7c7.js");case"./handlers/survival.ts":return import("./survival-538cddc2.js");default:return new Promise((function(t,i){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(i.bind(null,new Error("Unknown variable dynamic import: "+e)))}))}}function ze(e){switch(e){case"./handlers/categorical.ts":return import("./categorical-f67752ed.js");case"./handlers/condition.ts":return import("./condition-dcc70001.js");case"./handlers/density.ts":return import("./density-e023c28f.js");case"./handlers/geneExpression.ts":return import("./geneExpression-e4a5a2cd.js");case"./handlers/geneVariant.ts":return import("./geneVariant-447d6af9.js");case"./handlers/groupsetting.ts":return import("./groupsetting-697a1503.js");case"./handlers/metaboliteIntensity.ts":return import("./metaboliteIntensity-f407ad0c.js");case"./handlers/numeric.binary.ts":return import("./numeric.binary-da92d665.js");case"./handlers/numeric.continuous.ts":return import("./numeric.continuous-92d1dea8.js");case"./handlers/numeric.discrete.ts":return import("./numeric.discrete-cd8f09b1.js");case"./handlers/numeric.spline.ts":return import("./numeric.spline-9a9987b6.js");case"./handlers/numeric.toggle.ts":return import("./numeric.toggle-8f68f077.js");case"./handlers/numeric.ts":return import("./numeric-eb1d29b3.js");case"./handlers/samplelst.ts":return import("./samplelst-27115b0e.js");case"./handlers/singleCellCellType.ts":return import("./singleCellCellType-b4061c59.js");case"./handlers/singleCellGeneExpression.ts":return import("./singleCellGeneExpression-547149f2.js");case"./handlers/snp.ts":return import("./snp-6bbefa83.js");case"./handlers/snplocus.ts":return import("./snplocus-84450f3d.js");case"./handlers/snplst.sampleSum.ts":return import("./snplst.sampleSum-e47d05f0.js");case"./handlers/snplst.ts":return import("./snplst-6865d7c7.js");case"./handlers/survival.ts":return import("./survival-538cddc2.js");default:return new Promise((function(t,i){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(i.bind(null,new Error("Unknown variable dynamic import: "+e)))}))}}const Je=`_ts_${(+new Date).toString().slice(-8)}`;let Ze=0;function Ke(e){return i(this,void 0,void 0,(function*(){if(!e)return`${Ze++}${Je}`;delete e.$id;return yield tt(JSON.stringify(e))}))}const et=new TextEncoder;function tt(e){return i(this,void 0,void 0,(function*(){const t=et.encode(e);const i=yield crypto.subtle.digest("SHA-1",t);const n=Array.from(new Uint8Array(i));const r=n.map((e=>e.toString(16).padStart(2,"0"))).join("");return it(r).replace("=","-")}))}function it(e){return btoa([...e].reduce(((t,i,n)=>t+=!(n-1&1)?String.fromCharCode(parseInt(e.substring(n-1,n+1),16)):""),""))}const nt={menuOptions:"edit",menuLayout:"vertical"};class rt{constructor(e){this.opts=this.validateOpts(e);this.vocabApi=e.vocabApi;this.activeCohort=e.activeCohort;this.placeholder=e.placeholder;this.durations={exit:0};this.disable_terms=e.disable_terms;this.usecase=e.usecase;this.abbrCutoff=e.abbrCutoff;this.numqByTermIdModeType={};this.dom={holder:e.holder,tip:e.tip||new d({padding:"0px",parent_menu:this.opts.holder&&this.opts.holder.node()&&this.opts.holder.node().closest(".sja_menu_div")})};this.dom.tip2=new d({padding:"0px",parent_menu:this.dom.tip.d.node()});at(this);ot(this);this.initUI();const t=dt(this);this.handlerByType={default:t};this.handler=t;this.hasError=false;this.api={main:this.main.bind(this),runCallback:this.runCallback.bind(this),showTree:this.showTree,showMenu:this.showMenu.bind(this),showGeneSearch:this.showGeneSearch,hasError:()=>this.hasError,validateQ:e=>{if(!this.handler||!this.handler.validateQ)return;try{this.handler.validateQ(e)}catch(e){this.hasError=true;throw e}}}}runCallback(e=null){var t,i;const n=this.term?{term:this.term,q:this.q,isAtomic:true}:{};if("$id"in this)n.$id=this.$id;if(((t=n.q)===null||t===void 0?void 0:t.reuseId)&&n.q.reuseId===((i=this.data.q)===null||i===void 0?void 0:i.reuseId)){if(!p(n.q,this.data.q)){delete n.q.reuseId;delete n.q.name}}const r=e?JSON.parse(JSON.stringify(e)):{};if(this.opts.callback)this.opts.callback(e?o(JSON.stringify(n),r):n)}validateOpts(e){const t=Object.assign({},nt,e);if(!t.holder&&t.renderAs!="none")throw".holder missing";if(typeof t.callback!="function")throw".callback() is not a function";if(!t.vocabApi)throw".vocabApi missing";if(typeof t.vocabApi!="object");if("placeholder"in t&&!t.placeholder&&"placeholderIcon"in t&&!t.placeholderIcon)throw"must specify a non-empty opts.placeholder and/or .placeholderIcon";if(!("placeholder"in t))t.placeholder="Select term&nbsp;";if(!("placeholderIcon"in t))t.placeholderIcon="+";if(!Number.isInteger(t.abbrCutoff))t.abbrCutoff=18;this.validateMenuOptions(t);if(!t.numericEditMenuVersion)t.numericEditMenuVersion=["discrete"];this.mayValidate_noTermPromptOptions(t);return t}main(e={}){return i(this,void 0,void 0,(function*(){try{if(this.doNotHideTipInMain){delete this.doNotHideTipInMain}else{this.dom.tip.hide()}this.hasError=false;delete this.error;this.validateMainData(e);this.data=e;this.term=e.term;this.q=JSON.parse(JSON.stringify(e.q));if("$id"in e)this.$id=e.$id;if("disable_terms"in e)this.disable_terms=e.disable_terms;if("filter"in e)this.filter=e.filter;if("activeCohort"in e)this.activeCohort=e.activeCohort;if("sampleCounts"in e)this.sampleCounts=e.sampleCounts;if("menuOptions"in e)this.opts.menuOptions=e.menuOptions;yield this.setHandler(this.term?this.term.type:null);if(e.term&&this.handler&&this.handler.validateQ)this.handler.validateQ(e);if(this.handler.postMain)yield this.handler.postMain();if(this.opts.renderAs!="none")this.updateUI()}catch(e){this.hasError=true;throw e}}))}validateMainData(e){if(e.term){if(!e.term.type)throw"data.term.type missing";if(x(e.term.type)){if(!e.term.id&&e.term.type!=m.SAMPLELST)throw"data.term.id missing";if(!e.term.name)throw"data.term.name missing"}}if(!e.q)e.q={};if(typeof e.q!="object")throw"data.q{} is not object";if(e.disable_terms){if(!Array.isArray(e.disable_terms))throw"data.disable_terms[] is not array"}this.mayValidate_noTermPromptOptions(e)}validateMenuOptions(e){if(!e.menuOptions)e.menuOptions=nt.menuOptions;if(e.menuOptions=="all")e.menuOptions="*";for(const t of["edit","replace","remove"]){if(F(t,e.menuOptions))return}throw`no matches found for termsetting opts.menuOptions='${e.menuOptions}'`}mayValidate_noTermPromptOptions(e){if(!e.noTermPromptOptions)return;if(!Array.isArray(e.noTermPromptOptions))throw"noTermPromptOptions[] is not array";for(const t of e.noTermPromptOptions){if(t.isDictionary);else{if(!t.termtype)throw"element of noTermPromptOptions[] missing both isDictionary=true and .termtype"}if(!t.text&&!t.html)throw"element of noTermPromptOptions[] missing both .text and .html";if(t.q&&typeof t.q!="object")throw"type.q{} is not object"}this.noTermPromptOptions=e.noTermPromptOptions}setHandler(e){return i(this,void 0,void 0,(function*(){if(!e){this.handler=this.handlerByType.default;return}const t=e=="integer"||e=="float"?"numeric":e;if(!this.handlerByType[t]){try{const e=yield ze(`./handlers/${t}.ts`);this.handlerByType[t]=yield e.getHandler(this)}catch(e){throw`error with handler='./handlers/${t}.ts': ${e}`}}this.handler=this.handlerByType[t]}))}}const st=l(rt);function ot(e){e.initUI=()=>{if(e.opts.$id){e.dom.tip.d.attr("id",e.opts.$id+"-ts-tip")}if(!e.dom.holder)return;e.dom.nopilldiv=e.dom.holder.append("div").style("cursor","pointer").on("click",e.clickNoPillDiv).on(`keyup.sjpp-termdb`,(t=>{if(t.key=="Enter")e.showTree(t)}));e.dom.pilldiv=e.dom.holder.append("div");if(e.opts.placeholder){e.dom.nopilldiv.append("div").html(e.placeholder).attr("class","sja_clbtext2").style("padding","3px 6px 3px 6px").style("display","inline-block")}if(e.opts.placeholderIcon){e.dom.nopilldiv.append("div").attr("class","sja_filter_tag_btn add_term_btn").style("padding","3px 6px 3px 6px").style("display","inline-block").style("border-radius","6px").style("background-color","#4888BF").text(e.opts.placeholderIcon)}e.dom.btnDiv=e.dom.holder.append("div");e.dom.content_holder=u(e.dom.holder.node().parentNode).append("div")};e.updateUI=()=>i(this,void 0,void 0,(function*(){e.dom.btnDiv.selectAll("*").remove();e.dom.content_holder.selectAll("*").remove();if(!e.term){e.dom.nopilldiv.style("display","block");e.dom.pilldiv.style("display","none");e.dom.btnDiv.style("display","none");return}if(e.term.hashtmldetail){if(e.opts.buttons&&!e.opts.buttons.includes("info"))e.opts.buttons.unshift("info");else e.opts.buttons=["info"]}else{e.opts.buttons=[]}if(e.opts.buttons.length){e.dom.btnDiv.selectAll("div").data(e.opts.buttons).enter().append("div").style("display","inline-block").style("padding","0px 5px").style("cursor","pointer").style("color","#999").style("font-size",".8em").html((e=>e.toUpperCase())).on("click",((t,i)=>{if(i=="delete")e.removeTerm();else if(i=="replace"){e.showTree(t.target)}else throw"unknown button"}));if(e.term.hashtmldetail){const t=e.dom.btnDiv.selectAll("div").filter((function(){return u(this).text()==="INFO"}));const i=yield import("./termInfo-4d954045.js");i.termInfoInit({vocabApi:e.opts.vocabApi,icon_holder:t,content_holder:e.dom.content_holder,id:e.term.id,state:{term:e.term}})}}e.dom.nopilldiv.style("display","none");e.dom.pilldiv.style("display",e.opts.buttons?"inline-block":"block");e.dom.btnDiv.style("display",e.opts.buttons?"inline-block":"none");const t=e.dom.pilldiv.selectAll(".ts_pill").data([e.term],(e=>e.id));t.exit().each(e.exitPill);t.transition().duration(200).each(e.updatePill);t.enter().append("div").attr("class","ts_pill").style("display","grid").style("grid-template-columns","auto").style("grid-template-areas",'"left right"').style("cursor","pointer").style("margin","2px").on("click",e.showMenu).transition().duration(200).each(e.enterPill)}));e.enterPill=function(){return i(this,void 0,void 0,(function*(){const t=u(this);e.dom.pill_termname=t.append("div").attr("class","term_name_btn  sja_filter_tag_btn").attr("tabindex",0).style("display","flex").style("grid-area","left").style("position","relative").style("align-items","center").style("padding","3px 6px 3px 6px").style("border-radius","6px").html(e.handler.getPillName).on(`keyup.sjpp-termdb`,(e=>{if(e.key=="Enter")e.target.click()}));e.updatePill.call(this)}))};e.updatePill=function(){return i(this,void 0,void 0,(function*(){const t=u(this);const i=e.handler.getPillStatus()||{};e.dom.pill_termname.style("border-radius",i.text?"6px 0 0 6px":"6px").html(e.handler.getPillName);const n=t.selectAll(".ts_summary_btn").data(i.text?[{txt:i.text}]:[],(e=>e.txt));n.exit().remove();const r=n.enter().append("div").attr("class","ts_summary_btn sja_filter_tag_btn").style("display","flex").style("grid-area","right").style("position","relative").style("align-items","center").style("padding","3px 6px 3px 6px").style("border-radius","0 6px 6px 0").style("font-style","italic").html((e=>e.txt)).style("opacity",0).transition().duration(200).style("opacity",1);if(i.bgcolor){r.transition().duration(200).style("background-color",i.bgcolor)}}))};e.exitPill=function(){u(this).style("opacity",1).transition().duration(e.durations.exit).style("opacity",0).remove()}}function at(e){e.removeTerm=()=>{e.opts.callback(null)};e.cancelGroupsetting=()=>{e.opts.callback({id:e.term.id,term:e.term,q:{mode:"discrete",type:"values",isAtomic:true}})};e.clickNoPillDiv=()=>i(this,void 0,void 0,(function*(){if(!e.noTermPromptOptions||e.noTermPromptOptions.length==0){yield e.showTree(e.dom.nopilldiv.node());return}e.dom.tip.clear().showunder(e.dom.nopilldiv.node());for(const t of e.noTermPromptOptions){const n=e.dom.tip.d.append("div").attr("class","sja_menuoption sja_sharp_border").on("click",(()=>i(this,void 0,void 0,(function*(){e.dom.tip.clear();if(t.isDictionary){yield e.showTree(e.dom.tip.d.node())}else if(t.termtype){if(t.q)e.q=structuredClone(t.q);yield e.setHandler(t.termtype);if(q(e.term)&&!e.term.bins&&e.term.type!="survival"){yield e.vocabApi.setTermBins({term:e.term,q:e.q})}e.handler.showEditMenu(e.dom.tip.d)}else{throw"termtype missing"}}))));if(t.text)n.text(t.text);else if(t.html)n.html(t.html)}}));e.showTree=function(t,n){return i(this,void 0,void 0,(function*(){e.dom.tip.clear();if(t)e.dom.tip.showunder(t instanceof Element?t:this instanceof Element?this:e.dom.holder.node());else e.dom.tip.show(n.clientX,n.clientY);if(!e.usecase)e.usecase={target:"default"};const r=yield import("./app-5aa892cb.js");r.appInit({holder:e.dom.tip.d,vocabApi:e.vocabApi,state:{activeCohort:e.activeCohort,tree:{usecase:e.usecase}},tree:{disable_terms:e.disable_terms,click_term:t=>i(this,void 0,void 0,(function*(){e.dom.tip.hide();let i;if(t.term)i=t;else{const e=t;i={term:e,q:{isAtomic:true},isAtomic:true}}if(e.opts.customFillTw)e.opts.customFillTw(i);yield yt(i,e.vocabApi,e.opts.defaultQ4fillTW);e.opts.callback(i)}))}})}))};e.showMenu=(t,n=null,r=null)=>{var s,o,a;const l=e.dom.tip;l.clear();if(e.opts.renderAs=="none"&&n)e.dom.holder=u(n);if(e.dom.holder){const i=(s=e.dom.holder)===null||s===void 0?void 0:s.node();if(i)l.showunder(i);else l.show(t.clientX,t.clientY)}const d=[];if(e.q.type=="predefined-groupset"||e.q.type=="custom-groupset"){if(e.q.mode!="binary"&&e.term.type!="geneVariant"){d.push({label:"Cancel grouping",callback:e.cancelGroupsetting})}}if(e.q&&!((o=e.term.groupsetting)===null||o===void 0?void 0:o.disabled)&&F("edit",e.opts.menuOptions)){d.push({label:"Edit",callback:t=>i(this,void 0,void 0,(function*(){if(e.term&&q(e.term)&&!e.term.bins&&e.term.type!="survival"){yield e.vocabApi.setTermBins({term:e.term,q:e.q})}e.handler.showEditMenu(t)}))})}if(F("replace",e.opts.menuOptions)){d.push({label:"Replace",callback:e.showTree})}if(F("remove",e.opts.menuOptions)){d.push({label:"Remove",callback:e.removeTerm})}if(e.opts.customMenuOptions)d.push(...e.opts.customMenuOptions);e.openMenu=r||l.d;e.openMenu.selectAll("div").data(d).enter().append("div").attr("class","sja_menuoption sja_sharp_border").attr("tabindex",((e,t)=>t+1)).style("display",e.opts.menuLayout=="horizontal"?"inline-block":"block").text((e=>e.label)).on("click",((t,i)=>{e.dom.tip.clear();i.callback(e.dom.tip.d)})).on("keyup",(e=>{if(e.key=="Enter")e.target.click()}));(a=e.openMenu.select(".sja_menuoption").node())===null||a===void 0?void 0:a.focus()};e.showReuseMenu=function(t){return i(this,void 0,void 0,(function*(){const n=t.append("div");n.style("display","block").style("padding","10px").append("span").style("color","#aaa").html("Save current setting as ");const r=e.vocabApi.getCustomTermQLst(e.term);const s=n.append("input").attr("type","text").attr("placeholder",r.nextReuseId).attr("value",e.q.reuseId||r.nextReuseId);n.append("button").style("margin-left","5px").html("Save").on("click",(()=>{const t=s.property("value").trim()||r.nextReuseId;e.q.reuseId=t;e.vocabApi.cacheTermQ(e.term,e.q);e.runCallback();e.dom.tip.hide()}));const o=t.append("div").style("margin","10px");const a={term:e.term,q:{}};yield ht(a,e.vocabApi);a.q.reuseId="Default";r.push(a.q);if(r.length>1){o.append("div").style("color","#aaa").html("Previously saved settings")}o.append("table").selectAll("tr").data(r).enter().append("tr").style("margin","2px 5px").each((function(t){const n=u(this);const r=lt(e.q,t);const s=t.name||t.reuseId;n.append("td").style("min-width","180px").style("text-align","center").html(s);const o=n.append("td").style("text-align","center");if(r){o.html(`In use <span style='color:#5a5;font-weight:600'>&check;</span>`)}else{o.append("button").style("min-width","80px").html("Use").on("click",(()=>{if(t.reuseId==="Default"){delete t.reuseId;delete t.name}e.q=t;e.dom.tip.hide();e.runCallback()}))}const a=n.append("td").style("text-align","center");if(!r&&t.reuseId!="Default"){a.append("button").style("min-width","80px").html("Delete").on("click",(()=>i(this,void 0,void 0,(function*(){yield e.vocabApi.uncacheTermQ(e.term,t);e.dom.tip.hide();e.runCallback()}))))}}));t.append("div").style("margin","20px 5px 5px 5px").style("padding","5px").style("font-size","0.8em").style("color","#aaa").html(`Saving the setting will allow it to be reused at another chart.<br/>`+`The setting will be reusable in your current or saved session.`)}))};e.showGeneSearch=function(t,n){e.dom.tip.clear();if(t)e.dom.tip.showunder(t instanceof Element?t:this instanceof Element?this:e.dom.holder.node());else e.dom.tip.show(n.clientX,n.clientY);const r=new Set;const s=e.dom.tip.d.append("div").style("padding","5px");const o=s.append("label");o.append("span").text("Search: ");const a=o.append("input").attr("type","text").on("input",(()=>i(this,void 0,void 0,(function*(){const t=a.property("value");try{const i=!t?{lst:[]}:yield e.vocabApi.findTerm(t,e.activeCohort,e.usecase,"gene");l.selectAll("*").remove();l.selectAll("div").data(i.lst.filter((e=>!r.has(e)))).enter().append("div").attr("class","ts_pill sja_filter_tag_btn sja_tree_click_term").style("display","block").style("margin","2px 3px").style("width","fit-content").text((e=>e.name)).on("click",(t=>{e.dom.tip.hide();e.runCallback({term:{name:t.name,type:"geneVariant"},q:{exclude:[]}})}))}catch(e){alert("Search error: "+e)}}))));const l=e.dom.tip.d.append("div").style("margin","5px").style("padding-left","5px").style("border-left","2px solid #ccc")}}function lt(e,t){const i=[e,t].map((e=>JSON.parse(JSON.stringify(e))));for(const e of i){delete e.binLabelFormatter;if(e.reuseId==="Default")delete e.reuseId;if(e.mode==="continuous")delete e.mode;if(e.mode==="discrete"&&e.type=="custom-bin"&&e.lst){for(const t of e.lst){delete t.range}}}return p(...i)}function dt(e){return{showEditMenu(){},getPillStatus(){},getPillName(t){return pt(e,t)}}}function pt(e,t){if(!e.opts.abbrCutoff)return t.name;return t.name.length<=e.opts.abbrCutoff+2?t.name:'<label title="'+t.name+'">'+t.name.substring(0,e.opts.abbrCutoff)+"..."+"</label>"}function ut(e,t,n){return i(this,void 0,void 0,(function*(){yield ct(e,t);const i=[];for(const r of e){i.push(ht(r,t,n))}yield Promise.all(i)}))}function ct(e,t){return i(this,void 0,void 0,(function*(){const i=[];for(const t of e){if(t.term)continue;if(t.id===undefined||t.id==="")throw".id is required";i.push(t.id)}const n=i.length?yield t.getTerms(i):{};for(const t of i){if(!n[t])throw`missing dictionary term for id=${t}`;for(const t of e){if(t.id&&t.id in n)t.term=n[t.id]}}}))}const ft=new Set(["categorical","integer","float"]);function ht(e,t,n){var r;return i(this,void 0,void 0,(function*(){e.isAtomic=true;if(!e.term&&e.id){yield ct([e],t)}if(ft.has((r=e.term)===null||r===void 0?void 0:r.type)){const i=yield Fe.fill(e,{vocabApi:t,defaultQByTsHandler:n});Object.assign(e,i);gt(e);if(!e.$id)e.$id=yield Ke(t.getTwMinCopy(e));if(e.q)e.q.isAtomic=true;return e}delete e.id;if(!e.q)e.q={};e.q.isAtomic=true;mt(e);yield yt(e,t,n);gt(e);if(!e.$id)e.$id=yield Ke(t.getTwMinCopy(e));return e}))}function mt(e){if(Object.keys(e.q).includes("groupsetting")){if(e.q["groupsetting"]["inuse"]){if(e.q.type=="predefined-groupset"){e.q["predefined_groupset_idx"]=e.q["groupsetting"]["predefined_groupset_idx"]}else if(e.q.type=="custom-groupset"){e.q["customset"]=e.q["groupsetting"]["customset"]}else{throw"invalid q.type"}}else{e.q.type="values"}delete e.q["groupsetting"]}}function yt(e,t,n){return i(this,void 0,void 0,(function*(){if(!e.$id)e.$id=yield Ke(t.getTwMinCopy(e));const i=e.term.type;const r=i=="float"||i=="integer"?"numeric":i;let s;if(e.term.type){try{s=yield Xe(`./handlers/${r}.ts`)}catch(e){throw`Type ${r} does not exist`}}else throw`Type not defined for ${JSON.stringify(e)}`;yield s.fillTW(e,t,n?n[r]:null)}))}function gt(e){if(!("mode"in e.q)){return}if(typeof e.q.mode!="string")throw"q.mode not string"}function vt(e,t){if(!e.hiddenValues){e.hiddenValues={};if(t.values){for(const i in t.values){if(t.values[i].uncomputable)e.hiddenValues[i]=1}}}}export{h as N,f as R,m as T,T as a,x as b,Oe as c,E as d,S as e,ht as f,Ke as g,st as h,q as i,je as j,y as k,Fe as l,ut as m,b as n,pt as o,Ce as r,vt as s,g as t};