@sjcrh/proteinpaint-client 2.201.0 → 2.202.0

package/dist/chunk-JKMN7XOP.js

@@ -1,1114 +0,0 @@
-import {
-  InputValuesTable
-} from "./chunk-C2JHLAKV.js";
-import {
-  mayRunSnplstTask
-} from "./chunk-7OYOC7XY.js";
-import {
-  RegressionResults
-} from "./chunk-Q4AP5L7R.js";
-import {
-  PlotBase,
-  fillTermWrapper,
-  get$id,
-  getCombinedTermFilter,
-  make_one_checkbox,
-  sayerror,
-  termsettingInit
-} from "./chunk-K6OVOHIZ.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  dictionaryNumericTypes,
-  isDictionaryType,
-  isNumericTerm,
-  numericTypes
-} from "./chunk-X6VTVZY7.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import {
-  get_bin_label
-} from "./chunk-L44P5N4U.js";
-import {
-  getValueConversionFactor
-} from "./chunk-75T7ESEO.js";
-import {
-  roundValue
-} from "./chunk-TLT4YIG3.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// plots/regression.inputs.term.js
-var InputTerm = class {
-  constructor(opts) {
-    this.opts = opts;
-    this.section = opts.section;
-    this.term = opts.term;
-    this.parent = opts.parent;
-    this.vocabApi = this.parent.parent.vocabApi || this.parent.app.vocabApi;
-  }
-  async init(holder) {
-    const termRow = holder.append("div");
-    const pillDiv = termRow.append("span").style("display", "inline-block");
-    const interactionDiv = termRow.append("span").style("margin-left", "20px");
-    this.dom = {
-      holder,
-      termRow,
-      pillDiv,
-      interactionDiv,
-      err_div: holder.append("div").style("display", "none").style("padding", "5px").style("background-color", "rgba(255,100,100,0.2)"),
-      infoDiv: holder.append("div"),
-      tip: new Menu()
-    };
-    try {
-      const { app, config, state, disable_terms } = this.parent;
-      const arg = {
-        placeholder: this.section.selectPrompt,
-        placeholderIcon: this.section.placeholderIcon,
-        holder: this.dom.pillDiv,
-        vocabApi: this.vocabApi,
-        noTermPromptOptions: this.opts.noTermPromptOptions,
-        activeCohort: state.activeCohort,
-        debug: app.opts.debug,
-        menuOptions: this.section.configKey == "outcome" ? "{edit,reuse,replace}" : "{edit,reuse,remove}",
-        usecase: { target: "regression", detail: this.section.configKey, regressionType: config.regressionType },
-        disable_terms,
-        abbrCutoff: 50,
-        genomeObj: this.parent.parent.genomeObj,
-        // required for snplocus
-        defaultQ4fillTW: get_defaultQ4fillTW(config.regressionType, this.section.configKey),
-        callback: (term) => {
-          this.parent.editConfig(this, term);
-        }
-      };
-      this.furbishTsConstructorArg(arg);
-      this.pill = await termsettingInit(arg);
-      if (this.section.configKey == "outcome") {
-        this.setQ = getQSetter4outcome(config.regressionType);
-      }
-      this.valuesTable = new InputValuesTable({
-        holder: this.dom.infoDiv,
-        input: this,
-        callback: (term) => {
-          this.parent.editConfig(this, term);
-        }
-      });
-    } catch (e) {
-      this.displayError([e]);
-    }
-  }
-  furbishTsConstructorArg(arg) {
-    const type = this.parent.config.regressionType;
-    if (this.section.configKey == "outcome") {
-      if (type == "logistic") {
-        arg.numericEditMenuVersion = ["binary"];
-        return;
-      }
-      if (type == "linear") {
-        arg.numericEditMenuVersion = ["continuous"];
-        return;
-      }
-      if (type == "cox") {
-        return;
-      }
-      throw "unknown regressionType";
-    }
-    if (this.section.configKey == "independent") {
-      arg.numericEditMenuVersion = ["continuous", "discrete", "spline"];
-      arg.geneVariantEditMenuOnlyGrp = true;
-      return;
-    }
-    throw "unknown section.configKey: " + this.section.configKey;
-  }
-  displayError(errors) {
-    this.hasError = true;
-    this.dom.err_div.selectAll("*").remove();
-    this.dom.err_div.style("display", "block").selectAll("div").data(Array.isArray(errors) ? errors : [errors]).enter().append("div").text((e) => e);
-    this.parent.handleError();
-    console.error(errors);
-  }
-  async main() {
-    const tw = this.term;
-    if (tw) {
-      delete tw.error;
-    }
-    this.dom.err_div.style("display", "none").text("");
-    this.hasError = false;
-    const errors = [];
-    try {
-      if (tw && this.setQ) {
-        const { app, state } = this.parent;
-        await this.setQ[tw.term.type](tw, this.vocabApi, this.parent.parent.filter, state);
-      }
-      try {
-        await this.updateTerm();
-      } catch (e2) {
-        errors.push(e2);
-      }
-      await this.pill.main(this.getPillArgs());
-      this.renderInteractionPrompt();
-      await this.valuesTable.main();
-      if (tw && !tw.$id) tw.$id = await get$id(this.vocabApi.getTwMinCopy(tw));
-      const e = tw && tw.error || this.pill.error;
-      if (e) errors.push(e);
-      if (errors.length) throw errors;
-    } catch (errors2) {
-      this.displayError(errors2);
-    }
-  }
-  async updateTerm() {
-    const tw = this.term;
-    if (!tw) return;
-    if (!tw.q) throw ".term.q missing on this input";
-    if (!tw.q.mode && isDictionaryType(tw.term.type)) {
-      if (tw.term.type == "categorical" || tw.term.type == "condition" || tw.term.type == "survival" || tw.term.type == "samplelst")
-        tw.q.mode = "discrete";
-      else tw.q.mode = "continuous";
-    }
-    const body = tw.term.type == "snplst" || tw.term.type == "snplocus" ? { cacheid: tw.q.cacheid } : { term1_q: tw.q };
-    const wait = this.dom.holder.append("div").style("padding", "5px").text("Loading...");
-    let data;
-    try {
-      data = await this.vocabApi.getCategories(tw.term, this.parent.parent.filter, body);
-      if (!data) throw `no data for term.id='${tw.term.id}'`;
-      if (data.error) throw data.error;
-    } finally {
-      wait.remove();
-    }
-    mayRunSnplstTask(tw, data);
-    this.termStatus = {
-      topInfoStatus: [],
-      bottomSummaryStatus: void 0,
-      sampleCounts: void 0,
-      excludeCounts: void 0,
-      allowToSelectRefGrp: false
-    };
-    if (tw.q.numOfSampleWithAnyValidGT) {
-      const invalid_snps_count = tw.term.snps.reduce((i, j) => i + (j.invalid ? 1 : 0), 0);
-      this.termStatus.topInfoStatus.push(
-        `${tw.q.numOfSampleWithAnyValidGT} samples with valid genotypes` + (invalid_snps_count > 0 ? ` ${invalid_snps_count} invalid SNP${invalid_snps_count > 1 ? "s" : ""}.` : "")
-      );
-    }
-    if ("geneticModel" in tw.q) {
-      this.termStatus.topInfoStatus.push(
-        "Genetic model: " + (tw.q.geneticModel == 0 ? "Additive" : tw.q.geneticModel == 1 ? "Dominant" : tw.q.geneticModel == 2 ? "Recessive" : "By genotype")
-      );
-    }
-    if (tw.q.restrictAncestry) {
-      this.termStatus.topInfoStatus.push("Analyzing " + tw.q.restrictAncestry.name);
-      if (tw.q.restrictAncestry.PCcount) {
-        this.termStatus.topInfoStatus.push(
-          `Adjusting for top ${tw.q.restrictAncestry.PCcount} ancestry principal components`
-        );
-      }
-    }
-    if (tw.term.reachedVariantLimit) {
-      this.termStatus.topInfoStatus.push(
-        `<span class=sja_mcdot style="background:#aaa;font-size:1em">
-				&nbsp;&#9888; Restricted to first ${tw.term.snps.length}
-				variants of this region.&nbsp;</span> Try zooming in.`
-      );
-    }
-    this.orderedLabels = data.orderedLabels;
-    if (data.lst) {
-      this.summarizeSample(tw, data.lst);
-      if (isNumericTerm(tw.term)) {
-        if (tw.q.mode != "continuous" && tw.q.mode != "spline") {
-          this.termStatus.allowToSelectRefGrp = true;
-        }
-        if (tw.q.scale && tw.q.scale != 1) this.termStatus.topInfoStatus.push(`Scale: Per ${tw.q.scale}`);
-        if (tw.q.mode == "discrete") {
-          this.termStatus.topInfoStatus.push(`Discrete variable with ${this.termStatus.sampleCounts.length} bins`);
-        }
-        const vc = tw.term.valueConversion;
-        const isConverted = vc && (tw.q.mode == "continuous" || tw.q.mode == "spline");
-        if (isConverted) {
-          this.termStatus.topInfoStatus.push(`Analyzed by the unit of ${vc.toUnit}, converted from ${vc.fromUnit}`);
-        }
-        if (tw.q.mode == "spline") {
-          const f = getValueConversionFactor(tw.term);
-          this.termStatus.topInfoStatus.push(
-            `Cubic spline variable with ${tw.q.knots.length} knots: ${tw.q.knots.map((x) => Number(x.value) * f).sort((a, b) => a - b).map((v) => f == 1 ? v : roundValue(v, 2)).join(", ")}${isConverted ? ` ${vc.toUnit}s` : ""}`
-          );
-        }
-      } else if (tw.term.type == "categorical" || tw.term.type == "geneVariant" || tw.term.type == "samplelst") {
-        this.termStatus.allowToSelectRefGrp = true;
-      } else if (tw.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(tw.q.timeScale)) throw "invalid q.timeScale";
-          const tdb = this.vocabApi.termdbConfig;
-          this.termStatus.topInfoStatus.push(`Time axis: ${tw.q.timeScale == "time" ? tdb.timeUnit : "age"}`);
-          this.termStatus.topInfoStatus.push(
-            `<span style="padding-left: 10px;">-start: ${tw.q.timeScale == "time" ? " " : "age at "}entry into the cohort (i.e., ${tdb.cohortStartTimeMsg})</span>`
-          );
-          this.termStatus.topInfoStatus.push(
-            `<span style="padding-left: 10px;">-end: ${tw.q.timeScale == "time" ? " " : "age at "}event or censoring/death</span>`
-          );
-          const grades = Object.keys(tw.term.values).map(Number);
-          const maxgrade = Math.max(...grades);
-          this.termStatus.topInfoStatus.push(
-            `<div style="padding-top: 8px;">Event: first occurrence of grade ${tw.q.breaks[0] === maxgrade ? tw.q.breaks[0] : `${tw.q.breaks[0]}-${maxgrade}</div>`}`
-          );
-        }
-      }
-      this.maySet_refGrp(tw);
-      if (this.section.configKey == "outcome") {
-        if (this.parent.config.regressionType == "logistic") {
-          tw.nonRefGrp = getLogisticOutcomeNonref(tw);
-        } else if (this.parent.config.regressionType == "cox") {
-          tw.eventLabel = getCoxOutcomeEventLabel(tw);
-        }
-      }
-    }
-  }
-  summarizeSample(tw, datalst) {
-    const excluded_values = /* @__PURE__ */ new Set();
-    if (tw.term.values) {
-      for (const i in tw.term.values) {
-        if (tw.term.values[i].uncomputable) excluded_values.add(tw.term.values[i].label);
-      }
-    }
-    if (tw.q.mode == "cox") {
-      const toExclude = datalst.find((x) => x.key == -1);
-      if (toExclude) excluded_values.add(toExclude.label);
-    }
-    const sampleCounts = this.termStatus.sampleCounts = datalst.filter((v) => !excluded_values.has(v.label));
-    const excludeCounts = this.termStatus.excludeCounts = datalst.filter((v) => excluded_values.has(v.label));
-    const totalCount = { included: 0, excluded: 0, total: 0 };
-    sampleCounts.forEach((v) => totalCount.included += v.samplecount);
-    excludeCounts.forEach((v) => totalCount.excluded += v.samplecount);
-    totalCount.total = totalCount.included + totalCount.excluded;
-    if (tw.term.type == "condition" && totalCount.total) {
-      totalCount.excluded = totalCount.total - totalCount.included;
-    }
-    this.termStatus.bottomSummaryStatus = `${totalCount.included} samples included` + (totalCount.excluded ? `. ${totalCount.excluded} samples excluded:` : "");
-    if (tw && tw.q.mode !== "continuous" && sampleCounts.length < 2)
-      throw `there should be two or more discrete values with samples for variable='${tw.term.name}'`;
-  }
-  maySet_refGrp(tw) {
-    if (this.section.configKey == "outcome" && this.parent.config.regressionType == "cox") {
-      return;
-    }
-    if (tw.q.mode == "continuous") {
-      tw.refGrp = "NA";
-      return;
-    }
-    const sc = this.termStatus.sampleCounts;
-    if (!("refGrp" in tw) || !sc.find((i) => i.key == tw.refGrp)) {
-      const o = this.orderedLabels;
-      if (o && o.length) sc.sort((a, b) => o.indexOf(a.key) - o.indexOf(b.key));
-      else sc.sort((a, b) => a.samplecount < b.samplecount ? 1 : -1);
-      tw.refGrp = sc[0].key;
-    }
-  }
-  getPillArgs() {
-    const section = this.section;
-    const { config, state, disable_terms } = this.parent;
-    const args = Object.assign(
-      {
-        activeCohort: state.activeCohort,
-        disable_terms,
-        usecase: {
-          target: "regression",
-          detail: section.configKey,
-          regressionType: config.regressionType
-        }
-      },
-      this.term
-    );
-    args.filter = this.parent.parent.filter;
-    return args;
-  }
-  remove() {
-    this.dom.termRow.transition().duration(500).style("opacity", 0).remove();
-    for (const key in this.dom) {
-      delete this.dom[key];
-    }
-  }
-  renderInteractionPrompt() {
-    this.dom.interactionDiv.style("display", "none");
-    if (!this.term) return;
-    if (this.section.configKey != "independent") return;
-    if (this.term.q.mode == "spline") return;
-    if (this.vocabApi.termdbConfig.regression?.settings?.disableInteractions) return;
-    {
-      let count = 0;
-      for (const input of this.section.inputLst) {
-        if (input.term && input.term.q.mode != "spline") {
-          count++;
-        }
-      }
-      if (count < 2) return;
-    }
-    const n = this.term.interactions.length;
-    this.dom.interactionDiv.style("display", "inline").html(n == 0 ? "Add interactions" : `${n} interaction${n > 1 ? "s" : ""}`).style("padding", "5px").style("background-color", n == 0 ? null : "#ececec").style("border-radius", n == 0 ? null : "6px").style("color", n == 0 ? "rgb(153, 153, 153)" : "#000").style("font-size", n == 0 ? "0.8em" : "").style("cursor", "pointer").on("click", () => this.renderInteractionOptions());
-  }
-  renderInteractionOptions() {
-    const self = this;
-    self.dom.tip.clear().showunder(self.dom.interactionDiv.node());
-    if (self.parent.config.includeUnivariate) {
-      const label = self.parent.dom.univariateCheckboxDiv.select("label").text().trim();
-      self.dom.tip.d.append("div").text(`Cannot add interactions. Please uncheck the "${label}" checkbox.`);
-      return;
-    }
-    self.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 ${this.term.term.name}`);
-    self.dom.tip.d.append("div").selectAll("div").data(self.parent.config.independent.filter((tw) => tw && tw.$id != self.term.$id && tw.q.mode != "spline")).enter().append("div").style("margin", "5px").each(function(tw) {
-      const elem = select_default(this).append("label");
-      const checkbox = elem.append("input").attr("type", "checkbox").property("checked", self.term.interactions.includes(tw.$id));
-      elem.append("span").text(" " + tw.term.name);
-    });
-    self.dom.tip.d.append("button").text("Apply").style("margin", "5px").on("click", () => {
-      self.dom.tip.hide();
-      self.term.interactions = [];
-      self.dom.tip.d.selectAll("input").each(function(tw) {
-        if (select_default(this).property("checked")) self.term.interactions.push(tw.$id);
-      });
-      for (const tw of self.parent.config.independent) {
-        const interactions = new Set(tw.interactions);
-        self.term.interactions.includes(tw.$id) ? interactions.add(self.term.$id) : interactions.delete(self.term.$id);
-        tw.interactions = [...interactions];
-      }
-      self.parent.editConfig(self, self.term);
-    });
-  }
-};
-function getQSetter4outcome(regressionType) {
-  return {
-    integer: regressionType == "logistic" ? maySetTwoBins : setContMode,
-    float: regressionType == "logistic" ? maySetTwoBins : setContMode,
-    geneExpression: regressionType == "logistic" ? maySetTwoBins : setContMode,
-    //Added geneExpression, but still breaks, need to fix
-    categorical: maySetTwoGroups,
-    condition: setQ4tteOutcome,
-    survival: setQ4tteOutcome
-  };
-}
-async function maySetTwoBins(tw, vocabApi, filter, state) {
-  if (tw.q.mode == "binary" && tw.q.lst && tw.q.lst.length == 2) {
-    tw.q.mode = "binary";
-    return;
-  }
-  const data = await vocabApi.getPercentile(tw.term, [50], state.termfilter);
-  if (data.error || !data.values.length || !Number.isFinite(data.values[0]))
-    throw "cannot get median value: " + (data.error || "no data");
-  const median = tw.term.type == "integer" ? Math.round(data.values[0]) : Number(data.values[0].toFixed(2));
-  tw.q = {
-    mode: "binary",
-    type: "custom-bin",
-    lst: [
-      {
-        startunbounded: true,
-        stopinclusive: true,
-        stop: median
-      },
-      {
-        stopunbounded: true,
-        startinclusive: false,
-        start: median
-      }
-    ]
-  };
-  tw.q.lst.forEach((bin) => {
-    bin.label = get_bin_label(bin, tw.q);
-  });
-  tw.refGrp = tw.q.lst[0].label;
-}
-function setQ4tteOutcome(tw, vocabApi, filter, state) {
-  if (state.config.regressionType == "logistic") {
-    if (!tw.refGrp) tw.refGrp = tw.q.groups[0].name;
-  }
-  if (state.config.regressionType == "cox") {
-    if (!tw.q.timeScale) tw.q.timeScale = "time";
-  }
-}
-async function maySetTwoGroups(tw, vocabApi, filter, state) {
-  const { term, q } = tw;
-  if (q.mode == "binary") {
-    if (q.type == "values" && Object.keys(term.values).length == 2) return;
-    if (q.type == "predefined-groupset") {
-      const idx = q.predefined_groupset_idx;
-      const t_gs2 = term.groupsetting;
-      if (t_gs2[idx] && Object.keys(t_gs2[idx]).length == 2) return;
-    }
-    if (q.type == "custom-groupset") {
-      const gs = q.customset;
-      if (gs.groups.filter((g) => !g.uncomputable).length == 2) return;
-    }
-  }
-  const data = await vocabApi.getCategories(term, filter);
-  if (data.error) throw "cannot get categories: " + data.error;
-  const category2samplecount = /* @__PURE__ */ new Map();
-  const computableCategories = [];
-  const uncomputableCategories = [];
-  for (const i of data.lst) {
-    category2samplecount.set(i.key, i.samplecount);
-    if (term.values && term.values[i.key] && term.values[i.key].uncomputable) uncomputableCategories.push(i.key);
-    else computableCategories.push(i.key);
-  }
-  if (computableCategories.length < 2) {
-    q.type = "values";
-    tw.error = "less than 2 categories/grades - cannot create separate groups";
-    return;
-  }
-  if (computableCategories.length == 2) {
-    q.type = "values";
-    return;
-  }
-  const t_gs = term.groupsetting;
-  if (q.customset && q.customset.groups && q.customset.groups.length == 2 && groupsetNoEmptyGroup(q.customset, category2samplecount)) {
-    q.type = "custom-groupset";
-    return;
-  }
-  if (t_gs && t_gs.lst) {
-    if (q.predefined_groupset_idx >= 0 && t_gs.lst[q.predefined_groupset_idx] && t_gs.lst[q.predefined_groupset_idx].groups.length == 2 && groupsetNoEmptyGroup(t_gs.lst[q.predefined_groupset_idx], category2samplecount)) {
-      q.type = "predefined-groupset";
-      return;
-    }
-    const i = t_gs.lst.findIndex((g) => g.groups.length == 2);
-    if (i != -1 && groupsetNoEmptyGroup(t_gs.lst[i], category2samplecount)) {
-      q.predefined_groupset_idx = i;
-      q.type = "predefined-groupset";
-      return;
-    }
-  }
-  const customset = {
-    activeCohort: state.activeCohort,
-    // creating 3 groups instead of 2 groups since current groupset UI expects first group to be excluded group
-    // TODO: refactor client/termsetting/handlers/qualitative.ts to not consider the first group (i.e. group.currentIdx === 0) as the excluded group, but rather to consider group.excluded=true as the excluded group
-    groups: [
-      {
-        name: "Excluded categories",
-        type: "values",
-        values: uncomputableCategories.map((v) => {
-          return { key: v };
-        })
-      },
-      {
-        name: "Group 1",
-        type: "values",
-        values: []
-      },
-      {
-        name: "Group 2",
-        type: "values",
-        values: []
-      }
-    ]
-  };
-  const group_i_cutoff = Math.round(computableCategories.length / 2);
-  for (const [i, v] of computableCategories.entries()) {
-    if (i < group_i_cutoff) customset.groups[1].values.push({ key: v });
-    else customset.groups[2].values.push({ key: v });
-  }
-  q.customset = customset;
-  q.type = "custom-groupset";
-}
-function setContMode(tw) {
-  tw.q.mode = "continuous";
-}
-function groupsetNoEmptyGroup(gs, c2s) {
-  for (const g of gs.groups) {
-    let total = 0;
-    if (g.type == "values") {
-      for (const i of g.values) total += c2s.get(i.key) || 0;
-      if (total == 0) return false;
-    }
-  }
-  return true;
-}
-function getLogisticOutcomeNonref(outcome) {
-  if (outcome.term.type == "condition") {
-    for (const i of outcome.q.groups) {
-      if (i.name != outcome.refGrp) return i.name;
-    }
-    throw "nonref group not found for logistic outcome";
-  }
-  if (outcome.q.type == "predefined-groupset") {
-    if (!Number.isInteger(outcome.q.predefined_groupset_idx))
-      throw 'outcome.q.predefined_groupset_idx not integer when q.type is "predefined-groupset"';
-    if (!outcome.term.groupsetting) throw "outcome.term.groupsetting missing";
-    const grpset = outcome.term.groupsetting.lst[outcome.q.predefined_groupset_idx];
-    if (!grpset) throw "groupset not found by outcome.q.predefined_groupset_idx";
-    const nonrefgrp = grpset.groups.find((i) => i.name != outcome.refGrp);
-    if (!nonrefgrp) throw "non-ref group not found for predefined-groupset";
-    return nonrefgrp.name;
-  }
-  if (outcome.q.type == "custom-groupset") {
-    if (!outcome.q.customset) throw "outcome.q.customset missing";
-    const nonrefgrp = outcome.q.customset.groups.find((i) => i.name != outcome.refGrp);
-    if (!nonrefgrp) throw "non-ref group not found for custom-groupset";
-    return nonrefgrp.name;
-  }
-  if (outcome.q.type == "values") {
-    if (!outcome.term.values) throw "outcome.term.values{} missing";
-    for (const k in outcome.term.values) {
-      const v = outcome.term.values[k];
-      if (v.label != outcome.refGrp) return v.label;
-    }
-    throw "unknown nonref group from outcome.term.values";
-  }
-  if (outcome.q.type == "custom-bin") {
-    const nonrefbin = outcome.q.lst.find((i) => i.label != outcome.refGrp);
-    if (!nonrefbin) throw "non-ref bin is not found for custom-bin";
-    return nonrefbin.label;
-  }
-  if (outcome.q.type == "regular-bin") {
-    throw "do not know a way to find computed bin list for type=regular-bin";
-  }
-  throw "unknown outcome.q.type";
-}
-function getCoxOutcomeEventLabel(tw) {
-  let eventLabel;
-  if (!tw.term.values) throw "tw.term.values missing";
-  if (tw.term.type == "condition") {
-    const grades = Object.keys(tw.term.values).map((k) => {
-      const grade = Number(k);
-      if (!Number.isFinite(grade)) throw "grade is not a number";
-      return grade;
-    });
-    const startGrade = tw.q.breaks[0];
-    const endGrade = Math.max(...grades);
-    eventLabel = `Grades ${startGrade}-${endGrade}`;
-  } else if (tw.term.type == "survival") {
-    const exitCodes = Object.keys(tw.term.values).map((k) => {
-      const code = Number(k);
-      if (!Number.isFinite(code)) throw "exit code is not a number";
-      return code;
-    });
-    eventLabel = tw.term.values[Math.max(...exitCodes)].label;
-  } else {
-    throw "unexpected tw.term.type";
-  }
-  return eventLabel;
-}
-
-// plots/regression.inputs.js
-var allNonDictionaryTerms = [
-  {
-    termtype: "snplst",
-    //html: 'A list of SNPs <span style="font-size:.7em">All SNPs are analyzed in one model</span>'
-    html: "A list of variants"
-  },
-  {
-    termtype: "snplocus",
-    //html: 'Variants in a locus <span style="font-size:.7em">Variants are analyzed individually</span>'
-    html: "Variants in a locus"
-  },
-  {
-    termtype: "prs",
-    text: "Polygenic risk score"
-  }
-];
-var RegressionInputs = class {
-  constructor(opts) {
-    this.opts = opts;
-    this.app = opts.app;
-    this.parent = opts.parent;
-    setInteractivity(this);
-    setRenderers(this);
-    this.createSectionConfigs();
-    this.initUI();
-  }
-  createSectionConfigs() {
-    this.outcome = {
-      /*** static configuration ***/
-      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" },
-      /*** dynamic configuration ***/
-      inputLst: [],
-      /*** tracker for this section's DOM elements ***/
-      dom: {}
-    };
-    this.independent = {
-      /*** static configuration ***/
-      heading: "Independent variable(s)",
-      selectPrompt: "Add independent variable",
-      placeholderIcon: "",
-      configKey: "independent",
-      limit: 10,
-      usecase: { target: "regression", regressionType: this.opts.regressionType, detail: "independent" },
-      /*** dynamic configuration ***/
-      inputLst: [],
-      /*** tracker for this section's DOM elements ***/
-      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 updates = [];
-      for (const section of this.sections) {
-        await this.renderSection(section);
-        for (const input of section.inputLst) {
-          input.dom.holder.style("border-left", input.term ? "1px solid #bbb" : "");
-          updates.push(input.main());
-        }
-      }
-      await Promise.all(updates);
-      for (const section of this.sections) {
-        for (const input of section.inputLst) {
-          if (input.term && input.term.error || input.hasError) {
-            this.hasError = true;
-          }
-        }
-      }
-    } catch (e) {
-      this.hasError = true;
-      throw e;
-    }
-  }
-  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 vb of this.config.independent) {
-        this.disable_terms.push(vb.term);
-      }
-    }
-  }
-  handleError() {
-    this.hasError = true;
-    this.dom.submitBtn.property("disabled", true);
-  }
-  getNoTermPromptOptions(section) {
-    if (section.configKey != "independent") return;
-    const lst = [];
-    for (const item of structuredClone(allNonDictionaryTerms)) {
-      if (!this.state.allowedTermTypes.includes(item.termtype)) {
-        continue;
-      }
-      if (section.inputLst.find((i) => i.term && i.term.term.type == item.termtype)) {
-        continue;
-      }
-      if (item.termtype == "snplocus") {
-        if (this.config.includeUnivariate) {
-          item.invalid = true;
-          const label = this.dom.univariateCheckboxDiv.select("label").text().trim();
-          item.invalidMsg = `Cannot add this variable. Please uncheck the "${label}" checkbox.`;
-        }
-      }
-      lst.push(item);
-    }
-    if (lst.length) {
-      lst.unshift({
-        isDictionary: true,
-        text: "Dictionary variable"
-      });
-    }
-    return lst;
-  }
-};
-function setRenderers(self) {
-  self.initUI = () => {
-    const controls = self.opts.holder.append("div").style("display", "block");
-    self.dom = {
-      div: self.opts.holder,
-      //.style('margin', '10px 0px'),
-      controls,
-      body: controls.append("div"),
-      foot: controls.append("div").style("margin", "0px 20px").style("display", "flex").style("align-items", "center").style("gap", "20px")
-    };
-    self.dom.submitBtn = self.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", self.submit);
-    self.dom.univariateCheckboxDiv = self.dom.foot.append("div").style("display", "none");
-    self.dom.univariateCheckbox = make_one_checkbox({
-      labeltext: "Include univariate results",
-      checked: false,
-      holder: self.dom.univariateCheckboxDiv,
-      callback: (checked) => {
-        const invalid = self.config.independent.find((v) => v.interactions.length || v.term.type == "snplocus");
-        if (invalid) {
-          self.dom.univariateCheckbox.property("checked", false);
-          const tip = new Menu();
-          tip.showunder(self.dom.univariateCheckboxDiv.node());
-          const msg = `Cannot include univariate results. Please remove ${invalid.interactions.length ? "all interactions" : `the "${invalid.term.name}" variable`}.`;
-          tip.d.append("div").text(msg);
-          return;
-        }
-        self.app.dispatch({
-          type: "plot_edit",
-          id: self.parent.id,
-          chartType: "regression",
-          config: {
-            hasUnsubmittedEdits: true,
-            includeUnivariate: checked
-          }
-        });
-      }
-    });
-    self.dom.submitMsgs = self.dom.foot.append("div").style("color", "#cc0000").style("font-style", "italic").style("font-size", "0.8em");
-    self.submitMsgs = {};
-    for (const section of self.sections) {
-      const div = self.dom.body.append("div");
-      self.addSection(section, div);
-    }
-  };
-  self.addSection = function(section, div) {
-    div.style("display", "none").style("margin", "3px 5px").style("padding", "3px 5px").attr("data-testid", section.configKey);
-    section.dom = {
-      holder: div,
-      headingDiv: div.append("div").style("margin", "3px 5px 20px 5px").style("font-size", "17px").style("color", "#bbb").text(section.heading),
-      inputsDiv: div.append("div")
-    };
-  };
-  self.renderSection = function(section) {
-    section.dom.holder.style("display", section.configKey == "outcome" || self.config.outcome ? "block" : "none");
-    syncInputsWithConfig(section);
-    const inputs = section.dom.inputsDiv.selectAll(":scope > div").data(section.inputLst, (input) => input.term && (input.term.term.id || input.term.term.name));
-    inputs.exit().each(removeInput);
-    inputs.enter().append("div").each(addInput);
-  };
-  function syncInputsWithConfig(section) {
-    const selected = self.config[section.configKey];
-    const selectedArray = Array.isArray(selected) ? selected : selected ? [selected] : [];
-    mayConvertInteractionIds(selectedArray, section);
-    for (const variable of selectedArray) {
-      if (section.configKey == "independent") {
-        if (!variable.interactions) variable.interactions = [];
-        for (const id of variable.interactions) {
-          const tw = selectedArray.find((i) => i.$id == id);
-          if (!tw) throw "interacting partner not found in independents: " + id;
-          if (!tw.interactions) tw.interactions = [];
-          if (!tw.interactions.includes(variable.$id)) tw.interactions.push(variable.$id);
-        }
-      }
-      const input = section.inputLst.find((input2) => input2.term?.$id == variable.$id);
-      if (!input) {
-        section.inputLst.push(
-          new InputTerm({
-            section,
-            term: variable,
-            parent: self
-          })
-        );
-      } else {
-        input.term = variable;
-      }
-    }
-    mayAddBlankInput(section, self);
-  }
-  function mayConvertInteractionIds(selectedArray, section) {
-    if (section.configKey != "independent") return;
-    const id2$id = /* @__PURE__ */ new Map();
-    for (const v of selectedArray) {
-      if (v.id) id2$id.set(v.id, v.$id);
-    }
-    for (const v of selectedArray) {
-      if (v.interactions?.length) {
-        for (const [i, id] of v.interactions.entries()) {
-          const $id = id2$id.get(id);
-          if ($id) v.interactions[i] = $id;
-        }
-      }
-    }
-  }
-  async function addInput(input) {
-    await input.init(
-      select_default(this).style("width", "fit-content").style("margin", "0px 15px 35px 25px").style("padding", "0px 5px")
-    );
-  }
-  function removeInput(input) {
-    input.remove();
-    for (const key in input.dom) {
-      delete input.dom[key];
-    }
-    const div = select_default(this);
-    div.transition().duration(500).style("opacity", 0).remove();
-  }
-  self.resetSubmitButton = () => {
-    self.dom.submitBtn.text("Run analysis").style("display", self.config.outcome && self.config.independent.length ? "block" : "none").property("disabled", self.hasError);
-  };
-  self.mayShowUnivariateCheckbox = () => {
-    if (!self.config.outcome || self.config.independent.length < 2) {
-      self.dom.univariateCheckboxDiv.style("display", "none");
-      return;
-    }
-    self.dom.univariateCheckboxDiv.style("display", "block");
-    self.dom.univariateCheckbox.property("checked", self.config.includeUnivariate);
-  };
-  self.mayShowSubmitMsgs = () => {
-    self.dom.submitMsgs.selectAll("div").data(Object.values(self.submitMsgs)).join("div").text((d) => d);
-  };
-}
-function setInteractivity(self) {
-  self.editConfig = async (input, variable) => {
-    if (!variable) {
-      const i = input.section.inputLst.findIndex((d) => d === input);
-      if (i == -1) throw `deleting an unknown input`;
-      input.section.inputLst.splice(i, 1);
-      if (input.term) {
-        for (const other of input.section.inputLst) {
-          if (!other.term || !other.term.interactions?.length) continue;
-          const i2 = other.term.interactions.indexOf(input.term.$id);
-          if (i2 != -1) other.term.interactions.splice(i2, 1);
-        }
-      }
-    } else {
-      const prevTerm = input.term;
-      if (prevTerm && variable.term.id === prevTerm.term.id) {
-        for (const k in prevTerm) {
-          if (!(k in variable)) variable[k] = prevTerm[k];
-        }
-      }
-      input.term = variable;
-      if (variable.q.mode == "spline" && variable.interactions) {
-        for (const other of input.section.inputLst) {
-          if (!other.term || !other.term.interactions) continue;
-          const i = other.term.interactions.indexOf(input.term.$id);
-          if (i != -1) other.term.interactions.splice(i, 1);
-        }
-        variable.interactions = [];
-      }
-    }
-    const selected = [];
-    for (const i of input.section.inputLst) {
-      if (i.term) selected.push(i.term);
-    }
-    const key = input.section.configKey;
-    const configValue = Array.isArray(self.config[key]) ? selected : selected[0];
-    self.app.dispatch({
-      type: "plot_edit",
-      id: self.parent.id,
-      chartType: "regression",
-      config: {
-        hasUnsubmittedEdits: true,
-        // replace config.outcome or config.independent
-        [key]: JSON.parse(JSON.stringify(configValue))
-      }
-    });
-  };
-  self.submit = () => {
-    self.dom.submitBtn.property("disabled", true);
-    if (self.hasError) {
-      alert("Please fix the input variable errors (highlighted in red background).");
-      return;
-    }
-    const config = JSON.parse(JSON.stringify(self.config));
-    config.hasUnsubmittedEdits = false;
-    self.app.dispatch({
-      type: "plot_edit",
-      id: self.parent.id,
-      chartType: "regression",
-      config
-    });
-  };
-}
-function mayAddBlankInput(section, self) {
-  if (section.inputLst.length >= section.limit) {
-    return;
-  }
-  const blankInput = section.inputLst.find((i) => !i.term);
-  if (blankInput) {
-    const noTermPromptOptions = self.getNoTermPromptOptions(section);
-    if (noTermPromptOptions) {
-      blankInput.pill.main({ noTermPromptOptions });
-    }
-    return;
-  }
-  section.inputLst.push(
-    new InputTerm({
-      section,
-      parent: self,
-      noTermPromptOptions: self.getNoTermPromptOptions(section)
-    })
-  );
-}
-
-// plots/regression.js
-var Regression = class _Regression extends PlotBase {
-  static type = "regression";
-  constructor(opts) {
-    super(opts);
-    this.type = _Regression.type;
-    this.genomeObj = opts.app.opts.genome;
-  }
-  async init(appState) {
-    this.dom = {
-      header: this.opts.header,
-      // header is optional
-      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 config = appState.plots.find((p) => p.id === this.id);
-    this.inputs = new RegressionInputs({
-      app: this.app,
-      parent: this,
-      id: this.id,
-      holder: this.dom.inputs,
-      regressionType: config.regressionType
-    });
-    this.results = new RegressionResults({
-      app: this.app,
-      parent: this,
-      id: this.id,
-      holder: this.dom.results,
-      regressionType: config.regressionType
-    });
-  }
-  getState(appState, sub) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    if (!config.regressionType) throw "regressionType is required";
-    const parentConfig = this.parentId && appState.plots.find((p) => p.id === this.parentId);
-    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
-    return {
-      vocab: appState.vocab,
-      formIsComplete: config.outcome && config.independent.length,
-      activeCohort: appState.activeCohort,
-      termfilter,
-      config,
-      allowedTermTypes: appState.termdbConfig.allowedTermTypes,
-      minTimeSinceDx: appState.termdbConfig.minTimeSinceDx
-    };
-  }
-  /* do not set reactsTo
-  so it reacts to all actions matching with the plot id (controlled by store method)
-  including filter/cohort change
-  */
-  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();
-      this.inputs.mayShowUnivariateCheckbox();
-      this.inputs.mayShowSubmitMsgs();
-    } catch (e) {
-      if (this.inputs.hasError) {
-        this.results.main();
-      }
-      sayerror(this.dom.errordiv, "Error: " + (e.error || e));
-      if (e.stack) console.log(e.stack);
-    }
-  }
-  mayUpdateSandboxHeader() {
-    if (!this.dom.header) return;
-    const o = this.config.outcome;
-    this.dom.header.html(
-      (o ? o.term.name : "") + '<span style="opacity:.6;font-size:.7em;margin-left:10px;">' + this.config.regressionType.toUpperCase() + " REGRESSION</span>"
-    );
-  }
-  getFilter() {
-    const filters = [];
-    if (this.state.termfilter?.filter) filters.push(this.state.termfilter.filter);
-    const tws = [this.config.outcome, ...this.config.independent];
-    const tws_restrictAncestry = tws.filter((tw) => tw?.q.restrictAncestry);
-    if (tws_restrictAncestry.length) {
-      if (tws_restrictAncestry.length > 1) {
-        const ancestries = new Set(tws_restrictAncestry.map((tw2) => tw2.q.restrictAncestry.name));
-        if (ancestries.size > 1) throw "samples cannot be restricted to more than 1 ancestry";
-      }
-      const tw = tws_restrictAncestry[0];
-      filters.push({ type: "tvs", tvs: tw.q.restrictAncestry.tvs });
-      this.inputs.submitMsgs.restrictAncestry = `Restricting analysis to samples of ${tw.q.restrictAncestry.name}`;
-    } else {
-      delete this.inputs.submitMsgs.restrictAncestry;
-    }
-    this.filter = { type: "tvslst", join: "and", lst: filters };
-  }
-};
-var regressionInit = getCompInit(Regression);
-var componentInit = regressionInit;
-var _ID_ = 1;
-async function getPlotConfig(opts, app) {
-  if (!opts.outcome) opts.outcome = {};
-  await fillTermWrapper(opts.outcome, app.vocabApi, get_defaultQ4fillTW(opts.regressionType, "outcome"));
-  const id = "id" in opts ? opts.id : `_REGRESSION_${_ID_++}`;
-  const config = { id };
-  config.outcome = opts.outcome;
-  if (opts.independent) {
-    if (!Array.isArray(opts.independent)) throw ".independent[] is not array";
-    for (const t of opts.independent) {
-      await fillTermWrapper(
-        t,
-        app.vocabApi,
-        t.q?.mode ? void 0 : get_defaultQ4fillTW(opts.regressionType, "independent")
-      );
-    }
-    config.independent = opts.independent;
-  } else {
-    config.independent = [];
-  }
-  return copyMerge(config, opts);
-}
-function get_defaultQ4fillTW(regressionType, useCase = "") {
-  const defaultQ = {};
-  defaultQ["numeric"] = regressionType == "logistic" && useCase == "outcome" ? { mode: "binary" } : { mode: "discrete" };
-  for (const t of numericTypes) {
-    if (dictionaryNumericTypes.has(t)) continue;
-    defaultQ[t] = regressionType == "logistic" && useCase == "outcome" ? { mode: "binary" } : { mode: "discrete", type: "custom-bin", preferredBins: "median" };
-  }
-  defaultQ["categorical"] = regressionType == "logistic" && useCase == "outcome" ? { mode: "binary" } : { mode: "discrete" };
-  if (useCase == "outcome") {
-    if (regressionType == "cox") {
-      defaultQ.condition = { mode: "cox" };
-    }
-    if (regressionType == "logistic") {
-      defaultQ.condition = { mode: "binary" };
-    }
-  }
-  defaultQ["geneVariant"] = { type: "predefined-groupset" };
-  return defaultQ;
-}
-function makeChartBtnMenu(holder, chartsInstance) {
-  const allMethods = [
-    { label: "Linear", type: "linear" },
-    { label: "Logistic", type: "logistic" },
-    { label: "Cox", type: "cox" }
-  ];
-  const useMethods = allMethods.filter((i) => chartsInstance.state.currentCohortChartTypes.includes(i.type));
-  if (useMethods.length == 0) return holder.append("div").text("Error: no methods available");
-  if (useMethods.length == 1) {
-    chartsInstance.dom.tip.hide();
-    chartsInstance.prepPlot({
-      config: {
-        chartType: "regression",
-        regressionType: useMethods[0].type,
-        independent: []
-      }
-    });
-    return;
-  }
-  for (const { label, type } of useMethods) {
-    holder.append("div").attr("class", "sja_menuoption sja_sharp_border").text(label).on("click", () => {
-      chartsInstance.dom.tip.hide();
-      chartsInstance.prepPlot({
-        config: {
-          chartType: "regression",
-          regressionType: type,
-          independent: []
-        }
-      });
-    });
-  }
-}
-
-export {
-  regressionInit,
-  componentInit,
-  getPlotConfig,
-  get_defaultQ4fillTW,
-  makeChartBtnMenu,
-  InputTerm,
-  RegressionInputs
-};
-//# sourceMappingURL=chunk-JKMN7XOP.js.map