@sjcrh/proteinpaint-client 2.211.0 → 2.212.0

package/dist/chunk-ZMSTQP6O.js

@@ -0,0 +1,299 @@
+import {
+  first_genetrack_tolist,
+  gmmode,
+  sayerror
+} from "./chunk-VHDYIOWU.js";
+import {
+  dofetch3
+} from "./chunk-RMUK3TLD.js";
+import {
+  codon_stop,
+  nt2aa,
+  proteinDomainColorScale
+} from "./chunk-57Z4VYLM.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// common/snp.js
+async function string2snp(genome, str) {
+  const data = await dofetch3("snp", {
+    method: "POST",
+    body: JSON.stringify({ byName: true, genome: genome.name, lst: [str] })
+  });
+  if (data.error) throw data.error;
+  if (!data.results || data.results.length == 0) throw str + ": not a SNP";
+  for (const i of data.results) {
+    const chr = genome.chrlookup[i.chrom.toUpperCase()];
+    if (chr && chr.major) {
+      return {
+        chr: i.chrom,
+        start: i.chromStart,
+        stop: i.chromEnd
+      };
+    }
+  }
+  const r = data.results[0];
+  return {
+    chr: r.chrom,
+    start: r.chromStart,
+    stop: r.chromEnd
+  };
+}
+
+// src/block.init.js
+async function block_init_default(arg) {
+  if (!arg.holder) throw "No holder for block.init";
+  if (!arg.genome) throw "no genome";
+  if (arg.holder instanceof Element) arg.holder = select_default(arg.holder);
+  if (!arg.tklst) arg.tklst = [];
+  if (arg.query) {
+    await step1_findgm(arg);
+    return;
+  }
+  if (arg.model && arg.allmodels) {
+    await step2_getseq(arg);
+    return;
+  }
+}
+async function step1_findgm(arg) {
+  const wait = arg.holder.append("p").style("font-size", "2em").style("color", "#858585").text("Searching for " + arg.query + " ...");
+  const data = await dofetch3("genelookup", {
+    body: { deep: 1, input: arg.query, genome: arg.genome.name }
+  });
+  if (!data) throw "querying genes: server error";
+  if (data.error) throw "error querying genes: " + data.error;
+  if (!data.gmlst || data.gmlst.length == 0) {
+    if (arg.genome.hasSNP) {
+      try {
+        const r = await string2snp(arg.genome, arg.query);
+        wait.remove();
+        const par = {
+          genome: arg.genome,
+          holder: arg.holder,
+          chr: r.chr,
+          start: Math.max(0, r.start - 300),
+          stop: r.start + 300,
+          nobox: true,
+          tklst: arg.tklst,
+          debugmode: arg.debugmode
+        };
+        first_genetrack_tolist(arg.genome, par.tklst);
+        const b = await import("./block-7WZWBQVA.js");
+        const block = new b.Block(par);
+        block.addhlregion(r.chr, r.start, r.stop - 1);
+      } catch (e) {
+        wait.text("Not a gene or SNP: " + arg.query);
+      }
+    } else {
+      wait.text("No match to gene: " + arg.query);
+    }
+    return;
+  }
+  wait.remove();
+  arg.allmodels = data.gmlst;
+  for (const m of arg.allmodels) {
+    if (m.isoform.toUpperCase() == (data.found_isoform ? data.found_isoform.toUpperCase() : arg.query.toUpperCase())) {
+      arg.model = m;
+      await step2_getseq(arg);
+      return;
+    }
+  }
+  const defaultisoforms = [];
+  for (const m of arg.allmodels) {
+    if (!m.isoform) throw "isoform missing from one gene model: " + JSON.stringify(m);
+    const n = m.isoform.toUpperCase();
+    if (arg.genome.isoformcache.has(n)) {
+      let nothas = true;
+      for (const m2 of arg.genome.isoformcache.get(n)) {
+        if (m2.chr == m.chr && m2.start == m.start && m2.stop == m.stop && m2.strand == m.strand) {
+          nothas = false;
+          break;
+        }
+      }
+      if (nothas) {
+        arg.genome.isoformcache.get(n).push(m);
+      }
+    } else {
+      arg.genome.isoformcache.set(n, [m]);
+    }
+    if (m.isoform.toUpperCase() == arg.query.toUpperCase()) {
+      defaultisoforms.push(m);
+      break;
+    }
+    if (m.isdefault) {
+      defaultisoforms.push(m);
+    }
+  }
+  if (defaultisoforms.length == 1) {
+    arg.model = defaultisoforms[0];
+  } else if (defaultisoforms.length > 1) {
+    for (const m of defaultisoforms) {
+      if (m.chr == "chrY") {
+        continue;
+      }
+      const chr = arg.genome.chrlookup[m.chr.toUpperCase()];
+      if (!chr) {
+        continue;
+      }
+      if (!chr.major) {
+        continue;
+      }
+      arg.model = m;
+      break;
+    }
+    if (!arg.model) {
+      arg.model = defaultisoforms[0];
+    }
+  }
+  if (!arg.model) {
+    arg.model = arg.allmodels[0];
+  }
+  await step2_getseq(arg);
+}
+async function step2_getseq(arg) {
+  if (arg.model.genomicseq) {
+    checker();
+    step2_getpdomain(arg);
+    return;
+  }
+  const par = {
+    genome: arg.genome.name,
+    coord: arg.model.chr + ":" + (arg.model.start + 1) + "-" + arg.model.stop
+  };
+  const data = await dofetch3("ntseq", { method: "POST", body: JSON.stringify(par) });
+  if (!data) throw "getting sequence: server error";
+  if (data.error) throw "getting sequence: " + data.error;
+  if (!data.seq) throw "no nt seq???";
+  arg.model.genomicseq = data.seq.toUpperCase();
+  arg.model.aaseq = nt2aa(arg.model);
+  checker();
+  await step2_getpdomain(arg);
+  function checker() {
+    if (arg.model.aaseq) {
+      const stop = arg.model.aaseq.indexOf(codon_stop);
+      const cdslen = arg.model.cdslen - (arg.model.startCodonFrame ? 3 - arg.model.startCodonFrame : 0);
+      if (stop != -1 && stop < cdslen / 3 - 1) {
+        sayerror(arg.holder, "Translating " + arg.model.isoform + " ends at " + stop + " AA, expecting " + cdslen / 3);
+      }
+    }
+  }
+}
+async function step2_getpdomain(arg) {
+  const isoform2gm = /* @__PURE__ */ new Map();
+  for (const m of arg.allmodels) {
+    if (!m.pdomains) {
+      m.pdomains = [];
+      m.domain_hidden = {};
+      if (!isoform2gm.has(m.isoform)) isoform2gm.set(m.isoform, []);
+      isoform2gm.get(m.isoform).push(m);
+    }
+  }
+  if (isoform2gm.size == 0) {
+    await step3(arg);
+    return;
+  }
+  const data = await dofetch3("pdomain", {
+    method: "POST",
+    body: JSON.stringify({ genome: arg.genome.name, isoforms: [...isoform2gm.keys()] })
+  });
+  if (data.error) throw "error getting protein domain: " + data.error;
+  if (!Array.isArray(data.lst)) throw ".lst[] not array";
+  for (const a of data.lst) {
+    for (const m of isoform2gm.get(a.name)) {
+      m.pdomains = a.pdomains;
+      if (arg.hidePdomain) {
+        for (const i of a.pdomains) {
+          m.domain_hidden[i.name + i.description] = 1;
+        }
+      }
+    }
+  }
+  if (arg.geneDomains) {
+    if (typeof arg.geneDomains != "object") throw "geneDomains not object";
+    for (const isoform in arg.geneDomains) {
+      const lst = isoform2gm.get(isoform);
+      if (!lst) throw `unknown isoform ${isoform} from geneDomains{}`;
+      for (const g of lst) {
+        if (!g.pdomains) g.pdomains = [];
+        if (!Array.isArray(arg.geneDomains[isoform])) throw `geneDomains[${isoform}] not array`;
+        for (const b of arg.geneDomains[isoform]) {
+          if (typeof b != "object") throw "element from geneDomains[] not object";
+          if (!Number.isInteger(b.start)) throw "start not integer from geneDomains[]";
+          if (!Number.isInteger(b.stop)) throw "stop not integer from geneDomains[]";
+          if (b.start > b.stop) throw "start>stop from geneDomains[]";
+          if (!b.name) b.name = "Custom domain";
+          if (!g.pdomains.find((a) => a.start == b.start && a.stop == b.stop && a.name == b.name)) g.pdomains.push(b);
+        }
+      }
+    }
+  }
+  const s = proteinDomainColorScale();
+  for (const lst of isoform2gm.values()) {
+    for (const g of lst) {
+      for (const d of g.pdomains || []) {
+        if (!d.color) d.color = s(d.name + d.description);
+      }
+    }
+  }
+  await step3(arg);
+}
+async function step3(arg) {
+  let mode = arg.gmmode;
+  if (!mode) {
+    if (arg.model.cdslen) {
+      mode = gmmode.protein;
+    } else {
+      mode = gmmode.exononly;
+    }
+  }
+  if (arg.dataset) {
+    if (!Array.isArray(arg.dataset)) throw "dataset is not array";
+    for (const dsname of arg.dataset) {
+      if (arg.genome.datasets[dsname] && !arg.genome.datasets[dsname].legacyDsIsUninitiated) continue;
+      const d = await dofetch3(`getDataset?genome=${arg.genome.name}&dsname=${dsname}`);
+      if (d.error) throw `invalid name from dataset[]: ${d.error}`;
+      if (!d.ds) throw ".ds missing";
+      const ds = arg.genome.datasets[d.ds.label];
+      Object.assign(ds, d.ds);
+      const _ = await import("./legacyDataset-IEFWFVS6.js");
+      _.validate_oldds(ds);
+      delete ds.legacyDsIsUninitiated;
+    }
+  }
+  const b = await import("./block-7WZWBQVA.js");
+  arg.__blockInstance = new b.Block({
+    genome: arg.genome,
+    holder: arg.holder,
+    nobox: true,
+    usegm: arg.model,
+    gmstackheight: 37,
+    allgm: arg.allmodels,
+    datasetlst: arg.dataset,
+    legacyDsFilter: arg.legacyDsFilter,
+    mset: arg.mset,
+    hlaachange: arg.hlaachange,
+    hlvariants: arg.hlvariants,
+    hlregions: arg.hlregions,
+    aarange: arg.aarange,
+    gmmode: mode,
+    hidedatasetexpression: arg.hidedatasetexpression,
+    hidegenecontrol: arg.hidegenecontrol,
+    hidegenelegend: arg.hidegenelegend,
+    variantPageCall_snv: arg.variantPageCall_snv,
+    datasetqueries: arg.datasetqueries,
+    samplecart: arg.samplecart,
+    debugmode: arg.debugmode,
+    tklst: arg.tklst,
+    mclassOverride: arg.mclassOverride,
+    hide_dsHandles: arg.hide_dsHandles,
+    onloadalltk_always: arg.onloadalltk_always,
+    onAddRemoveTk: arg.onAddRemoveTk
+  });
+}
+
+export {
+  string2snp,
+  block_init_default
+};
+//# sourceMappingURL=chunk-ZMSTQP6O.js.map

package/dist/cohort-CWGZR37O.js

@@ -0,0 +1,70 @@
+import {
+  appInit,
+  vocabInit
+} from "./chunk-VHDYIOWU.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-5WIA4KFA.js";
+import "./chunk-7XZA2XR2.js";
+import "./chunk-DD3DWHUY.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-RMUK3TLD.js";
+import "./chunk-HH5JKOE6.js";
+import "./chunk-RU2UHH7M.js";
+import {
+  TermTypes
+} from "./chunk-57Z4VYLM.js";
+import "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-6XKAOSQE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// termdb/handlers/cohort.ts
+var SearchHandler = class {
+  init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    const cohorts = this.app.vocabApi.app?.opts?.opts?.cohorts0;
+    if (!cohorts?.length) return;
+    const terms = cohorts.map((cohort) => {
+      const term = {
+        id: cohort.id,
+        name: cohort.name,
+        type: TermTypes.COHORT,
+        filter0: cohort.filter,
+        isleaf: true,
+        parent_id: null
+      };
+      return term;
+    });
+    const vocabApi = vocabInit({ vocab: { terms } });
+    appInit({
+      holder,
+      vocabApi,
+      state: {
+        nav: { header_mode: "hide_search" }
+      },
+      tree: {
+        click_term: (term) => {
+          this.callback(term);
+        }
+      }
+    });
+  }
+};
+export {
+  SearchHandler
+};
+//# sourceMappingURL=cohort-CWGZR37O.js.map

package/dist/condition-B6XBQML4.js

@@ -0,0 +1,327 @@
+import {
+  getPillNameDefault,
+  make_radios,
+  sayerror,
+  set_hiddenvalues,
+  throwMsgWithFilePathAndFnName
+} from "./chunk-VHDYIOWU.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-5WIA4KFA.js";
+import "./chunk-7XZA2XR2.js";
+import "./chunk-DD3DWHUY.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-RMUK3TLD.js";
+import "./chunk-HH5JKOE6.js";
+import "./chunk-RU2UHH7M.js";
+import "./chunk-57Z4VYLM.js";
+import {
+  copyMerge
+} from "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-6XKAOSQE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// termsetting/handlers/condition.ts
+var cutoffGrades = [1, 2, 3, 4, 5];
+function getHandler(self) {
+  return {
+    getPillName(d) {
+      return getPillNameDefault(self, d);
+    },
+    getPillStatus() {
+      return getPillStatus(self);
+    },
+    showEditMenu(div) {
+      if (self.q.mode == "discrete") {
+        return showMenu_discrete(self, div);
+      }
+      if (self.q.mode == "binary" || self.q.mode == "cuminc" || self.q.mode == "cox") {
+        return showMenu_cutoff(self, div);
+      }
+      console.error("invalid q.mode:", self.q.mode);
+      throw "invalid q.mode";
+    }
+    // async postMain() {
+    // 	const body = self.opts.getBodyParams?.() || {} //make sure term1_q is added
+    // 	const data = await self.vocabApi.getCategories(self.term, self.filter!, body)
+    // 	//not really sure this is necessary but it's consistent across other handlers
+    // 	self.category2samplecount = []
+    // 	for (const d of data.lst) {
+    // 		self.category2samplecount.push({
+    // 			key: d.key,
+    // 			label: d.label,
+    // 			count: d.samplecount
+    // 		})
+    // 		// }
+    // 	}
+    // }
+  };
+}
+function getPillStatus(self) {
+  const text = self.q?.name;
+  if (text) return { text };
+  if (self.q.mode == "discrete") {
+    if (self.q.breaks?.length) {
+      return { text: self.q.breaks.length + 1 + " groups" };
+    } else {
+      if (self.q.bar_by_grade) {
+        if (self.q.value_by_max_grade) return { text: "Max. Grade" };
+        if (self.q.value_by_most_recent) return { text: "Most Recent Grade" };
+        if (self.q.value_by_computable_grade) return { text: "Any Grade" };
+        return { text: "Error: unknown grade setting", bgcolor: "red" };
+      }
+      if (self.q.bar_by_children) return { text: "Sub-condition" };
+    }
+  }
+  if (self.q.mode == "binary") {
+    return {
+      text: self.usecase?.target == "regression" ? self.data.q.groups.find((x) => x.name != self.data.refGrp).name : "binary"
+    };
+  }
+  if (self.q.mode == "cuminc" || self.q.mode == "cox") {
+    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
+    return { text: `Grades ${self.q.breaks[0]}-5` };
+  }
+  return {};
+}
+async function showMenu_discrete(self, div) {
+  const value_type_div = div.append("div").style("margin", "10px 0px 10px 5px").style("border-left", "solid 1px #ededed");
+  value_type_div.append("div").style("display", "inline-block").style("margin", "0px 0px 5px 5px").style("color", "rgb(136, 136, 136)").text("Grade type:");
+  const value_type_select = value_type_div.append("select").style("display", "inline").style("margin", "0px 10px").on("change", () => {
+    const i = value_type_select.property("selectedIndex");
+    self.q.bar_by_grade = i != 3;
+    self.q.bar_by_children = i == 3;
+    self.q.value_by_max_grade = i == 0;
+    self.q.value_by_most_recent = i == 1;
+    self.q.value_by_computable_grade = i == 2 || i == 3;
+    self.dom.tip.hide();
+    self.api.runCallback();
+  });
+  value_type_select.append("option").text("Max grade per patient");
+  value_type_select.append("option").text("Most recent grade per patient");
+  value_type_select.append("option").text("Any grade per patient");
+  if (self.term.subconditions) {
+    value_type_select.append("option").text("Sub-conditions");
+  }
+  value_type_select.property(
+    "selectedIndex",
+    self.q.bar_by_children ? 3 : self.q.value_by_computable_grade ? 2 : self.q.value_by_most_recent ? 1 : 0
+  );
+  if (self.q.bar_by_children) {
+    return;
+  }
+  const breaksSelectorDiv = div.append("div").style("margin", "20px 0px 10px 5px").style("border-left", "solid 1px #ededed");
+  breaksSelectorDiv.append("div").text("Divide grades into groups (optional):").style("margin", "0px 0px 10px 5px").style("color", "rgb(136, 136, 136)");
+  const holder = breaksSelectorDiv.append("div").style("display", "flex").style("align-items", "start").style("margin-left", "10px").style("width", "100%");
+  const gradeValuesDiv = holder.append("div").style("margin-right", "20px");
+  const rangeNameDiv = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center").style("margin-right", "5px");
+  gradeValuesDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Cutoff grades");
+  const textarea = gradeValuesDiv.append("textarea").style("width", "100px").style("height", "70px").on("keyup", textarea2gradeUI);
+  gradeValuesDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
+  if (self.q.breaks?.length) {
+    textarea.property("value", self.q.breaks.join("\n"));
+  }
+  textarea2gradeUI();
+  function textarea2gradeUI() {
+    rangeNameDiv.selectAll("*").remove();
+    const breaks = textarea2breaks();
+    if (!breaks.length) {
+      delete self.q.breaks;
+      delete self.q.groups;
+      return;
+    }
+    if (!self.term.values) throwMsgWithFilePathAndFnName(`Missing term values`);
+    const grades = Object.keys(self.term.values).filter((g) => !self.term.values?.[g].uncomputable).map(Number).sort((a, b) => a - b);
+    const groups = getGroups(grades, breaks);
+    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
+    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Label");
+    for (const [i, g] of groups.entries()) {
+      rangeNameDiv.append("div").text(g.name.replace(/Grades* /, ""));
+      rangeNameDiv.append("div").append("input").attr("type", "text").property("value", g.name).style("margin", "2px 0px").on("change", function() {
+        groups[i].name = this.value;
+      });
+    }
+    self.q.breaks = breaks;
+    self.q.groups = groups;
+  }
+  function textarea2breaks() {
+    const str = textarea.property("value").trim();
+    if (!str) return [];
+    const lst = [...new Set(str.split("\n"))];
+    const breaks = [];
+    for (const x of lst) {
+      const b = Number(x);
+      if (!Number.isInteger(b)) {
+        sayerror(div, "cutoff grade must be an integer value");
+        return [];
+      }
+      if (b < 1 || b > 5) {
+        sayerror(div, `cutoff grade must be within grades 1-5`);
+        return [];
+      }
+      breaks.push(b);
+    }
+    if (!breaks.length) return [];
+    return breaks.sort((i, j) => i - j);
+  }
+  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
+    event.target.disabled = true;
+    event.target.innerHTML = "Loading...";
+    self.api.runCallback();
+  });
+}
+function showMenu_cutoff(self, div) {
+  const holder = div.append("div").style("margin", "10px").style("display", "grid").style("grid-template-columns", "auto auto").style("gap", "20px");
+  holder.append("div").text("Grade cutoff").style("opacity", 0.4);
+  const sd = holder.append("div");
+  const gradeSelect = sd.append("select").on("change", changeGradeSelect);
+  for (const i of cutoffGrades) {
+    gradeSelect.append("option").text(self.term.values?.[i].label);
+  }
+  gradeSelect.property("selectedIndex", self.q.breaks[0] - 1);
+  holder.append("div").text(self.q.mode == "binary" ? "Group 1" : "Censored").style("opacity", 0.4);
+  const g1n = holder.append("div").style("opacity", 0.4);
+  holder.append("div").text(self.q.mode == "binary" ? "Group 2" : "Event").style("opacity", 0.4);
+  const g2n = holder.append("div").style("opacity", 0.4);
+  changeGradeSelect();
+  function changeGradeSelect() {
+    const grade = gradeSelect.property("selectedIndex") + 1;
+    g1n.selectAll("*").remove();
+    g2n.selectAll("*").remove();
+    const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
+    for (const i of grades) {
+      if (i < grade) {
+        g1n.append("div").text(self.term.values?.[i].label);
+      } else {
+        g2n.append("div").text(self.term.values?.[i].label);
+      }
+    }
+  }
+  const timeUnit = self.vocabApi.termdbConfig.timeUnit;
+  let timeScaleChoice;
+  if (self.q.mode == "cox") {
+    timeScaleChoice = self.q.timeScale;
+    holder.append("div").text("Time axis").style("opacity", 0.4);
+    const options = [
+      {
+        label: timeUnit.charAt(0).toUpperCase() + timeUnit.slice(1),
+        value: "time"
+      },
+      { label: "Age", value: "age" }
+    ];
+    if (self.q.timeScale == "age") {
+      options[1].checked = true;
+    } else {
+      options[0].checked = true;
+    }
+    make_radios({
+      holder: holder.append("div"),
+      options,
+      styles: { padding: "" },
+      callback: (v) => timeScaleChoice = v
+    });
+  }
+  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
+    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
+    const grade = gradeSelect.property("selectedIndex") + 1;
+    self.q.breaks[0] = grade;
+    if (self.q.mode == "binary") {
+      const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
+      self.q.groups = getGroups(grades, self.q.breaks);
+      self.refGrp = self.q.groups[0].name;
+    }
+    if (self.q.mode == "cox") self.q.timeScale = timeScaleChoice;
+    event.target.disabled = true;
+    event.target.innerHTML = "Loading...";
+    self.api.runCallback();
+  });
+}
+function getGroups(grades, breaks) {
+  grades.sort((a, b2) => a - b2);
+  const groups = [];
+  let group = { values: [] };
+  let b;
+  for (const g of grades) {
+    if (breaks.includes(g)) {
+      b = g;
+      const max = Math.max(...group.values);
+      if (!groups.length) {
+        if (group.values.length == 1) {
+          if (group.values[0] !== 0) throw "unexpected group value";
+          group.name = "Grade 0";
+        } else {
+          if (group.values.length == 2 && group.values.includes(-1) && group.values.includes(0)) {
+            group.name = "Not tested/Grade 0";
+          } else {
+            group.name = group.values.includes(-1) ? `Not tested/Grade 0 - Grade ${max}` : `Grades 0-${max}`;
+          }
+        }
+      } else {
+        group.name = group.values.length == 1 ? `Grade ${group.values[0]}` : `${group.name}-${max}`;
+      }
+      groups.push(group);
+      group = {
+        name: `Grade ${b}`,
+        values: [g]
+      };
+    } else {
+      group.values.push(g);
+    }
+  }
+  group.name = `Grades ${b}-5`;
+  groups.push(group);
+  return groups;
+}
+function fillTW(tw, vocabApi, defaultQ) {
+  set_hiddenvalues(tw.q, tw.term);
+  if (defaultQ) {
+    copyMerge(tw.q, defaultQ);
+  }
+  if (!Object.keys(tw.q).includes("mode")) tw.q.mode = "discrete";
+  if (!tw.q.valueFor) {
+    const q = tw.q;
+    if (!q.bar_by_grade && !q.bar_by_children) q.bar_by_grade = true;
+    tw.q.valueFor = tw.q.bar_by_children ? "children" : "grade";
+  }
+  if (tw.q.valueFor == "grade") {
+    if (tw.q.value_by_max_grade || tw.q.value_by_most_recent || tw.q.value_by_computable_grade) {
+    } else {
+      tw.q.value_by_max_grade = true;
+    }
+  }
+  if (tw.q.mode == "binary" || tw.q.mode == "cox" || tw.q.mode == "cuminc") {
+    const defaultBreak = tw.q.mode == "binary" ? 1 : 3;
+    if (!tw.q.breaks?.length) tw.q.breaks = [defaultBreak];
+    if (tw.q.breaks.length != 1 || ![1, 2, 3, 4, 5].includes(tw.q.breaks[0])) throw "invalid tw.q.breaks";
+  }
+  if (tw.q.valueFor == "grade") {
+    if (tw.q.breaks?.length) {
+      if (!tw.term.values) throw "missing term.values";
+      if (tw.q.mode == "discrete" || tw.q.mode == "binary") {
+        const grades = Object.keys(tw.term.values).filter((g) => tw.q.mode == "discrete" ? !tw.term.values?.[g].uncomputable : g).map(Number).sort((a, b) => a - b);
+        tw.q.groups = getGroups(grades, tw.q.breaks);
+      }
+    }
+    if (tw.q.mode == "cox") {
+      if (!tw.q.timeScale) tw.q.timeScale = "time";
+      if (!["age", "time"].includes(tw.q.timeScale)) throw "invalid q.timeScale";
+    }
+  }
+}
+export {
+  fillTW,
+  getHandler
+};
+//# sourceMappingURL=condition-B6XBQML4.js.map