@sjcrh/proteinpaint-client 2.205.0 → 2.206.0

package/dist/geneVariant-BHXTPUDC.js

@@ -0,0 +1,286 @@
+import {
+  excludeFilterByTag,
+  fillGroupsetGroups,
+  filterInit,
+  filterPromptInit,
+  getDtTermValues,
+  getNormalRoot,
+  getPillNameDefault,
+  make_radios,
+  renderTable,
+  vocabInit
+} from "./chunk-Q5SK3U2T.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-54KC7DAB.js";
+import "./chunk-N7DVQTPC.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-RPDVFM7E.js";
+import "./chunk-M4XXKTH2.js";
+import {
+  getDtsFromGroups
+} from "./chunk-5ILEFNXJ.js";
+import {
+  getColors
+} from "./chunk-IZUYLFOX.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-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import {
+  rgb
+} from "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// termsetting/handlers/geneVariant.ts
+var colorScale = getColors(5);
+function getHandler(self) {
+  return {
+    getPillName(d) {
+      let name = d.name;
+      if (!name) {
+        if (d.genes) name = d.genes.map((g) => g.gene).join(", ");
+        else if (d.chr) name = `${d.chr}:${d.start}-${d.stop}`;
+        else name = d.id || "geneVariant";
+      }
+      return getPillNameDefault(self, { name });
+    },
+    getPillStatus() {
+      let text;
+      const q = self.q;
+      if (q.type == "predefined-groupset") {
+        const groupsetting = self.term.groupsetting;
+        if (!groupsetting?.lst?.length) throw "no predefined groupsets found";
+        const groupset = groupsetting.lst[q.predefined_groupset_idx];
+        text = groupset.name;
+      } else if (q.type == "custom-groupset") {
+        const n = q.customset.groups.length;
+        text = `Divided into ${n} groups`;
+      } else {
+        text = "any variant class";
+      }
+      return { text };
+    },
+    async showEditMenu(div) {
+      await makeEditMenu(self, div);
+    }
+  };
+}
+async function makeEditMenu(self, _div) {
+  delete self.groups;
+  const div = _div.append("div").style("margin", "10px");
+  div.append("div").style("font-size", "1.2rem").text(self.term.name);
+  const optsDiv = div.append("div").style("margin-top", "10px").style("margin-bottom", "1px");
+  const groupsDiv = div.append("div").style("display", "none").style("margin", "10px").style("vertical-align", "top");
+  optsDiv.append("div").style("font-weight", "bold").text("Group samples");
+  const q = self.q;
+  const isGroupset = q.type == "predefined-groupset" || q.type == "custom-groupset";
+  make_radios({
+    holder: optsDiv,
+    options: [
+      { label: "No sample grouping", value: "noGroup", checked: !isGroupset },
+      { label: "Assign samples to groups", value: "group", checked: isGroupset }
+    ],
+    callback: async (v) => {
+      if (v == "group") {
+        if (q.type == "values") Object.assign(q, { type: "custom-groupset", customset: { groups: [] } });
+        await makeGroupUI(self, groupsDiv);
+      } else {
+        clearGroupset(self);
+        groupsDiv.style("display", "none");
+      }
+    }
+  });
+  if (isGroupset) await makeGroupUI(self, groupsDiv);
+  if (self.usecase?.detail && ["term", "term0", "term2"].includes(self.usecase.detail) || self.opts.geneVariantEditMenuOnlyGrp) {
+    optsDiv.style("display", "none");
+    groupsDiv.style("margin", "0px");
+  }
+  div.append("div").style("margin-top", "25px").append("button").attr("data-testid", "sjpp-ts-gv-editui-applyBtn").text("Apply").on("click", () => {
+    const q2 = self.q;
+    if (q2.type == "predefined-groupset" || q2.type == "custom-groupset") {
+      if (!self.groups?.length) {
+        window.alert("Samples must be assigned to at least one group.");
+        return;
+      } else {
+        const dtLst = getDtsFromGroups(self.groups);
+        Object.assign(q2, { type: "custom-groupset", customset: { groups: self.groups }, dtLst });
+        self.vocabApi.rememberGvQ?.(self.term, q2);
+      }
+    } else {
+      if (q2.type != "values") throw `q.type must be 'values'`;
+    }
+    self.api.runCallback();
+  });
+}
+async function makeGroupUI(self, div) {
+  div.style("display", "block");
+  div.selectAll("*").remove();
+  div.append("div").style("margin", "15px 0px").text(
+    "Group samples by mutation status. Samples are assigned to first possible group. Only tested samples are considered."
+  );
+  const filterTableDiv = div.append("div");
+  const addNewGroupBtnHolder = div.append("div");
+  const q = self.q;
+  if (q.type != "predefined-groupset" && q.type != "custom-groupset") throw "unexpected q.type";
+  if (!self.groups) {
+    let groupset;
+    if (q.type == "predefined-groupset") {
+      const groupsetting = self.term.groupsetting;
+      if (!groupsetting.lst?.length) throw "no predefined groupsets found";
+      await fillGroupsetGroups(self.term, q.predefined_groupset_idx, self.vocabApi);
+      groupset = groupsetting.lst[q.predefined_groupset_idx];
+    } else {
+      groupset = q.customset;
+    }
+    if (!groupset) throw "groupset is missing";
+    if (!Array.isArray(groupset.groups)) throw "groupset.groups is not array";
+    self.groups = structuredClone(groupset.groups);
+  }
+  const dtTerms = structuredClone(self.term.childTerms);
+  for (const dtTerm of dtTerms) {
+    await getDtTermValues(dtTerm, self.filter, self.vocabApi, { withMnames: true });
+  }
+  const vocabApi = vocabInit({ vocab: { terms: dtTerms } });
+  vocabApi.termdbConfig = { queries: self.vocabApi.termdbConfig.queries };
+  vocabApi.vocab.genome = self.vocabApi.vocab?.genome;
+  const filterPrompt = await filterPromptInit({
+    holder: addNewGroupBtnHolder,
+    vocabApi,
+    emptyLabel: "Add group",
+    header_mode: "hide_search",
+    callback: (f) => {
+      const filter2 = getNormalRoot(f);
+      addNewGroup(filter2, self.groups);
+      makeGroupUI(self, div);
+    },
+    debug: self.opts.debug
+  });
+  const filter = structuredClone(self.filter);
+  filterPrompt.main(excludeFilterByTag(filter, "cohortFilter"));
+  if (!self.groups.length) {
+    filterTableDiv.style("display", "none");
+    return;
+  }
+  filterTableDiv.style("display", "").selectAll("*").remove();
+  const tableArg = {
+    div: filterTableDiv,
+    columns: [
+      {},
+      // blank column to add delete buttons
+      {
+        label: "NAME",
+        editCallback: async (i, cell) => {
+          const newName = cell.value;
+          const index = self.groups.findIndex((group) => group.name == newName);
+          if (index != -1) {
+            alert(`Group named ${newName} already exists`);
+            makeGroupUI(self, div);
+          } else {
+            self.groups[i].name = newName;
+            makeGroupUI(self, div);
+          }
+        }
+      },
+      {
+        label: "COLOR",
+        editCallback: async (i, cell) => {
+          self.groups[i].color = cell.color;
+          makeGroupUI(self, div);
+        }
+      },
+      //{ label: '#SAMPLE' }, // will re-enable when filtered sample count can be supported for gdc
+      { label: "FILTER" }
+    ],
+    rows: [],
+    striped: false,
+    // no alternating row bg color so delete button appears more visible
+    showLines: false
+  };
+  for (const g of self.groups) {
+    tableArg.rows.push([
+      {},
+      // blank cell to add delete button
+      { value: g.name },
+      // to allow click to show <input>
+      { color: g.color },
+      // { value: 'n=' + (await self.vocabApi.getFilteredSampleCount(g.filter)) }, // will re-enable when filtered sample count can be supported for gdc
+      {}
+      // blank cell to show filter ui
+    ]);
+  }
+  renderTable(tableArg);
+  for (const [i, row] of tableArg.rows.entries()) {
+    row[0].__td.append("div").attr("class", "sja_menuoption").style("padding", "1px 6px").html("&times;").on("click", () => {
+      self.groups.splice(i, 1);
+      makeGroupUI(self, div);
+    });
+    const group = self.groups[i];
+    filterInit({
+      holder: row[3].__td,
+      vocabApi,
+      header_mode: "hide_search",
+      callback: (f) => {
+        if (!f || f.lst.length == 0) {
+          const i2 = self.groups.findIndex((g) => g.name == group.name);
+          self.groups.splice(i2, 1);
+        } else {
+          excludeGeneNameFromFilter(f);
+          group.filter = f;
+        }
+        makeGroupUI(self, div);
+      }
+    }).main(group.filter);
+  }
+}
+function addNewGroup(filter, groups, name) {
+  if (!groups) throw "groups is missing";
+  if (!name) {
+    const base = "New group";
+    name = base;
+    for (let i = 0; ; i++) {
+      name = base + (i === 0 ? "" : " " + i);
+      if (!groups.find((g) => g.name === name)) break;
+    }
+  }
+  excludeGeneNameFromFilter(filter);
+  const newGroup = {
+    name,
+    type: "filter",
+    filter,
+    color: rgb(colorScale(groups.length)).formatHex()
+  };
+  groups.push(newGroup);
+}
+function excludeGeneNameFromFilter(filter) {
+  for (const item of filter.lst) {
+    if (item.type == "tvslst") {
+      excludeGeneNameFromFilter(item);
+    } else if (item.type == "tvs") {
+      item.tvs.excludeGeneName = true;
+    } else {
+      throw "unexpected item.type";
+    }
+  }
+}
+function clearGroupset(self) {
+  self.q.type = "values";
+  delete self.q.predefined_groupset_idx;
+  delete self.q.customset;
+  delete self.q.dtLst;
+  self.q.hiddenValues = {};
+}
+export {
+  getHandler
+};
+//# sourceMappingURL=geneVariant-BHXTPUDC.js.map

package/dist/geneVariant.integration.spec-ICFHVFIR.js

@@ -0,0 +1,388 @@
+import {
+  hg38
+} from "./chunk-7VB2BKXW.js";
+import {
+  sleep
+} from "./chunk-FYXIK6Y6.js";
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import {
+  SearchHandler,
+  vocabInit
+} from "./chunk-Q5SK3U2T.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-54KC7DAB.js";
+import "./chunk-N7DVQTPC.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-RPDVFM7E.js";
+import "./chunk-M4XXKTH2.js";
+import "./chunk-5ILEFNXJ.js";
+import {
+  dtsnvindel
+} from "./chunk-IZUYLFOX.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-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import {
+  __toESM
+} from "./chunk-HS5PO5ZQ.js";
+
+// termdb/handlers/test/geneVariant.integration.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+async function getVocabApi() {
+  const vocabApi2 = vocabInit({ state: { vocab: { genome: "hg38-test", dslabel: "TermdbTest" } } });
+  if (!vocabApi2) throw "vocabApi is missing";
+  await vocabApi2.getTermdbConfig();
+  return vocabApi2;
+}
+var vocabApi = await getVocabApi();
+var handler = new SearchHandler();
+function getHolder() {
+  const holder = select_default("body").append("div");
+  return holder;
+}
+async function initializeSearchHandler(opts) {
+  const callback = opts.callback || (() => {
+  });
+  await handler.init({
+    holder: opts.holder,
+    app: { vocabApi: opts.vocabApi || vocabApi },
+    genomeObj: hg38,
+    keepsQ: opts.keepsQ,
+    msg: opts.msg,
+    callback
+  });
+}
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- geneVariant search handler -***-");
+  test.end();
+});
+(0, import_tape.default)("Search handler layout", async (test) => {
+  const holder = getHolder();
+  await initializeSearchHandler({ holder });
+  const mutationTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]');
+  test.ok(
+    mutationTypeRadiosDiv.selectAll('input[type="radio"]').size() > 0,
+    "Mutation type radio buttons should be present"
+  );
+  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
+  test.equal(
+    inputTypeRadiosDiv.selectAll('input[type="radio"]').size(),
+    2,
+    "Input type radio buttons should be present"
+  );
+  const searchDiv = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]');
+  test.equal(searchDiv.selectAll('input[type="search"]').size(), 1, "Gene search input should be present");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Single gene input", async (test) => {
+  let tw;
+  const callback = (_tw) => {
+    tw = _tw;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = "TP53";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(tw.term.type, "geneVariant", "term.type should be geneVariant");
+  test.equal(tw.q.type, "predefined-groupset", "q.type should be predefined-groupset");
+  test.equal(tw.q.predefined_groupset_idx, 0, "q.predefined_groupset_idx should be 0");
+  test.equal(tw.term.genes.length, 1, "term.genes[] should have length of 1");
+  test.deepEqual(
+    tw.term.genes[0],
+    { kind: "gene", id: "TP53", gene: "TP53", name: "TP53", type: "geneVariant" },
+    "term.genes[0] should have expected structure"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Change mutation type", async (test) => {
+  let tw;
+  const callback = (_tw) => {
+    tw = _tw;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const mutationTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]');
+  const mutationTypeRadios = mutationTypeRadiosDiv.selectAll('input[type="radio"]');
+  const thirdRadio = mutationTypeRadios.nodes()[2];
+  thirdRadio.click();
+  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
+  const geneSetDiv = inputTypeRadiosDiv.selectAll("div").filter((d) => d.value == "geneset");
+  test.equal(geneSetDiv.style("display"), "none", "Gene set option should be hidden for CNV");
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = "TP53";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(tw.q.predefined_groupset_idx, 2, "q.predefined_groupset_idx should be 2 upon selecting third radio button");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Gene set input", async (test) => {
+  let tw;
+  const callback = (_tw) => {
+    tw = _tw;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
+  const inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type="radio"]');
+  const secondRadio = inputTypeRadios.nodes()[1];
+  secondRadio.click();
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = "TP53";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  geneSearchInput.value = "KRAS";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  const buttons = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').selectAll("button").nodes();
+  const submitButton = buttons.find((btn) => btn.textContent.trim() === "Submit");
+  await sleep(100);
+  submitButton.click();
+  await sleep(100);
+  test.equal(tw.term.genes.length, 2, "term.genes[] should have length of 2");
+  test.equal(tw.term.name, "TP53, KRAS", "term.name should concatenate gene names");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Gene set input - custom name", async (test) => {
+  let tw;
+  const callback = (_tw) => {
+    tw = _tw;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
+  const inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type="radio"]');
+  const secondRadio = inputTypeRadios.nodes()[1];
+  secondRadio.click();
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = "TP53";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  geneSearchInput.value = "KRAS";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  const nameInput = holder.select('[data-testid="sja_genesetinput_name"]').node();
+  nameInput.value = "Test gene set";
+  const buttons = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').selectAll("button").nodes();
+  const submitButton = buttons.find((btn) => btn.textContent.trim() === "Submit");
+  await sleep(100);
+  submitButton.click();
+  await sleep(100);
+  test.equal(tw.term.genes.length, 2, "term.genes[] should have length of 2");
+  test.equal(tw.term.name, "Test gene set", "term.name should be custom name");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+function getVocabApiWithRememberedQ(lst) {
+  return Object.assign(Object.create(vocabApi), { getGvQLst: () => structuredClone(lst) });
+}
+function getRememberedQ(name) {
+  return {
+    type: "custom-groupset",
+    customset: {
+      groups: [
+        {
+          name,
+          filter: {
+            type: "tvslst",
+            join: "",
+            in: true,
+            lst: [{ type: "tvs", tvs: { term: { id: "snvindel_somatic", dt: dtsnvindel, origin: "somatic" } } }]
+          }
+        }
+      ]
+    }
+  };
+}
+var rememberedLst = [
+  { label: "TP53 missense", q: getRememberedQ("TP53 missense") },
+  { label: "TP53 truncating", q: getRememberedQ("TP53 truncating") }
+];
+async function pickGene(holder, gene = "TP53") {
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = gene;
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+}
+(0, import_tape.default)("Remembered settings are offered for the picked gene", async (test) => {
+  let tw;
+  const holder = getHolder();
+  await initializeSearchHandler({
+    holder,
+    callback: (_tw) => tw = _tw,
+    vocabApi: getVocabApiWithRememberedQ(rememberedLst),
+    keepsQ: true,
+    // as client/plots/summarizeMutationSurvival.ts supplies it
+    msg: "Hit ENTER to launch plot."
+  });
+  await pickGene(holder);
+  test.equal(tw, void 0, "should not apply the mutation type while the settings are offered");
+  const msgDiv = holder.selectAll("div").nodes().find((n) => n.textContent == "Hit ENTER to launch plot.");
+  test.equal(msgDiv?.style.display, "none", "should hide a caller message that no longer describes what happens");
+  const remembered = holder.selectAll('[data-testid="sjpp-genevariant-rememberedQ"]');
+  test.equal(remembered.size(), 2, "should offer both remembered settings");
+  test.deepEqual(
+    remembered.nodes().map((n) => n.textContent),
+    ["TP53 missense", "TP53 truncating"],
+    "should label each by its remembered label"
+  );
+  const options = holder.selectAll(".sja_menuoption").nodes();
+  test.equal(options.length, 3, "should offer a way to continue with the mutation type instead");
+  test.ok(
+    options.every((n) => n.getAttribute("tabindex") == "0"),
+    "should make every option keyboard focusable"
+  );
+  test.equal(document.activeElement, options[0], "should focus the most recent setting");
+  options[0].dispatchEvent(new KeyboardEvent("keydown", { key: "ArrowDown", bubbles: true }));
+  test.equal(document.activeElement, options[1], "should move focus down");
+  options[1].dispatchEvent(new KeyboardEvent("keydown", { key: "ArrowUp", bubbles: true }));
+  test.equal(document.activeElement, options[0], "should move focus up");
+  options[0].dispatchEvent(new KeyboardEvent("keydown", { key: "ArrowUp", bubbles: true }));
+  test.equal(document.activeElement, options[2], "should wrap to the last option");
+  options[2].dispatchEvent(new KeyboardEvent("keydown", { key: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(tw?.q?.type, "predefined-groupset", "should continue with the mutation type on Enter");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Remembered settings are applied on Enter", async (test) => {
+  let tw;
+  const holder = getHolder();
+  await initializeSearchHandler({
+    holder,
+    callback: (_tw) => tw = _tw,
+    vocabApi: getVocabApiWithRememberedQ(rememberedLst),
+    keepsQ: true
+  });
+  await pickGene(holder);
+  const first = holder.selectAll('[data-testid="sjpp-genevariant-rememberedQ"]').nodes()[0];
+  first.dispatchEvent(new KeyboardEvent("keydown", { key: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(tw.q.type, "custom-groupset", "should apply the remembered q");
+  test.deepEqual(
+    tw.q.customset.groups.map((g) => g.name),
+    ["TP53 missense"],
+    "should apply the groups of the setting that was focused"
+  );
+  test.equal(tw.term.name, "TP53", "should apply it to the gene that was picked");
+  test.equal(
+    holder.select('[data-testid="sjpp-genevariant-rememberedQ"]').empty(),
+    true,
+    "should clear the offered settings once one is applied"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Remembered settings of another mutation type do not lead", async (test) => {
+  let tw;
+  const holder = getHolder();
+  await initializeSearchHandler({
+    holder,
+    callback: (_tw) => tw = _tw,
+    vocabApi: getVocabApiWithRememberedQ(rememberedLst),
+    keepsQ: true
+  });
+  const cnvRadio = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]').selectAll('input[type="radio"]').nodes()[2];
+  cnvRadio.click();
+  await pickGene(holder);
+  const options = holder.selectAll(".sja_menuoption").nodes();
+  test.deepEqual(
+    options.map((n) => n.textContent),
+    ["Continue with CNV", "TP53 missense", "TP53 truncating"],
+    "should lead with the selected mutation type, followed by the settings of other mutation types"
+  );
+  test.equal(document.activeElement, options[0], "should focus the way to continue with the mutation type");
+  options[0].dispatchEvent(new KeyboardEvent("keydown", { key: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(tw?.q?.predefined_groupset_idx, 2, "should continue with the selected mutation type on Enter");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Remembered settings are cleared on changing the mutation type", async (test) => {
+  let tw;
+  const holder = getHolder();
+  await initializeSearchHandler({
+    holder,
+    callback: (_tw) => tw = _tw,
+    vocabApi: getVocabApiWithRememberedQ(rememberedLst),
+    keepsQ: true,
+    msg: "Hit ENTER to launch plot."
+  });
+  await pickGene(holder);
+  test.equal(holder.selectAll(".sja_menuoption").size(), 3, "should offer the settings of the picked gene");
+  const cnvRadio = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]').selectAll('input[type="radio"]').nodes()[2];
+  cnvRadio.click();
+  await sleep(100);
+  test.equal(holder.selectAll(".sja_menuoption").size(), 0, "should clear the offered settings");
+  test.equal(tw, void 0, "should not apply anything on its own");
+  const msgDiv = holder.selectAll("div").nodes().find((n) => n.textContent == "Hit ENTER to launch plot.");
+  test.equal(msgDiv?.style.display, "block", "should put back the caller message that describes picking a gene again");
+  await pickGene(holder);
+  const options = holder.selectAll(".sja_menuoption").nodes();
+  test.equal(
+    options[0]?.textContent,
+    "Continue with CNV",
+    "should offer the settings against the mutation type now selected"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Remembered settings are cleared on changing the input type", async (test) => {
+  let tw;
+  const holder = getHolder();
+  await initializeSearchHandler({
+    holder,
+    callback: (_tw) => tw = _tw,
+    vocabApi: getVocabApiWithRememberedQ(rememberedLst),
+    keepsQ: true
+  });
+  await pickGene(holder);
+  test.equal(holder.selectAll(".sja_menuoption").size(), 3, "should offer the settings of the picked gene");
+  const geneSetRadio = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]').selectAll('input[type="radio"]').nodes()[1];
+  geneSetRadio.click();
+  await sleep(100);
+  test.equal(holder.selectAll(".sja_menuoption").size(), 0, "should clear the offered settings");
+  test.equal(tw, void 0, "should not apply anything on its own");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Remembered settings are not offered where the q would be dropped", async (test) => {
+  let tw;
+  const holder = getHolder();
+  await initializeSearchHandler({
+    holder,
+    callback: (_tw) => tw = _tw,
+    vocabApi: getVocabApiWithRememberedQ(rememberedLst)
+  });
+  await pickGene(holder);
+  test.equal(
+    holder.select('[data-testid="sjpp-genevariant-rememberedQ"]').empty(),
+    true,
+    "should offer no remembered setting"
+  );
+  test.equal(tw.q.type, "predefined-groupset", "should apply the mutation type directly");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+//# sourceMappingURL=geneVariant.integration.spec-ICFHVFIR.js.map