@sjcrh/proteinpaint-client 2.208.0 → 2.209.0

package/dist/geneVariant.integration.spec-O36JK4B7.js

@@ -0,0 +1,503 @@
+import {
+  hg38
+} from "./chunk-7VB2BKXW.js";
+import {
+  sleep
+} from "./chunk-FYXIK6Y6.js";
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import {
+  SearchHandler,
+  vocabInit
+} from "./chunk-C3HEDQPT.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-B6UXFX73.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-3FEP6B5T.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-OBDIJ4QS.js";
+import "./chunk-6FG6JFZP.js";
+import "./chunk-3XBG5HIV.js";
+import {
+  dtcnv,
+  dtsnvindel
+} from "./chunk-SB36AUG7.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();
+function getHolder() {
+  const holder = select_default("body").append("div");
+  return holder;
+}
+async function initializeSearchHandler(opts) {
+  const handler = new SearchHandler();
+  const callback = opts.callback || (() => {
+  });
+  await handler.init({
+    holder: opts.holder,
+    app: { vocabApi: opts.vocabApi || vocabApi },
+    genomeObj: hg38,
+    keepsQ: opts.keepsQ,
+    msg: opts.msg,
+    callback
+  });
+  return handler;
+}
+(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 getVocabApiWithSampleTypes() {
+  const termdbConfig = structuredClone(vocabApi.termdbConfig);
+  termdbConfig.sampleTypes = {
+    1: { name: "Primary" },
+    2: { name: "Relapse" }
+  };
+  termdbConfig.assayAvailability ??= { byDt: {} };
+  termdbConfig.assayAvailability.byDt ??= {};
+  termdbConfig.assayAvailability.byDt[dtsnvindel] = {
+    ...termdbConfig.assayAvailability.byDt[dtsnvindel],
+    bySampleType: { 1: { hasSamples: true }, 2: { hasSamples: true } }
+  };
+  delete termdbConfig.assayAvailability.byDt[dtsnvindel].byOrigin;
+  termdbConfig.assayAvailability.byDt[dtcnv] = {
+    ...termdbConfig.assayAvailability.byDt[dtcnv],
+    bySampleType: { 1: { hasSamples: true } }
+  };
+  termdbConfig.queries.snvindel = { ...termdbConfig.queries.snvindel, mafFilter: true };
+  termdbConfig.queries.cnv = { ...termdbConfig.queries.cnv, cnvGainCutoff: 1 };
+  return Object.assign(Object.create(vocabApi), { termdbConfig });
+}
+(0, import_tape.default)("Sample types are derived from current assay availability", async (test) => {
+  const holder = getHolder();
+  const handler = await initializeSearchHandler({ holder, vocabApi: getVocabApiWithSampleTypes() });
+  test.deepEqual(handler.getQuerySampleTypes(), [1, 2], "should return available SNV/indel sample types");
+  delete handler.opts.app.vocabApi.termdbConfig.assayAvailability.byDt[dtsnvindel].bySampleType;
+  test.equal(handler.getQuerySampleTypes(), void 0, "should not retain sample types after availability is removed");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Sample types are intersected for a multi-DT mutation type", async (test) => {
+  const holder = getHolder();
+  const handler = await initializeSearchHandler({ holder, vocabApi: getVocabApiWithSampleTypes() });
+  const allelicRadio = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]').selectAll('input[type="radio"]').nodes().slice(-1)[0];
+  allelicRadio.click();
+  test.deepEqual(handler.getQuerySampleTypes(), [1], "should return only sample types available for SNV/indel and CNV");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Sample type selection is cleared when changing to a mutation type without a selector", async (test) => {
+  let tw;
+  const holder = getHolder();
+  const handler = await initializeSearchHandler({
+    holder,
+    callback: (_tw) => tw = _tw,
+    vocabApi: getVocabApiWithSampleTypes()
+  });
+  const sampleTypeCheckboxes = holder.selectAll(".sjpp-genesearch-sampletype-checkboxes input");
+  test.equal(sampleTypeCheckboxes.size(), 2, "should render sample type choices for SNV/indel");
+  sampleTypeCheckboxes.nodes()[1].checked = true;
+  await pickGene(holder);
+  test.deepEqual(tw.term.sampleTypes, [2], "should submit the selected sample type");
+  const cnvMutationTypeIdx = handler.mutationTypeTerms.findIndex((term) => term.dt == dtcnv);
+  const cnvRadio = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]').selectAll('input[type="radio"]').nodes()[cnvMutationTypeIdx];
+  cnvRadio.click();
+  test.equal(
+    holder.selectAll(".sjpp-genesearch-sampletype-checkboxes input").size(),
+    0,
+    "should remove stale sample type choices"
+  );
+  await pickGene(holder, "KRAS");
+  test.deepEqual(tw.term.sampleTypes, [1], "should carry the only available CNV sample type");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Continuing past remembered settings does not retain sample types from another mutation type", async (test) => {
+  let tw;
+  const holder = getHolder();
+  const sampleTypeVocabApi = getVocabApiWithSampleTypes();
+  const vocabApiWithRememberedKrasQ = Object.assign(Object.create(sampleTypeVocabApi), {
+    getGvQLst: (term) => term.name == "KRAS" ? structuredClone(rememberedLst) : []
+  });
+  const handler = await initializeSearchHandler({
+    holder,
+    callback: (_tw) => tw = _tw,
+    vocabApi: vocabApiWithRememberedKrasQ,
+    keepsQ: true
+  });
+  holder.selectAll(".sjpp-genesearch-sampletype-checkboxes input").nodes()[1].checked = true;
+  await pickGene(holder);
+  test.deepEqual(tw.term.sampleTypes, [2], "should submit the selected SNV/indel sample type");
+  const cnvMutationTypeIdx = handler.mutationTypeTerms.findIndex((term) => term.dt == dtcnv);
+  const cnvRadio = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]').selectAll('input[type="radio"]').nodes()[cnvMutationTypeIdx];
+  cnvRadio.click();
+  await pickGene(holder, "KRAS");
+  const continueWithCnv = holder.selectAll(".sja_menuoption").nodes().find((option) => option.textContent == `Continue with ${handler.mutationTypeTerms[cnvMutationTypeIdx].name}`);
+  continueWithCnv.dispatchEvent(new KeyboardEvent("keydown", { key: "Enter", bubbles: true }));
+  await sleep(100);
+  test.deepEqual(tw.term.sampleTypes, [1], "should not retain the prior SNV/indel sample type");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+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)("Applying remembered settings applies the selected sample type", async (test) => {
+  let tw;
+  const holder = getHolder();
+  const sampleTypeVocabApi = getVocabApiWithSampleTypes();
+  await initializeSearchHandler({
+    holder,
+    callback: (_tw) => tw = _tw,
+    vocabApi: Object.assign(Object.create(sampleTypeVocabApi), {
+      getGvQLst: () => structuredClone(rememberedLst)
+    }),
+    keepsQ: true
+  });
+  holder.selectAll(".sjpp-genesearch-sampletype-checkboxes input").nodes()[1].checked = 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.deepEqual(tw.term.sampleTypes, [2], "should apply the selected sample type with the remembered q");
+  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-O36JK4B7.js.map

package/dist/geneVariant.integration.spec-O36JK4B7.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termdb/handlers/test/geneVariant.integration.spec.ts"],
+  "sourcesContent": ["import tape from 'tape'\nimport * as d3s from 'd3-selection'\nimport { SearchHandler } from '../geneVariant.ts'\nimport { dtcnv, dtsnvindel } from '#shared/common.js'\nimport { hg38 } from '../../../test/testdata/genomes'\nimport { sleep } from '../../../test/test.helpers.js'\nimport { vocabInit } from '../../vocabulary'\n\n/*\nTests:\n\tSearch handler layout\n    Single gene input\n    Change mutation type\n    Gene set input\n\tGene set input - custom name\n\tRemembered settings are offered for the picked gene\n\tRemembered settings are applied on Enter\n\tRemembered settings of another mutation type do not lead\n\tRemembered settings are cleared on changing the mutation type\n\tRemembered settings are cleared on changing the input type\n\tRemembered settings are not offered where the q would be dropped\n*/\n\n/*************************\n reusable helper functions\n**************************/\n\nasync function getVocabApi() {\n\tconst vocabApi = vocabInit({ state: { vocab: { genome: 'hg38-test', dslabel: 'TermdbTest' } } })\n\tif (!vocabApi) throw 'vocabApi is missing'\n\tawait vocabApi.getTermdbConfig()\n\treturn vocabApi\n}\n\nconst vocabApi: any = await getVocabApi()\n\nfunction getHolder() {\n\tconst holder = d3s.select('body').append('div')\n\treturn holder\n}\n\nasync function initializeSearchHandler(opts) {\n\tconst handler = new SearchHandler()\n\tconst callback = opts.callback || (() => {})\n\tawait handler.init({\n\t\tholder: opts.holder,\n\t\tapp: { vocabApi: opts.vocabApi || vocabApi },\n\t\tgenomeObj: hg38,\n\t\tkeepsQ: opts.keepsQ,\n\t\tmsg: opts.msg,\n\t\tcallback\n\t})\n\treturn handler\n}\n\n/**************\n test sections\n***************/\n\ntape('\\n', function (test) {\n\ttest.comment('-***- geneVariant search handler -***-')\n\ttest.end()\n})\n\ntape('Search handler layout', async test => {\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder })\n\tconst mutationTypeRadiosDiv = holder.select('[data-testid=\"sjpp-genevariant-mutationTypeRadios\"]')\n\ttest.ok(\n\t\tmutationTypeRadiosDiv.selectAll('input[type=\"radio\"]').size() > 0,\n\t\t'Mutation type radio buttons should be present'\n\t)\n\tconst inputTypeRadiosDiv = holder.select('[data-testid=\"sjpp-genevariant-genesetTypeRadios\"]')\n\ttest.equal(\n\t\tinputTypeRadiosDiv.selectAll('input[type=\"radio\"]').size(),\n\t\t2,\n\t\t'Input type radio buttons should be present'\n\t)\n\tconst searchDiv = holder.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]')\n\ttest.equal(searchDiv.selectAll('input[type=\"search\"]').size(), 1, 'Gene search input should be present')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Single gene input', async test => {\n\tlet tw\n\tconst callback = _tw => {\n\t\ttw = _tw\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst geneSearchInput: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]')\n\t\t.select('input[type=\"search\"]')\n\t\t.node()\n\t// gene name input\n\tgeneSearchInput.value = 'TP53'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(tw.term.type, 'geneVariant', 'term.type should be geneVariant')\n\ttest.equal(tw.q.type, 'predefined-groupset', 'q.type should be predefined-groupset')\n\ttest.equal(tw.q.predefined_groupset_idx, 0, 'q.predefined_groupset_idx should be 0')\n\ttest.equal(tw.term.genes.length, 1, 'term.genes[] should have length of 1')\n\ttest.deepEqual(\n\t\ttw.term.genes[0],\n\t\t{ kind: 'gene', id: 'TP53', gene: 'TP53', name: 'TP53', type: 'geneVariant' },\n\t\t'term.genes[0] should have expected structure'\n\t)\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Change mutation type', async test => {\n\tlet tw\n\tconst callback = _tw => {\n\t\ttw = _tw\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst mutationTypeRadiosDiv = holder.select('[data-testid=\"sjpp-genevariant-mutationTypeRadios\"]')\n\tconst mutationTypeRadios = mutationTypeRadiosDiv.selectAll('input[type=\"radio\"]')\n\t// select CNV mutation type\n\tconst thirdRadio: any = mutationTypeRadios.nodes()[2]\n\tthirdRadio.click()\n\t// verify gene set option is hidden for CNV\n\tconst inputTypeRadiosDiv = holder.select('[data-testid=\"sjpp-genevariant-genesetTypeRadios\"]')\n\tconst geneSetDiv = inputTypeRadiosDiv.selectAll('div').filter((d: any) => d.value == 'geneset')\n\ttest.equal(geneSetDiv.style('display'), 'none', 'Gene set option should be hidden for CNV')\n\t// enter gene to search\n\tconst geneSearchInput: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]')\n\t\t.select('input[type=\"search\"]')\n\t\t.node()\n\tgeneSearchInput.value = 'TP53'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(tw.q.predefined_groupset_idx, 2, 'q.predefined_groupset_idx should be 2 upon selecting third radio button')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Gene set input', async test => {\n\tlet tw\n\tconst callback = _tw => {\n\t\ttw = _tw\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst inputTypeRadiosDiv = holder.select('[data-testid=\"sjpp-genevariant-genesetTypeRadios\"]')\n\tconst inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type=\"radio\"]')\n\tconst secondRadio: any = inputTypeRadios.nodes()[1]\n\tsecondRadio.click()\n\tconst geneSearchInput: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]')\n\t\t.select('input[type=\"search\"]')\n\t\t.node()\n\tgeneSearchInput.value = 'TP53'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100) // wait for dispatch event\n\tgeneSearchInput.value = 'KRAS'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tconst buttons = holder.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]').selectAll('button').nodes()\n\tconst submitButton: any = buttons.find((btn: any) => btn.textContent.trim() === 'Submit')\n\tawait sleep(100) // wait until submit button is enabled\n\tsubmitButton.click()\n\tawait sleep(100) // wait until tw is populated\n\ttest.equal(tw.term.genes.length, 2, 'term.genes[] should have length of 2')\n\ttest.equal(tw.term.name, 'TP53, KRAS', 'term.name should concatenate gene names')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Gene set input - custom name', async test => {\n\tlet tw\n\tconst callback = _tw => {\n\t\ttw = _tw\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst inputTypeRadiosDiv = holder.select('[data-testid=\"sjpp-genevariant-genesetTypeRadios\"]')\n\tconst inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type=\"radio\"]')\n\tconst secondRadio: any = inputTypeRadios.nodes()[1]\n\tsecondRadio.click()\n\tconst geneSearchInput: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]')\n\t\t.select('input[type=\"search\"]')\n\t\t.node()\n\tgeneSearchInput.value = 'TP53'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100) // wait for dispatch event\n\tgeneSearchInput.value = 'KRAS'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100) // wait for dispatch event\n\tconst nameInput: any = holder.select('[data-testid=\"sja_genesetinput_name\"]').node()\n\tnameInput.value = 'Test gene set'\n\tconst buttons = holder.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]').selectAll('button').nodes()\n\tconst submitButton: any = buttons.find((btn: any) => btn.textContent.trim() === 'Submit')\n\tawait sleep(100) // wait until submit button is enabled\n\tsubmitButton.click()\n\tawait sleep(100) // wait until tw is populated\n\ttest.equal(tw.term.genes.length, 2, 'term.genes[] should have length of 2')\n\ttest.equal(tw.term.name, 'Test gene set', 'term.name should be custom name')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\n/* the settings a mass store remembers for a gene, see remember_gvq() in client/mass/store.ts.\nSupplied through a derived vocabApi, so that the shared one is left alone */\nfunction getVocabApiWithRememberedQ(lst) {\n\treturn Object.assign(Object.create(vocabApi), { getGvQLst: () => structuredClone(lst) })\n}\n\nfunction getVocabApiWithSampleTypes() {\n\tconst termdbConfig = structuredClone(vocabApi.termdbConfig)\n\ttermdbConfig.sampleTypes = {\n\t\t1: { name: 'Primary' },\n\t\t2: { name: 'Relapse' }\n\t}\n\ttermdbConfig.assayAvailability ??= { byDt: {} }\n\ttermdbConfig.assayAvailability.byDt ??= {}\n\ttermdbConfig.assayAvailability.byDt[dtsnvindel] = {\n\t\t...termdbConfig.assayAvailability.byDt[dtsnvindel],\n\t\tbySampleType: { 1: { hasSamples: true }, 2: { hasSamples: true } }\n\t}\n\tdelete termdbConfig.assayAvailability.byDt[dtsnvindel].byOrigin\n\ttermdbConfig.assayAvailability.byDt[dtcnv] = {\n\t\t...termdbConfig.assayAvailability.byDt[dtcnv],\n\t\tbySampleType: { 1: { hasSamples: true } }\n\t}\n\ttermdbConfig.queries.snvindel = { ...termdbConfig.queries.snvindel, mafFilter: true }\n\ttermdbConfig.queries.cnv = { ...termdbConfig.queries.cnv, cnvGainCutoff: 1 }\n\treturn Object.assign(Object.create(vocabApi), { termdbConfig })\n}\n\ntape('Sample types are derived from current assay availability', async test => {\n\tconst holder = getHolder()\n\tconst handler = await initializeSearchHandler({ holder, vocabApi: getVocabApiWithSampleTypes() })\n\ttest.deepEqual(handler.getQuerySampleTypes(), [1, 2], 'should return available SNV/indel sample types')\n\n\tdelete handler.opts.app.vocabApi.termdbConfig.assayAvailability.byDt[dtsnvindel].bySampleType\n\ttest.equal(handler.getQuerySampleTypes(), undefined, 'should not retain sample types after availability is removed')\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Sample types are intersected for a multi-DT mutation type', async test => {\n\tconst holder = getHolder()\n\tconst handler = await initializeSearchHandler({ holder, vocabApi: getVocabApiWithSampleTypes() })\n\tconst allelicRadio: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-mutationTypeRadios\"]')\n\t\t.selectAll('input[type=\"radio\"]')\n\t\t.nodes()\n\t\t.slice(-1)[0]\n\tallelicRadio.click()\n\ttest.deepEqual(handler.getQuerySampleTypes(), [1], 'should return only sample types available for SNV/indel and CNV')\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Sample type selection is cleared when changing to a mutation type without a selector', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\tconst handler = await initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithSampleTypes()\n\t})\n\tconst sampleTypeCheckboxes: any = holder.selectAll('.sjpp-genesearch-sampletype-checkboxes input')\n\ttest.equal(sampleTypeCheckboxes.size(), 2, 'should render sample type choices for SNV/indel')\n\tsampleTypeCheckboxes.nodes()[1].checked = true\n\tawait pickGene(holder)\n\ttest.deepEqual(tw.term.sampleTypes, [2], 'should submit the selected sample type')\n\n\tconst cnvMutationTypeIdx = handler.mutationTypeTerms.findIndex((term: any) => term.dt == dtcnv)\n\tconst cnvRadio: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-mutationTypeRadios\"]')\n\t\t.selectAll('input[type=\"radio\"]')\n\t\t.nodes()[cnvMutationTypeIdx]\n\tcnvRadio.click()\n\ttest.equal(\n\t\tholder.selectAll('.sjpp-genesearch-sampletype-checkboxes input').size(),\n\t\t0,\n\t\t'should remove stale sample type choices'\n\t)\n\tawait pickGene(holder, 'KRAS')\n\ttest.deepEqual(tw.term.sampleTypes, [1], 'should carry the only available CNV sample type')\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\n/* The initial selection writes sampleTypes to the handler term. A remembered setting on the\nnext selection exercises the \"Continue with ...\" path, which must replace those values. */\ntape('Continuing past remembered settings does not retain sample types from another mutation type', async test => {\n\tlet tw\n\tconst holder: any = getHolder()\n\tconst sampleTypeVocabApi = getVocabApiWithSampleTypes()\n\tconst vocabApiWithRememberedKrasQ = Object.assign(Object.create(sampleTypeVocabApi), {\n\t\tgetGvQLst: (term: any) => (term.name == 'KRAS' ? structuredClone(rememberedLst) : [])\n\t})\n\tconst handler = await initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: vocabApiWithRememberedKrasQ,\n\t\tkeepsQ: true\n\t})\n\tholder.selectAll('.sjpp-genesearch-sampletype-checkboxes input').nodes()[1].checked = true\n\tawait pickGene(holder)\n\ttest.deepEqual(tw.term.sampleTypes, [2], 'should submit the selected SNV/indel sample type')\n\n\tconst cnvMutationTypeIdx = handler.mutationTypeTerms.findIndex((term: any) => term.dt == dtcnv)\n\tconst cnvRadio: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-mutationTypeRadios\"]')\n\t\t.selectAll('input[type=\"radio\"]')\n\t\t.nodes()[cnvMutationTypeIdx]\n\tcnvRadio.click()\n\tawait pickGene(holder, 'KRAS')\n\tconst continueWithCnv: any = holder\n\t\t.selectAll('.sja_menuoption')\n\t\t.nodes()\n\t\t.find((option: any) => option.textContent == `Continue with ${handler.mutationTypeTerms[cnvMutationTypeIdx].name}`)\n\tcontinueWithCnv.dispatchEvent(new KeyboardEvent('keydown', { key: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.deepEqual(tw.term.sampleTypes, [1], 'should not retain the prior SNV/indel sample type')\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\n/* a grouping of the first mutation type of this dataset, SNV/indel (somatic), as it is\nremembered: a customset whose group filter carries the dt term of each tvs */\nfunction getRememberedQ(name) {\n\treturn {\n\t\ttype: 'custom-groupset',\n\t\tcustomset: {\n\t\t\tgroups: [\n\t\t\t\t{\n\t\t\t\t\tname,\n\t\t\t\t\tfilter: {\n\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\tin: true,\n\t\t\t\t\t\tlst: [{ type: 'tvs', tvs: { term: { id: 'snvindel_somatic', dt: dtsnvindel, origin: 'somatic' } } }]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n}\n\nconst rememberedLst = [\n\t{ label: 'TP53 missense', q: getRememberedQ('TP53 missense') },\n\t{ label: 'TP53 truncating', q: getRememberedQ('TP53 truncating') }\n]\n\nasync function pickGene(holder, gene = 'TP53') {\n\tconst geneSearchInput: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]')\n\t\t.select('input[type=\"search\"]')\n\t\t.node()\n\tgeneSearchInput.value = gene\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100)\n}\n\ntape('Remembered settings are offered for the picked gene', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithRememberedQ(rememberedLst),\n\t\tkeepsQ: true,\n\t\t// as client/plots/summarizeMutationSurvival.ts supplies it\n\t\tmsg: 'Hit ENTER to launch plot.'\n\t})\n\tawait pickGene(holder)\n\n\ttest.equal(tw, undefined, 'should not apply the mutation type while the settings are offered')\n\tconst msgDiv: any = holder\n\t\t.selectAll('div')\n\t\t.nodes()\n\t\t.find((n: any) => n.textContent == 'Hit ENTER to launch plot.')\n\ttest.equal(msgDiv?.style.display, 'none', 'should hide a caller message that no longer describes what happens')\n\tconst remembered = holder.selectAll('[data-testid=\"sjpp-genevariant-rememberedQ\"]')\n\ttest.equal(remembered.size(), 2, 'should offer both remembered settings')\n\ttest.deepEqual(\n\t\tremembered.nodes().map((n: any) => n.textContent),\n\t\t['TP53 missense', 'TP53 truncating'],\n\t\t'should label each by its remembered label'\n\t)\n\tconst options: any[] = holder.selectAll('.sja_menuoption').nodes()\n\ttest.equal(options.length, 3, 'should offer a way to continue with the mutation type instead')\n\ttest.ok(\n\t\toptions.every((n: any) => n.getAttribute('tabindex') == '0'),\n\t\t'should make every option keyboard focusable'\n\t)\n\ttest.equal(document.activeElement, options[0], 'should focus the most recent setting')\n\n\t// arrowing moves within the options and wraps, so focus cannot leave them by accident\n\toptions[0].dispatchEvent(new KeyboardEvent('keydown', { key: 'ArrowDown', bubbles: true }))\n\ttest.equal(document.activeElement, options[1], 'should move focus down')\n\toptions[1].dispatchEvent(new KeyboardEvent('keydown', { key: 'ArrowUp', bubbles: true }))\n\ttest.equal(document.activeElement, options[0], 'should move focus up')\n\toptions[0].dispatchEvent(new KeyboardEvent('keydown', { key: 'ArrowUp', bubbles: true }))\n\ttest.equal(document.activeElement, options[2], 'should wrap to the last option')\n\n\t/* activating on keydown and not keyup: the gene above is picked by pressing Enter in the\n\tsearch box, whose keyup would otherwise land on the option focused here */\n\toptions[2].dispatchEvent(new KeyboardEvent('keydown', { key: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(tw?.q?.type, 'predefined-groupset', 'should continue with the mutation type on Enter')\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Remembered settings are applied on Enter', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithRememberedQ(rememberedLst),\n\t\tkeepsQ: true\n\t})\n\tawait pickGene(holder)\n\n\tconst first: any = holder.selectAll('[data-testid=\"sjpp-genevariant-rememberedQ\"]').nodes()[0]\n\tfirst.dispatchEvent(new KeyboardEvent('keydown', { key: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(tw.q.type, 'custom-groupset', 'should apply the remembered q')\n\ttest.deepEqual(\n\t\ttw.q.customset.groups.map((g: any) => g.name),\n\t\t['TP53 missense'],\n\t\t'should apply the groups of the setting that was focused'\n\t)\n\ttest.equal(tw.term.name, 'TP53', 'should apply it to the gene that was picked')\n\ttest.equal(\n\t\tholder.select('[data-testid=\"sjpp-genevariant-rememberedQ\"]').empty(),\n\t\ttrue,\n\t\t'should clear the offered settings once one is applied'\n\t)\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Applying remembered settings applies the selected sample type', async test => {\n\tlet tw\n\tconst holder: any = getHolder()\n\tconst sampleTypeVocabApi = getVocabApiWithSampleTypes()\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: Object.assign(Object.create(sampleTypeVocabApi), {\n\t\t\tgetGvQLst: () => structuredClone(rememberedLst)\n\t\t}),\n\t\tkeepsQ: true\n\t})\n\tholder.selectAll('.sjpp-genesearch-sampletype-checkboxes input').nodes()[1].checked = true\n\tawait pickGene(holder)\n\n\tconst first: any = holder.selectAll('[data-testid=\"sjpp-genevariant-rememberedQ\"]').nodes()[0]\n\tfirst.dispatchEvent(new KeyboardEvent('keydown', { key: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.deepEqual(tw.term.sampleTypes, [2], 'should apply the selected sample type with the remembered q')\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Remembered settings of another mutation type do not lead', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithRememberedQ(rememberedLst),\n\t\tkeepsQ: true\n\t})\n\t// the settings above group SNV/indel (somatic) variants, so select CNV instead\n\tconst cnvRadio: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-mutationTypeRadios\"]')\n\t\t.selectAll('input[type=\"radio\"]')\n\t\t.nodes()[2]\n\tcnvRadio.click()\n\tawait pickGene(holder)\n\n\tconst options: any[] = holder.selectAll('.sja_menuoption').nodes()\n\ttest.deepEqual(\n\t\toptions.map((n: any) => n.textContent),\n\t\t['Continue with CNV', 'TP53 missense', 'TP53 truncating'],\n\t\t'should lead with the selected mutation type, followed by the settings of other mutation types'\n\t)\n\ttest.equal(document.activeElement, options[0], 'should focus the way to continue with the mutation type')\n\n\toptions[0].dispatchEvent(new KeyboardEvent('keydown', { key: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(tw?.q?.predefined_groupset_idx, 2, 'should continue with the selected mutation type on Enter')\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Remembered settings are cleared on changing the mutation type', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithRememberedQ(rememberedLst),\n\t\tkeepsQ: true,\n\t\tmsg: 'Hit ENTER to launch plot.'\n\t})\n\tawait pickGene(holder)\n\ttest.equal(holder.selectAll('.sja_menuoption').size(), 3, 'should offer the settings of the picked gene')\n\n\t// the options were offered against the mutation type selected above, so they no longer apply\n\tconst cnvRadio: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-mutationTypeRadios\"]')\n\t\t.selectAll('input[type=\"radio\"]')\n\t\t.nodes()[2]\n\tcnvRadio.click()\n\tawait sleep(100)\n\n\ttest.equal(holder.selectAll('.sja_menuoption').size(), 0, 'should clear the offered settings')\n\ttest.equal(tw, undefined, 'should not apply anything on its own')\n\tconst msgDiv: any = holder\n\t\t.selectAll('div')\n\t\t.nodes()\n\t\t.find((n: any) => n.textContent == 'Hit ENTER to launch plot.')\n\ttest.equal(msgDiv?.style.display, 'block', 'should put back the caller message that describes picking a gene again')\n\n\t// the gene is picked again, now against the mutation type that was just selected\n\tawait pickGene(holder)\n\tconst options: any[] = holder.selectAll('.sja_menuoption').nodes()\n\ttest.equal(\n\t\toptions[0]?.textContent,\n\t\t'Continue with CNV',\n\t\t'should offer the settings against the mutation type now selected'\n\t)\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Remembered settings are cleared on changing the input type', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithRememberedQ(rememberedLst),\n\t\tkeepsQ: true\n\t})\n\tawait pickGene(holder)\n\ttest.equal(holder.selectAll('.sja_menuoption').size(), 3, 'should offer the settings of the picked gene')\n\n\t// the gene input is rebuilt empty, so the settings offered for the gene it held no longer apply\n\tconst geneSetRadio: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-genesetTypeRadios\"]')\n\t\t.selectAll('input[type=\"radio\"]')\n\t\t.nodes()[1]\n\tgeneSetRadio.click()\n\tawait sleep(100)\n\n\ttest.equal(holder.selectAll('.sja_menuoption').size(), 0, 'should clear the offered settings')\n\ttest.equal(tw, undefined, 'should not apply anything on its own')\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Remembered settings are not offered where the q would be dropped', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\t// a consumer that keeps only the term{}, see keepsQ in client/termdb/TermTypeSearch.ts\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithRememberedQ(rememberedLst)\n\t})\n\tawait pickGene(holder)\n\n\ttest.equal(\n\t\tholder.select('[data-testid=\"sjpp-genevariant-rememberedQ\"]').empty(),\n\t\ttrue,\n\t\t'should offer no remembered setting'\n\t)\n\ttest.equal(tw.q.type, 'predefined-groupset', 'should apply the mutation type directly')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n"],
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+  "names": ["vocabApi", "tape"]
+}