@sjcrh/proteinpaint-client 2.207.0 → 2.207.1

package/dist/geneVariant.integration.spec-2ATUV7NH.js

@@ -1,489 +0,0 @@
-import {
-  hg38
-} from "./chunk-7VB2BKXW.js";
-import {
-  sleep
-} from "./chunk-FYXIK6Y6.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import {
-  SearchHandler,
-  vocabInit
-} from "./chunk-NQDF3U2C.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-CCYVGZGI.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-N7DVQTPC.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-GRVO7RW4.js";
-import "./chunk-7CJKL3LK.js";
-import "./chunk-HZ3TCGBK.js";
-import {
-  dtcnv,
-  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();
-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 } }
-  };
-  termdbConfig.assayAvailability.byDt[dtcnv] = {
-    ...termdbConfig.assayAvailability.byDt[dtcnv],
-    bySampleType: { 1: { hasSamples: true } }
-  };
-  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 type selection is cleared when changing to a mutation type without a selector", async (test) => {
-  let tw;
-  const holder = getHolder();
-  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 cnvRadio = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]').selectAll('input[type="radio"]').nodes()[2];
-  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) : []
-  });
-  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 cnvRadio = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]').selectAll('input[type="radio"]').nodes()[2];
-  cnvRadio.click();
-  await pickGene(holder, "KRAS");
-  const continueWithCnv = holder.selectAll(".sja_menuoption").nodes()[0];
-  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-2ATUV7NH.js.map