@sjcrh/proteinpaint-client 2.221.0 → 2.223.0

package/dist/termCollection.unit.spec-G4HGOR7B.js

@@ -0,0 +1,295 @@
+import {
+  SearchHandler
+} from "./chunk-DKEH6FBC.js";
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import "./chunk-JP4IU7DO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-IRAB3OI7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import {
+  __toESM
+} from "./chunk-HS5PO5ZQ.js";
+
+// termdb/handlers/test/termCollection.unit.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+function getHolder() {
+  return select_default("body").append("div");
+}
+function getTermCollectionDetails(overrides = {}) {
+  return {
+    name: "Test Collection",
+    type: "gene",
+    memberType: "gene",
+    termlst: [
+      { id: "gene1", name: "TP53", values: { tissue: "Lung" } },
+      { id: "gene2", name: "KRAS", values: { tissue: "Colon" } },
+      { id: "gene3", name: "BRCA1", values: { tissue: "Breast" } }
+    ],
+    categoryKeys: [
+      { key: "tissue", shown: true },
+      { key: "expression", shown: false }
+    ],
+    propsByTermId: {
+      gene1: { color: "#FF0000" },
+      gene2: { color: "#00FF00" }
+    },
+    ...overrides
+  };
+}
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- termdb/handlers/termCollection -***-");
+  test.end();
+});
+(0, import_tape.default)("init() should render term list table with all terms from details.termlst", async (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  const details = getTermCollectionDetails();
+  await handler.init({
+    holder,
+    callback: () => {
+    },
+    app: {},
+    details
+  });
+  const table = holder.select("table");
+  test.ok(table.node(), "Should render a table");
+  const rows = table.selectAll("tbody tr");
+  test.equal(rows.size(), 3, "Should render three rows for three terms");
+  const rowTexts = rows.nodes().map((row) => row.textContent.trim());
+  test.ok(rowTexts[0].includes("TP53"), "First row should contain TP53");
+  test.ok(rowTexts[1].includes("KRAS"), "Second row should contain KRAS");
+  test.ok(rowTexts[2].includes("BRCA1"), "Third row should contain BRCA1");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("init() should render category table when details.categoryKeys is present", async (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  const details = getTermCollectionDetails();
+  await handler.init({
+    holder,
+    callback: () => {
+    },
+    app: {},
+    details
+  });
+  const tables = holder.selectAll("table");
+  test.equal(tables.size(), 2, "Should render two tables when categoryKeys is present");
+  const categoryTable = tables.nodes()[1];
+  const categoryRows = select_default(categoryTable).selectAll("tbody tr");
+  test.equal(categoryRows.size(), 2, "Should render two rows for two categories");
+  const categoryTexts = categoryRows.nodes().map((row) => row.textContent.trim());
+  test.ok(categoryTexts[0].includes("tissue"), "Should display tissue category key");
+  test.ok(categoryTexts[1].includes("expression"), "Should display expression category key");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("init() should call callback with selected terms, categoryKeys, and properties", async (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  const details = getTermCollectionDetails();
+  let callbackResult;
+  await handler.init({
+    holder,
+    callback: (result) => {
+      callbackResult = result;
+    },
+    app: {},
+    details
+  });
+  const termsTable = holder.selectAll("table").nodes()[0];
+  const checkboxes = termsTable.querySelectorAll('tbody input[type="checkbox"]');
+  checkboxes[0].checked = true;
+  checkboxes[1].checked = true;
+  checkboxes[2].checked = false;
+  const categoryTable = holder.selectAll("table").nodes()[1];
+  const categoryCheckboxes = categoryTable.querySelectorAll('tbody input[type="checkbox"]');
+  categoryCheckboxes[0].checked = true;
+  categoryCheckboxes[1].checked = false;
+  const selectBtn = holder.select('[data-testid="sjpp-term-collection-select"]').node();
+  selectBtn.click();
+  test.equal(callbackResult?.type, "termCollection", "Should set type to termCollection");
+  test.equal(callbackResult?.name, "Test Collection", "Should pass collection name");
+  test.equal(callbackResult?.memberType, "gene", "Should pass memberType");
+  test.deepEqual(callbackResult?.termIds, ["gene1", "gene2"], "Should pass selected term IDs");
+  test.equal(callbackResult?.termlst.length, 2, "Should pass selected term list with correct length");
+  test.equal(callbackResult?.termlst[0].name, "TP53", "First selected term should be TP53");
+  test.equal(callbackResult?.termlst[1].name, "KRAS", "Second selected term should be KRAS");
+  test.deepEqual(
+    callbackResult?.categoryKeys,
+    [
+      { key: "tissue", shown: true },
+      { key: "expression", shown: false }
+    ],
+    "Should pass updated categoryKeys with shown status"
+  );
+  test.deepEqual(
+    callbackResult?.propsByTermId,
+    { gene1: { color: "#FF0000" }, gene2: { color: "#00FF00" } },
+    "Should pass propsByTermId for selected terms only"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("init() should not render category table when details.categoryKeys is missing", async (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  const details = getTermCollectionDetails({ categoryKeys: void 0 });
+  await handler.init({
+    holder,
+    callback: () => {
+    },
+    app: {},
+    details
+  });
+  const tables = holder.selectAll("table");
+  test.equal(tables.size(), 1, "Should render only one table when categoryKeys is missing");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("init() disables the Select button for an invalid collection", async (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  const details = getTermCollectionDetails();
+  let callbackResult;
+  await handler.init({
+    holder,
+    callback: (result) => {
+      callbackResult = result;
+    },
+    app: {},
+    details
+  });
+  const selectBtn = holder.select('[data-testid="sjpp-term-collection-select"]').node();
+  const getChecks = (tableIdx) => [
+    ...holder.selectAll("table").nodes()[tableIdx].querySelectorAll('tbody input[type="checkbox"]')
+  ];
+  const terms = () => getChecks(0);
+  const categories = () => getChecks(1);
+  test.equal(selectBtn.disabled, false, "enables the button for the default selection");
+  terms()[0].click();
+  test.equal(selectBtn.disabled, false, "stays enabled with two selected variables");
+  terms()[1].click();
+  test.equal(selectBtn.disabled, true, "disables the button with a single selected variable");
+  test.ok(`${selectBtn.title}`.includes("two variables"), `titles the button with the reason: ${selectBtn.title}`);
+  selectBtn.click();
+  test.equal(callbackResult, void 0, "a disabled button does not submit the selection");
+  terms()[1].click();
+  test.equal(selectBtn.disabled, false, "re-enables the button with two selected variables");
+  categories()[0].click();
+  test.equal(selectBtn.disabled, false, "stays enabled with one selected category");
+  categories()[1].click();
+  test.equal(selectBtn.disabled, true, "disables the button without a selected category");
+  test.ok(`${selectBtn.title}`.includes("category"), `titles the button with the reason: ${selectBtn.title}`);
+  categories()[1].click();
+  test.equal(selectBtn.disabled, false, "re-enables the button for a valid collection");
+  selectBtn.click();
+  test.deepEqual(callbackResult?.termIds, ["gene2", "gene3"], "submits the selected variables");
+  test.deepEqual(
+    callbackResult?.categoryKeys,
+    [
+      { key: "tissue", shown: false },
+      { key: "expression", shown: true }
+    ],
+    "submits the selected categories"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("fraction selection returns a raw fraction wrapper and retains every member", async (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  const details = getTermCollectionDetails({
+    type: "numeric",
+    memberType: "numeric",
+    categoryKeys: void 0
+  });
+  let callbackResult;
+  await handler.init({
+    holder,
+    callback: (result) => {
+      callbackResult = result;
+    },
+    app: {},
+    details,
+    usecase: { target: "barchart", detail: "term2" },
+    termCollectionSelectionMode: "fraction"
+  });
+  test.ok(holder.text().includes("Denominator"), "renders the denominator selector");
+  test.ok(holder.text().includes("Numerator"), "renders the numerator selector");
+  const rows = holder.selectAll("tbody tr").nodes();
+  const numerator = rows[1].querySelector('[data-testid="sjpp-term-collection-numerator"]');
+  numerator.click();
+  holder.select('[data-testid="sjpp-term-collection-fraction-select"]').node().click();
+  test.equal(callbackResult?.type, "TermCollectionTWFraction", "returns a fraction wrapper");
+  test.deepEqual(callbackResult?.q.denominators, ["gene1", "gene2", "gene3"], "defaults all members as denominators");
+  test.deepEqual(callbackResult?.q.numerators, ["gene1", "gene2"], "returns the selected numerators");
+  test.equal(callbackResult?.term.termlst.length, 3, "keeps the complete source member list");
+  test.deepEqual(callbackResult?.term.termIds, ["gene1", "gene2", "gene3"], "keeps every source member ID");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("fraction selection clears and disables the numerator of a deselected denominator", async (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  const details = getTermCollectionDetails({
+    type: "numeric",
+    memberType: "numeric",
+    categoryKeys: void 0
+  });
+  let callbackResult;
+  await handler.init({
+    holder,
+    callback: (result) => {
+      callbackResult = result;
+    },
+    app: {},
+    details,
+    usecase: { target: "barchart", detail: "term2" },
+    termCollectionSelectionMode: "fraction"
+  });
+  const getNumerators = () => holder.selectAll('[data-testid="sjpp-term-collection-numerator"]').nodes();
+  const getDenominators = () => holder.selectAll('[data-testid="sjpp-term-collection-denominator"]').nodes();
+  getDenominators()[0].click();
+  test.equal(getNumerators()[0].checked, false, "clears the numerator of a deselected denominator");
+  test.equal(getNumerators()[0].disabled, true, "disables the numerator of a deselected denominator");
+  const selectBtn = holder.select('[data-testid="sjpp-term-collection-fraction-select"]').node();
+  test.equal(selectBtn.disabled, true, "disables the Select button without a numerator");
+  selectBtn.click();
+  test.equal(callbackResult, void 0, "does not submit a fraction without a numerator");
+  getDenominators()[0].click();
+  test.equal(getNumerators()[0].disabled, false, "enables the numerator when its denominator is restored");
+  test.equal(getNumerators()[0].checked, false, "does not silently restore the numerator");
+  getNumerators()[1].click();
+  holder.select('[data-testid="sjpp-term-collection-fraction-select"]').node().click();
+  test.deepEqual(callbackResult?.q.numerators, ["gene2"], "submits the edited numerator selection");
+  test.deepEqual(
+    callbackResult?.q.denominators,
+    ["gene1", "gene2", "gene3"],
+    "submits the restored denominator selection"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+//# sourceMappingURL=termCollection.unit.spec-G4HGOR7B.js.map

package/dist/termCollectionFractionSelection-F2VKGR2D.js

@@ -0,0 +1,38 @@
+import {
+  getDefaultFractionSelection,
+  getFractionSelectionError,
+  makeFractionTermWrapper,
+  mayRenderFractionSelection,
+  pickCollectionFraction,
+  renderFractionSelection
+} from "./chunk-JP4IU7DO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-IRAB3OI7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+export {
+  getDefaultFractionSelection,
+  getFractionSelectionError,
+  makeFractionTermWrapper,
+  mayRenderFractionSelection,
+  pickCollectionFraction,
+  renderFractionSelection
+};
+//# sourceMappingURL=termCollectionFractionSelection-F2VKGR2D.js.map

package/dist/termCollectionFractionSelection.unit.spec-46XS3WMX.js

@@ -0,0 +1,184 @@
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import {
+  mayRenderFractionSelection,
+  renderFractionSelection
+} from "./chunk-JP4IU7DO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-IRAB3OI7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import {
+  __toESM
+} from "./chunk-HS5PO5ZQ.js";
+
+// termdb/handlers/test/termCollectionFractionSelection.unit.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+function getDivs() {
+  const holder = select_default("body").append("div");
+  return { holder, listDiv: holder.append("div"), fractionDiv: holder.append("div").style("display", "none") };
+}
+function getCollectionTerm(overrides = {}) {
+  return {
+    type: "termCollection",
+    isCustom: true,
+    memberType: "numeric",
+    name: "Splice junction event",
+    termlst: [
+      { id: "junction-1", name: "junction-1" },
+      { id: "junction-2", name: "junction-2" }
+    ],
+    ...overrides
+  };
+}
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- termdb/handlers/termCollectionFractionSelection -***-");
+  test.end();
+});
+(0, import_tape.default)("mayRenderFractionSelection() renders the chooser for a numeric collection", (test) => {
+  const { holder, listDiv, fractionDiv } = getDivs();
+  let selected;
+  const term = getCollectionTerm();
+  const isStaged = mayRenderFractionSelection({
+    term,
+    selectionMode: "fraction",
+    listDiv,
+    fractionDiv,
+    callback: (tw) => selected = tw
+  });
+  test.equal(isStaged, true, "defers the selection to the chooser");
+  test.equal(listDiv.style("display"), "none", "hides the term list");
+  test.ok(fractionDiv.text().includes("Denominator"), "renders the denominator selector");
+  test.ok(fractionDiv.text().includes("Numerator"), "renders the numerator selector");
+  fractionDiv.select('[data-testid="sjpp-term-collection-fraction-select"]').node().click();
+  test.equal(selected?.type, "TermCollectionTWFraction", "submits a fraction wrapper");
+  test.deepEqual(selected?.q.denominators, ["junction-1", "junction-2"], "defaults all members as denominators");
+  test.deepEqual(selected?.q.numerators, ["junction-1"], "defaults only the first member as numerator");
+  test.equal(selected?.term, term, "wraps the clicked term as is");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("mayRenderFractionSelection() back button restores the term list", (test) => {
+  const { holder, listDiv, fractionDiv } = getDivs();
+  mayRenderFractionSelection({
+    term: getCollectionTerm(),
+    selectionMode: "fraction",
+    listDiv,
+    fractionDiv,
+    callback: () => {
+    }
+  });
+  fractionDiv.select('[data-testid="sjpp-term-collection-fraction-back"]').node().click();
+  test.notEqual(listDiv.style("display"), "none", "shows the term list again");
+  test.equal(fractionDiv.style("display"), "none", "hides the chooser");
+  test.equal(fractionDiv.selectAll("*").size(), 0, "clears the chooser");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("mayRenderFractionSelection() skips terms that do not require a fraction", (test) => {
+  const cases = [
+    { label: "no fraction selection mode", selectionMode: void 0, term: getCollectionTerm() },
+    {
+      label: "categorical collection",
+      selectionMode: "fraction",
+      term: getCollectionTerm({ memberType: "categorical" })
+    },
+    { label: "collection without members", selectionMode: "fraction", term: getCollectionTerm({ termlst: [] }) },
+    { label: "non-collection term", selectionMode: "fraction", term: { type: "junction", id: "junction-1" } }
+  ];
+  for (const c of cases) {
+    const { holder, listDiv, fractionDiv } = getDivs();
+    const isStaged = mayRenderFractionSelection({
+      term: c.term,
+      selectionMode: c.selectionMode,
+      listDiv,
+      fractionDiv,
+      callback: () => {
+      }
+    });
+    test.equal(isStaged, false, `does not stage a selection for ${c.label}`);
+    test.equal(fractionDiv.selectAll("*").size(), 0, `renders no chooser for ${c.label}`);
+    test.notEqual(listDiv.style("display"), "none", `keeps the term list visible for ${c.label}`);
+    if (test["_ok"]) holder.remove();
+  }
+  test.end();
+});
+(0, import_tape.default)("renderFractionSelection() only renders the Select button with a selectCallback", (test) => {
+  const holder = select_default("body").append("div");
+  const term = getCollectionTerm();
+  renderFractionSelection({
+    holder,
+    termlst: term.termlst,
+    selection: { numerators: ["junction-1"], denominators: ["junction-1", "junction-2"] }
+  });
+  test.equal(
+    holder.selectAll('[data-testid="sjpp-term-collection-fraction-select"]').size(),
+    0,
+    "renders no button for a caller with its own apply button"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("renderFractionSelection() disables the Select button for an inapplicable selection", (test) => {
+  const holder = select_default("body").append("div");
+  const term = getCollectionTerm({
+    termlst: [
+      { id: "junction-1", name: "junction-1" },
+      { id: "junction-2", name: "junction-2" },
+      { id: "junction-3", name: "junction-3" }
+    ]
+  });
+  const selected = [];
+  const selection = { numerators: ["junction-1"], denominators: term.termlst.map((t) => t.id) };
+  renderFractionSelection({
+    holder,
+    termlst: term.termlst,
+    selection,
+    selectCallback: (s) => selected.push(structuredClone(s))
+  });
+  const selectBtn = holder.select('[data-testid="sjpp-term-collection-fraction-select"]').node();
+  const numerators = holder.selectAll('[data-testid="sjpp-term-collection-numerator"]').nodes();
+  const denominators = holder.selectAll('[data-testid="sjpp-term-collection-denominator"]').nodes();
+  test.equal(selectBtn.disabled, false, "enables the button for the starting selection");
+  numerators[0].click();
+  test.equal(selectBtn.disabled, true, "disables the button without a numerator");
+  test.ok(`${selectBtn.title}`.includes("numerator"), `titles the button with the reason: ${selectBtn.title}`);
+  selectBtn.click();
+  test.equal(selected.length, 0, "a disabled button does not submit the selection");
+  numerators[0].click();
+  denominators[1].click();
+  test.equal(selectBtn.disabled, false, "stays enabled with two denominators");
+  denominators[2].click();
+  test.equal(selectBtn.disabled, true, "disables the button with a single denominator");
+  test.ok(`${selectBtn.title}`.includes("denominator"), `titles the button with the reason: ${selectBtn.title}`);
+  denominators[1].click();
+  test.equal(selectBtn.disabled, false, "re-enables the button for an applicable selection");
+  selectBtn.click();
+  test.deepEqual(
+    selected,
+    [{ numerators: ["junction-1"], denominators: ["junction-1", "junction-2"] }],
+    "submits the current selection"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+//# sourceMappingURL=termCollectionFractionSelection.unit.spec-46XS3WMX.js.map

package/dist/tk-JBLKYKKI.js

@@ -0,0 +1,37 @@
+import {
+  loadTk,
+  rangequery_rglst
+} from "./chunk-SZNEHG4C.js";
+import "./chunk-FE5TCBIT.js";
+import "./chunk-RRMAUPEA.js";
+import "./chunk-MU77WKSY.js";
+import "./chunk-V2OJLJSK.js";
+import "./chunk-4FTH4L3A.js";
+import "./chunk-VLIOMJDR.js";
+import "./chunk-JP4IU7DO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-IRAB3OI7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+export {
+  loadTk,
+  rangequery_rglst
+};
+//# sourceMappingURL=tk-JBLKYKKI.js.map