@sjcrh/proteinpaint-client 2.211.0 → 2.212.0

package/dist/matrix.sorterUi.unit.spec-4ZKNOV2L.js

@@ -1,338 +0,0 @@
-import {
-  getPlotConfig,
-  setComputedConfig
-} from "./chunk-6ECKCC4X.js";
-import "./chunk-HTZJQNHP.js";
-import "./chunk-C2MCQZWH.js";
-import {
-  getSorterUi
-} from "./chunk-PFRPC2SY.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-K7HFOAR7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-FSWBNSQD.js";
-import "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-GP4VLNMZ.js";
-import "./chunk-6AFMWQXZ.js";
-import "./chunk-CME6DYDH.js";
-import "./chunk-57Z4VYLM.js";
-import {
-  copyMerge
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/matrix/test/matrix.sorterUi.unit.spec.js
-var import_tape = __toESM(require_tape(), 1);
-var i = 0;
-async function getControls(_opts = {}) {
-  const holder = select_default("body").append("div").attr("class", "sja_root_holder").append("table").append("tr");
-  const parent = {
-    id: `_${i++}_${Math.random()}`,
-    app: {
-      dispatch: _opts.dispatch || ((action) => {
-        copyMerge(config, action.config);
-        setComputedConfig(config);
-        uiApi.main();
-      }),
-      vocabApi: {
-        termdbConfig: {}
-      }
-    },
-    dom: {
-      holder
-    }
-  };
-  const config = await getPlotConfig(_opts, parent.app);
-  setComputedConfig(config);
-  parent.config = config;
-  const controls = { parent };
-  const opts = { controls, holder, debug: true, setComputedConfig };
-  const uiApi = getSorterUi(opts);
-  return { uiApi, controls, config, parent: controls.parent, opts };
-}
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- plots/matrix.sorterUi -***-");
-  test.end();
-});
-(0, import_tape.default)("default setup", async (test) => {
-  const { uiApi, controls, config, parent, opts } = await getControls();
-  const s = parent.config.settings.matrix;
-  const activeOption = s.sortOptions[s.sortSamplesBy];
-  test.equal(
-    opts.holder.node().querySelectorAll("thead").length,
-    // 2 theads, 1 for hardcoded manual selected rows + 1 for sort by case names
-    // 1 thead for main table heading
-    activeOption.sortPriority.length + 2 + 1,
-    "should have the expected number of thead"
-  );
-  if (test._ok) uiApi.destroy();
-  test.end();
-});
-(0, import_tape.default)("section visibility toggling", async (test) => {
-  const { uiApi, controls, config, parent, opts } = await getControls();
-  const s = config.settings.matrix;
-  const ui = uiApi.Inner;
-  const activeOptionBeforeDrag = structuredClone(ui.activeOption);
-  const thead = opts.holder.selectAll("thead").filter((d) => d?.types?.includes("geneVariant")).node();
-  test.equal(
-    thead.nextSibling.style.display,
-    "none",
-    "should have a hiddden table section for gene mutation before toggling"
-  );
-  thead.firstChild.firstChild.click();
-  test.equal(
-    opts.holder.selectAll("thead").filter((d) => d?.types?.includes("geneVariant")).node().nextSibling.style.display,
-    "",
-    "should have a visible table section for gene mutation after toggling"
-  );
-  if (test._ok) uiApi.destroy();
-  test.end();
-});
-(0, import_tape.default)("simulated section drag/drop", async (test) => {
-  const { uiApi, controls, config, parent, opts } = await getControls();
-  const s = config.settings.matrix;
-  const prevSettings = structuredClone(s);
-  const ui = uiApi.Inner;
-  const activeOptionBeforeDrag = structuredClone(ui.activeOption);
-  const th = opts.holder.selectAll("th").filter((d) => d?.types?.includes("geneVariant")).node();
-  const sectionData = th.__data__;
-  ui.trackDraggedSection.call(th, {}, sectionData);
-  test.equal(
-    select_default(th.parentNode.parentNode).on("drop"),
-    ui.adjustSortPriority,
-    "should attach the correct drop handler for section thead"
-  );
-  const i2 = ui.activeOption.sortPriority.indexOf(sectionData);
-  ui.adjustSortPriority({}, ui.activeOption.sortPriority[i2 + 1]);
-  test.deepEqual(
-    activeOptionBeforeDrag.sortPriority,
-    prevSettings.sortOptions[s.sortSamplesBy].sortPriority,
-    "should not adjust the sortPriority/table before clicking apply, after drag/drop"
-  );
-  ui.apply();
-  test.deepEqual(
-    activeOptionBeforeDrag.sortPriority.reverse(),
-    config.settings.matrix.sortOptions[s.sortSamplesBy].sortPriority,
-    "should adjust the sortPriority/table after clicking apply"
-  );
-  if (test._ok) uiApi.destroy();
-  test.end();
-});
-(0, import_tape.default)("simulated tiebreaker drag/drop", async (test) => {
-  const { uiApi, controls, config, parent, opts } = await getControls();
-  const s = config.settings.matrix;
-  const prevSettings = structuredClone(s);
-  const ui = uiApi.Inner;
-  const activeOptionBeforeDrag = structuredClone(ui.activeOption);
-  const thead0 = opts.holder.selectAll("thead").filter((d) => d?.types?.includes("geneVariant")).node();
-  thead0.firstChild.firstChild.click();
-  const thead1 = opts.holder.selectAll("thead").filter((d) => d?.types?.includes("geneVariant")).node();
-  const trs = thead1.nextSibling.querySelectorAll("tr");
-  test.equal(
-    select_default(trs[0]).on("drop"),
-    ui.adjustTieBreakers,
-    "should attach the correct drop handler for tiebreaker label"
-  );
-  const tbData = trs[0].__data__;
-  ui.trackDraggedTieBreaker.call(trs[0], { target: trs[0].firstChild.nextSibling }, tbData);
-  const activeTieBreakers = ui.activeOption.sortPriority[0].tiebreakers;
-  const i2 = activeTieBreakers.indexOf(tbData);
-  ui.adjustTieBreakers({ preventDefault: () => void 0 }, activeTieBreakers[i2 + 1]);
-  const thead2 = opts.holder.selectAll("thead").filter((d) => d?.types?.includes("geneVariant")).node();
-  const trs2 = [...thead2.nextSibling.querySelectorAll("tr")];
-  test.deepEqual(
-    trs2.slice(0, 2).map((elem) => elem.__data__),
-    activeOptionBeforeDrag.sortPriority[0].tiebreakers.slice(1, 3).reverse(),
-    "should visibly switch the first two tiebreaker rows"
-  );
-  test.deepEqual(
-    activeOptionBeforeDrag.sortPriority[0].tiebreakers,
-    prevSettings.sortOptions[s.sortSamplesBy].sortPriority[0].tiebreakers,
-    "should not adjust the tiebreakers before clicking apply, after drag/drop"
-  );
-  ui.apply();
-  test.deepEqual(
-    activeTieBreakers,
-    config.settings.matrix.sortOptions[s.sortSamplesBy].sortPriority[0].tiebreakers,
-    "should adjust the tiebreakers after clicking apply"
-  );
-  if (test._ok) uiApi.destroy();
-  test.end();
-});
-(0, import_tape.default)("tiebreaker disabled", async (test) => {
-  const { uiApi, controls, config, parent, opts } = await getControls();
-  const s = config.settings.matrix;
-  const ui = uiApi.Inner;
-  const activeOptionBeforeDrag = structuredClone(ui.activeOption);
-  const thead0 = opts.holder.selectAll("thead").filter((d) => d?.types?.includes("geneVariant")).node();
-  thead0.firstChild.firstChild.click();
-  const thead1 = opts.holder.selectAll("thead").filter((d) => d?.types?.includes("geneVariant")).node();
-  const trs = thead1.nextSibling.querySelectorAll("tr");
-  test.equal(
-    select_default(trs[0].lastChild).select("button").node(),
-    null,
-    `should not have an enable/disable toggle button for the protein-changing tiebreaker that is not configured with 'mayToggle: true'`
-  );
-  test.equal(
-    select_default(trs[1].lastChild).select("button").html(),
-    "Enable",
-    "should indicate that the CNV tiebreaker is not active"
-  );
-  select_default(trs[1].lastChild).select("button").node().click();
-  const activeTieBreakers = ui.activeOption.sortPriority[0].tiebreakers;
-  ui.apply();
-  test.deepEqual(
-    activeTieBreakers[1].disabled,
-    config.settings.matrix.sortOptions[s.sortSamplesBy].sortPriority[0].tiebreakers[1]?.disabled,
-    "should adjust the CNV tiebreaker disabled after clicking apply"
-  );
-  if (test._ok) uiApi.destroy();
-  test.end();
-});
-(0, import_tape.default)("simulated value drag/drop", async (test) => {
-  const { uiApi, controls, config, parent, opts } = await getControls();
-  const ui = uiApi.Inner;
-  const a = structuredClone(config.settings.matrix.sortOptions.a);
-  ui.expandedSection = a.sortPriority[0].label;
-  a.sortPriority[0].tiebreakers[1].isOrdered = true;
-  uiApi.main({
-    sortOptions: { a }
-  });
-  const activeOptionBeforeDrag = structuredClone(ui.activeOption);
-  const thead1 = opts.holder.selectAll("thead").filter((d) => d?.types?.includes("geneVariant")).node();
-  const valuesDiv = thead1.nextSibling.querySelectorAll("tr")[0].querySelector(".sjpp-matrix-sorter-ui-value");
-  const lastVal = select_default(valuesDiv.lastChild);
-  test.equal(lastVal.on("drop"), ui.adjustValueOrder, "should attach the correct drop handler for value label");
-  const activeOrder = ui.activeOption.sortPriority[0].tiebreakers[1].order;
-  const activeOrderBeforeDrag = structuredClone(activeOrder);
-  const value = lastVal.datum();
-  ui.trackDraggedValue.call(lastVal.node(), { target: lastVal.node() }, value);
-  ui.adjustValueOrder({ preventDefault: () => void 0 }, valuesDiv.firstChild.__data__);
-  const thead2 = opts.holder.selectAll("thead").filter((d) => d?.types?.includes("geneVariant")).node();
-  const valuesDiv2 = thead2.nextSibling.querySelectorAll("tr")[0].querySelector(".sjpp-matrix-sorter-ui-value");
-  const lastVal2 = select_default(valuesDiv2.lastChild);
-  const n = activeOrderBeforeDrag.length;
-  test.deepEqual(
-    [valuesDiv2.firstChild.__data__?.key, valuesDiv2.lastChild.__data__?.key],
-    [activeOrderBeforeDrag[n - 1], activeOrderBeforeDrag[n - 2]],
-    "should visibly switch the last value to first"
-  );
-  const s = config.settings.matrix;
-  test.deepEqual(
-    activeOrderBeforeDrag,
-    s.sortOptions[s.sortSamplesBy].sortPriority[0].tiebreakers[1].order,
-    "should not adjust the tiebreaker.order before clicking apply, after drag/drop"
-  );
-  ui.apply();
-  test.deepEqual(
-    activeOrder,
-    s.sortOptions[s.sortSamplesBy].sortPriority[0].tiebreakers[1].order,
-    "should adjust the tiebreaker.order after clicking apply"
-  );
-  if (test._ok) uiApi.destroy();
-  test.end();
-});
-(0, import_tape.default)("hidden values", async (test) => {
-  const filterByClass = {
-    // CNV_amp: 'value',
-    // CNV_loss: 'value',
-    // Utr3: 'value',
-    // Utr5: 'value',
-    // S: 'value',
-    // Intron: 'value',
-    noncoding: "value"
-  };
-  const legendValueFilter = Object.freeze({
-    isAtomic: true,
-    type: "tvslst",
-    in: true,
-    join: "and",
-    lst: [
-      {
-        legendGrpName: "test",
-        type: "tvs",
-        tvs: {
-          isnot: true,
-          legendFilterType: "geneVariant_soft",
-          // indicates this matrix legend filter is soft filter
-          term: { type: "geneVariant" },
-          values: [{ dt: 1, mclasslst: Object.keys(filterByClass) }]
-        }
-      }
-    ]
-  });
-  const { uiApi, controls, config, parent, opts } = await getControls({
-    legendValueFilter: structuredClone(legendValueFilter)
-  });
-  const s = config.settings.matrix;
-  const ui = uiApi.Inner;
-  const tipNode = ui.dom.tip.d.node();
-  const a = config.settings.matrix.sortOptions.a;
-  ui.expandedSection = a.sortPriority[0].label;
-  a.sortPriority[0].tiebreakers[1].isOrdered = true;
-  a.sortPriority[0].tiebreakers[1].notUsed = ["S"];
-  uiApi.main({
-    sortOptions: { a }
-  });
-  const origConfig = structuredClone(config);
-  const thead1 = opts.holder.selectAll("thead").filter((d) => d?.types?.includes("geneVariant")).node();
-  const tr1 = thead1.nextSibling.querySelectorAll("tr")[0];
-  const valuesDiv = tr1.querySelector(".sjpp-matrix-sorter-ui-value");
-  const m = valuesDiv.querySelectorAll(":scope>div").length;
-  const hiddenBtn = tr1.querySelector("[data-testid=sjpp-matrix-sorter-ui-hidden-add]");
-  hiddenBtn.click();
-  const unusedVals = tipNode.querySelector("[data-testid=sjpp-matrix-sorter-ui-hidden-vals]");
-  const n = 1;
-  test.equal(
-    unusedVals.querySelectorAll(":scope>div").length,
-    1,
-    `should have the expected number of addable hidden values on load`
-  );
-  valuesDiv.firstChild.click();
-  const tr1_a = opts.holder.selectAll("thead").filter((d) => d?.types?.includes("geneVariant")).node().nextSibling.querySelectorAll("tr")[0];
-  const valuesDiv_a = tr1_a.querySelector(".sjpp-matrix-sorter-ui-value");
-  const hiddenBtn_a = tr1_a.querySelector("[data-testid=sjpp-matrix-sorter-ui-hidden-add]");
-  hiddenBtn_a.click();
-  const unusedVals_a = tipNode.querySelector("[data-testid=sjpp-matrix-sorter-ui-hidden-vals]");
-  test.deepEqual(
-    [valuesDiv_a.querySelectorAll(":scope>div").length, unusedVals_a.querySelectorAll(":scope>div").length],
-    [m - 1, n + 1],
-    `should increase the expected number of used and unused values by 1, after clicking on a visible sorter value`
-  );
-  test.deepEqual(origConfig, config, "should not adjust the tiebreaker.order + notUsed arrays before clicking apply");
-  ui.apply();
-  const s0 = origConfig.settings.matrix;
-  const tb = s0.sortOptions.a.sortPriority[0].tiebreakers[1];
-  if (!tb.notUsed) tb.notUsed = [];
-  tb.notUsed.unshift(tb.order.shift());
-  test.deepEqual(
-    config.settings.matrix.sortOptions.a,
-    origConfig.settings.matrix.sortOptions.a,
-    "should adjust the tiebreaker.order + notUsed after clicking apply"
-  );
-  if (test._ok) uiApi.destroy();
-  test.end();
-});
-//# sourceMappingURL=matrix.sorterUi.unit.spec-4ZKNOV2L.js.map

package/dist/matrix.unit.spec-V5XNLECG.js

@@ -1,150 +0,0 @@
-import {
-  Matrix
-} from "./chunk-VP2JWT5W.js";
-import "./chunk-IWVCFZHQ.js";
-import "./chunk-42VFF74T.js";
-import "./chunk-55T2AMJ3.js";
-import "./chunk-6ECKCC4X.js";
-import "./chunk-HTZJQNHP.js";
-import "./chunk-TGKWEAUE.js";
-import "./chunk-RHOMR2GY.js";
-import "./chunk-DQD4MTK4.js";
-import "./chunk-C2MCQZWH.js";
-import "./chunk-DDKS3MV3.js";
-import "./chunk-PFRPC2SY.js";
-import "./chunk-7ISAV37C.js";
-import "./chunk-MRPYHLFW.js";
-import "./chunk-SPFK5XZH.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-V2OJLJSK.js";
-import "./chunk-K7HFOAR7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-FSWBNSQD.js";
-import "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-GP4VLNMZ.js";
-import "./chunk-6AFMWQXZ.js";
-import "./chunk-CME6DYDH.js";
-import "./chunk-57Z4VYLM.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/matrix/test/matrix.unit.spec.js
-var import_tape = __toESM(require_tape(), 1);
-var filter0A = { op: "in", content: { field: "cases.project.project_id", value: "TCGA-PAAD" } };
-var filter0B = { op: "in", content: { field: "cases.project.project_id", value: "TCGA-LAML" } };
-var i = 0;
-function getMatrix() {
-  const id = `_${i++}`;
-  const holder = select_default("body").append("div").attr("class", "sja_root_holder");
-  return {
-    id,
-    app: {
-      vocabApi: {
-        hasVerifiedToken: () => true,
-        tokenVerificationMessage: void 0
-      }
-    },
-    // as assigned in main(), where settings.matrix is filled-in from config.settings
-    settings: { matrix: { showHints: ["genesetEdit"] } },
-    dom: {
-      cohortMsgDiv: holder.append("div").style("display", "none")
-    },
-    controlsRenderer: { btns: select_default(null) },
-    getState: Matrix.prototype.getState,
-    mayDisplayCohortMessage: Matrix.prototype.mayDisplayCohortMessage
-  };
-}
-function getAppState(filter0) {
-  return {
-    plots: [],
-    termfilter: {
-      filter: { type: "tvslst", join: "", in: 1, lst: [] },
-      filter0
-    },
-    termdbConfig: {},
-    vocab: {},
-    nav: {},
-    groups: []
-  };
-}
-function update(matrix, filter0) {
-  const appState = getAppState(filter0);
-  appState.plots.push({ id: matrix.id, settings: { matrix: {} } });
-  matrix.state = matrix.getState(appState);
-  matrix.mayDisplayCohortMessage();
-}
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- plots/matrix -***-");
-  test.end();
-});
-(0, import_tape.default)("cohort message on filter0 change", function(test) {
-  const matrix = getMatrix();
-  update(matrix, filter0A);
-  test.equal(
-    matrix.dom.cohortMsgDiv.style("display"),
-    "none",
-    "should not display the cohort message on the initial render with a filter0"
-  );
-  update(matrix, filter0A);
-  test.equal(
-    matrix.dom.cohortMsgDiv.style("display"),
-    "none",
-    "should not display the cohort message when filter0 does not change"
-  );
-  update(matrix, filter0B);
-  test.notEqual(
-    matrix.dom.cohortMsgDiv.style("display"),
-    "none",
-    "should display the cohort message when filter0 changes"
-  );
-  test.true(
-    matrix.dom.cohortMsgDiv.text().includes("The gene list is persisted across cohorts."),
-    "should display the expected cohort message text"
-  );
-  update(matrix, filter0B);
-  test.equal(
-    matrix.dom.cohortMsgDiv.style("display"),
-    "none",
-    "should hide the cohort message on the next update after a cohort change"
-  );
-  test.end();
-});
-(0, import_tape.default)("no cohort message without filter0", function(test) {
-  const matrix = getMatrix();
-  update(matrix, void 0);
-  test.equal(
-    matrix.dom.cohortMsgDiv.style("display"),
-    "none",
-    "should not display the cohort message on the initial render without a filter0"
-  );
-  update(matrix, void 0);
-  test.equal(
-    matrix.dom.cohortMsgDiv.style("display"),
-    "none",
-    "should not display the cohort message on a subsequent render without a filter0"
-  );
-  test.end();
-});
-//# sourceMappingURL=matrix.unit.spec-V5XNLECG.js.map