@sjcrh/proteinpaint-client 2.193.0 → 2.195.0

package/dist/hierCluster.integration.spec-OL4FLSBS.js

@@ -0,0 +1,488 @@
+import {
+  appInit
+} from "./chunk-5B5FZPZI.js";
+import "./chunk-YRXB3MKU.js";
+import "./chunk-SKMFMGCD.js";
+import {
+  detectOne,
+  sleep
+} from "./chunk-DJQTUDJM.js";
+import "./chunk-MAACMLMN.js";
+import {
+  require_tape
+} from "./chunk-TUMA63WX.js";
+import "./chunk-4KY4XKJV.js";
+import "./chunk-XNYATA6C.js";
+import "./chunk-3DS4HIEH.js";
+import "./chunk-O64WQLAV.js";
+import "./chunk-OEOYTMMY.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-HVZQYGQN.js";
+import "./chunk-MKAF2BHB.js";
+import "./chunk-WKNI3HRQ.js";
+import "./chunk-5DSLFEAN.js";
+import "./chunk-D3TU3RDU.js";
+import {
+  fillTermWrapper
+} from "./chunk-LYULXXGR.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-CPMOBFFR.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-B4VBTVVQ.js";
+import "./chunk-IQTEW3SK.js";
+import "./chunk-MNPTPENH.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import {
+  TermTypes
+} from "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/test/hierCluster.integration.spec.js
+var import_tape = __toESM(require_tape(), 1);
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- plots/hierCluster.js -***-");
+  test.end();
+});
+(0, import_tape.default)("basic render", async (test) => {
+  test.timeoutAfter(4e3);
+  const { app, hc } = await getHierClusterApp({ terms: getGenes() });
+  test.equal(hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(), 4, "should render 4 gene rows");
+  test.equal(hc.dom.sampleLabelG.selectAll(".sjpp-matrix-label").size(), 60, "should render 60 sample columns");
+  if (test._ok) app.destroy();
+  test.end();
+});
+(0, import_tape.default)("filter", async (test) => {
+  test.timeoutAfter(4e3);
+  const { app, hc } = await getHierClusterApp({
+    terms: getGenes(),
+    filter: {
+      type: "tvslst",
+      join: "",
+      in: true,
+      lst: [{ type: "tvs", tvs: { term: { id: "diaggrp" }, values: [{ key: "Acute lymphoblastic leukemia" }] } }]
+    }
+  });
+  test.equal(hc.dom.sampleLabelG.selectAll(".sjpp-matrix-label").size(), 36, "should render 36 sample columns");
+  if (test._ok) app.destroy();
+  test.end();
+});
+(0, import_tape.default)("avoid race condition - specified gene list", async (test) => {
+  test.timeoutAfter(4e3);
+  test.plan(4);
+  const { app, hc } = await getHierClusterApp({ terms: getGenes() });
+  const termgroups = structuredClone(hc.config.termgroups);
+  const lst = await Promise.all([
+    fillTermWrapper({ term: { gene: "KRAS", name: "KRAS", type: "geneExpression" } }, app.vocabApi),
+    fillTermWrapper({ term: { gene: "AKT1", name: "AKT1", type: "geneExpression" } }, app.vocabApi),
+    fillTermWrapper({ term: { gene: "TP53", name: "TP53", type: "geneExpression" } }, app.vocabApi),
+    fillTermWrapper({ term: { gene: "BCR", name: "BCR", type: "geneExpression" } }, app.vocabApi)
+  ]);
+  termgroups[0].lst = lst;
+  const responseDelay = 250;
+  hc.origRequestData = hc.requestData;
+  hc.requestData = async () => {
+    const lst2 = hc.config.termgroups[0].lst;
+    const data = await hc.origRequestData({});
+    if (lst2.length === 3) return data;
+    await sleep(250);
+    return data;
+  };
+  const prom = {};
+  const postRenderTest = new Promise((resolve) => {
+    prom.resolve = resolve;
+  });
+  app.on("postRender.test1", () => {
+    app.on("postRender.test1", null);
+    prom.resolve();
+  });
+  await Promise.all([
+    app.dispatch({
+      type: "plot_edit",
+      id: hc.id,
+      config: { termgroups }
+    }),
+    (async () => {
+      await sleep(0);
+      const termgroups2 = structuredClone(hc.config.termgroups);
+      termgroups2[0].lst = lst.slice(0, 3);
+      await app.dispatch({
+        type: "plot_edit",
+        id: hc.id,
+        config: { termgroups: termgroups2 }
+      });
+    })()
+  ]);
+  await postRenderTest;
+  await sleep(responseDelay + 500);
+  test.equal(hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(), 3, "should render 3 gene rows");
+  const rects = hc.dom.seriesesG.selectAll(".sjpp-mass-series-g rect");
+  const hits = rects.filter((d) => d.key !== "BCR" && d.value.class != "WT" && d.value.class != "Blank");
+  test.equal(
+    rects.size(),
+    180,
+    "should have the expected total number of matrix cell rects, inlcuding WT and not tested"
+  );
+  test.equal(hits.size(), 180, "should have the expected number of matrix cell rects with hits");
+  test.equal(
+    app.Inner.dom.holder.selectAll(".sja_errorbar").filter(function() {
+      return this.style.display != "none";
+    }).size(),
+    0,
+    "should not display errors"
+  );
+  if (test._ok) app.destroy();
+});
+(0, import_tape.default)("avoid race condition - reused fetch response cache", async (test) => {
+  test.timeoutAfter(4e3);
+  test.plan(4);
+  const { app, hc } = await getHierClusterApp({ terms: getGenes() });
+  const termgroups = structuredClone(hc.config.termgroups);
+  const responseDelay = 250;
+  hc.origRequestData = hc.requestData;
+  hc.requestData = async () => {
+    const lst = hc.config.termgroups[0].lst;
+    const data = await hc.origRequestData({});
+    if (lst.length === 3) return data;
+    return data;
+    await sleep(responseDelay);
+    return data;
+  };
+  const prom = {};
+  const postRenderTest = new Promise((resolve) => {
+    prom.resolve = resolve;
+  });
+  app.on("postRender.test1", () => {
+    app.on("postRender.test1", null);
+    prom.resolve();
+  });
+  await Promise.all([
+    app.dispatch({
+      type: "plot_edit",
+      id: hc.id,
+      config: { termgroups }
+    }),
+    (async () => {
+      await sleep(0);
+      const _termgroups = structuredClone(termgroups);
+      _termgroups[0].lst = _termgroups[0].lst.slice(0, 3);
+      await app.dispatch({
+        type: "plot_edit",
+        id: hc.id,
+        config: { termgroups: _termgroups }
+      });
+    })()
+  ]);
+  await postRenderTest;
+  await sleep(responseDelay + 500);
+  test.equal(hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(), 3, "should render 3 gene rows");
+  const rects = hc.dom.seriesesG.selectAll(".sjpp-mass-series-g rect");
+  const hits = rects.filter((d) => d.key !== "BCR" && d.value.class != "WT" && d.value.class != "Blank");
+  test.equal(
+    rects.size(),
+    180,
+    "should have the expected total number of matrix cell rects, inlcuding WT and not tested"
+  );
+  test.equal(hits.size(), 180, "should have the expected number of matrix cell rects with hits");
+  test.equal(
+    app.Inner.dom.holder.selectAll(".sja_errorbar").filter(function() {
+      return this.style.display != "none";
+    }).size(),
+    0,
+    "should not display errors"
+  );
+  if (test._ok) app.destroy();
+});
+(0, import_tape.default)("dendrogram click", async function(test) {
+  test.timeoutAfter(5e3);
+  test.plan(3);
+  let numRenders = 0;
+  const { app, hc } = await getHierClusterApp({ terms: getGenes() });
+  const img = await detectOne({ elem: hc.dom.topDendrogram.node(), selector: "image" });
+  const svgBox = hc.dom.svg.node().getBoundingClientRect();
+  const imgBox = img.getBBox();
+  img.dispatchEvent(
+    new MouseEvent("click", {
+      //'view': window,
+      bubbles: true,
+      cancelable: true,
+      clientX: svgBox.x + hc.dimensions.xOffset + imgBox.x + imgBox.width / 2,
+      clientY: svgBox.y + imgBox.y + imgBox.height / 2
+    })
+  );
+  test.deepEqual(
+    hc.clickedClusterIds,
+    [
+      46,
+      54,
+      37,
+      28,
+      27,
+      51,
+      53,
+      44,
+      49,
+      25,
+      34,
+      11,
+      20,
+      41,
+      45,
+      29,
+      33,
+      17,
+      15,
+      2,
+      38,
+      42,
+      30,
+      36,
+      22,
+      9,
+      14,
+      3,
+      4,
+      31,
+      13,
+      26,
+      1,
+      16,
+      8,
+      10,
+      5,
+      6,
+      7,
+      23,
+      47,
+      48,
+      35,
+      43,
+      21,
+      32,
+      18,
+      24,
+      56
+    ],
+    `should give the expected clickedClusterIds`
+  );
+  test.deepEqual(
+    ["Zoom in", "List 50 samples"],
+    [...hc.dom.dendroClickMenu.d.node().querySelectorAll(".sja_menuoption")].map((elem) => elem.__data__.label),
+    "should show the expected menu options on dendrogram click"
+  );
+  hc.dom.dendroClickMenu.d.node().querySelector(".sja_menuoption").parentNode.lastChild.click();
+  await sleep(5);
+  test.equal(
+    hc.dom.dendroClickMenu.d.node().querySelectorAll(".sjpp_row_wrapper").length,
+    50,
+    "should list the expected number of samples"
+  );
+  if (test._ok) {
+    hc.dom.dendroClickMenu.clear().hide();
+    app.destroy();
+  }
+});
+(0, import_tape.default)("numeric dictionary terms (float)", async function(test) {
+  const terms = [
+    {
+      id: "aaclassic_5",
+      // tw.id must be provided
+      term: { id: "aaclassic_5", name: "a1", type: "float" },
+      // requires {id,name,type}; term.name doesn't need to be real, unique name works
+      q: { mode: "continuous" }
+      // set to continuous to avoid validating tw.term.bins
+    },
+    { id: "hrtavg", term: { id: "hrtavg", name: "a2", type: "float" }, q: { mode: "continuous" } },
+    { id: "agedx", term: { id: "agedx", name: "a3", type: "float" }, q: { mode: "continuous" } }
+  ];
+  const { app, hc } = await getHierClusterApp({ terms, dataType: "float", termGroupName: "Numeric Dictionary Terms" });
+  test.equal(hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(), 3, "should render 3 rows");
+  if (test._ok) app.destroy();
+  test.end();
+});
+(0, import_tape.default)("isoform expression cluster", async function(test) {
+  test.timeoutAfter(4e3);
+  const terms = [
+    {
+      term: { isoform: "ENST00000370314", name: "ENST00000370314", type: "isoformExpression" }
+    },
+    {
+      term: { isoform: "ENST00000361510", name: "ENST00000361510", type: "isoformExpression" }
+    },
+    {
+      term: { isoform: "ENST00000229281", name: "ENST00000229281", type: "isoformExpression" }
+    }
+  ];
+  const { app, hc } = await getHierClusterApp({
+    terms,
+    dataType: "isoformExpression",
+    termGroupName: "Isoform Expression"
+  });
+  test.equal(hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(), 3, "should render 3 isoform rows");
+  if (test._ok) app.destroy();
+  test.end();
+});
+(0, import_tape.default)("ssGSEA cluster", async function(test) {
+  test.timeoutAfter(4e3);
+  const terms = [
+    { term: { id: "HALLMARK_ADIPOGENESIS", name: "HALLMARK_ADIPOGENESIS", type: "ssGSEA" } },
+    {
+      term: { id: "HALLMARK_ALLOGRAFT_REJECTION", name: "HALLMARK_ALLOGRAFT_REJECTION", type: "ssGSEA" }
+    },
+    {
+      term: { id: "HALLMARK_ANDROGEN_RESPONSE", name: "HALLMARK_ANDROGEN_RESPONSE", type: "ssGSEA" }
+    }
+  ];
+  const { app, hc } = await getHierClusterApp({
+    terms,
+    dataType: "ssGSEA",
+    termGroupName: "Gene Set Enrichment (ssGSEA)"
+  });
+  test.equal(hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(), 3, "should render 3 ssGSEA rows");
+  if (test._ok) app.destroy();
+  test.end();
+});
+(0, import_tape.default)("dnaMethylation cluster", async function(test) {
+  test.timeoutAfter(4e3);
+  const terms = [
+    {
+      term: { type: "dnaMethylation", chr: "chr17", start: 7673484, stop: 7681953, genomicFeatureType: "gene" }
+    },
+    {
+      term: { type: "dnaMethylation", chr: "chr17", start: 7663195, stop: 7671664, genomicFeatureType: "gene" }
+    },
+    {
+      term: { type: "dnaMethylation", chr: "chr17", start: 7673484, stop: 7681953, genomicFeatureType: "promoter" }
+    }
+  ];
+  const { app, hc } = await getHierClusterApp({ terms, dataType: "dnaMethylation", termGroupName: "DNA Methylation" });
+  test.equal(hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(), 3, "should render 3 methylation rows");
+  if (test._ok) app.destroy();
+  test.end();
+});
+(0, import_tape.default)("cluster rejects a non-continuous term mode", async function(test) {
+  test.timeoutAfter(4e3);
+  const terms = [
+    { term: { gene: "AKT1", name: "AKT1", type: "geneExpression" }, q: { mode: "discrete" } },
+    { term: { gene: "TP53", name: "TP53", type: "geneExpression" }, q: { mode: "continuous" } },
+    { term: { gene: "BCR", name: "BCR", type: "geneExpression" }, q: { mode: "continuous" } }
+  ];
+  const { app, hc } = await getHierClusterApp({ terms, dataType: "geneExpression" });
+  test.equal(
+    hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(),
+    0,
+    "should render no rows when a term is not in continuous mode"
+  );
+  if (test._ok) app.destroy();
+  test.end();
+});
+(0, import_tape.default)("cluster rejects incompatible numeric types", async function(test) {
+  test.timeoutAfter(4e3);
+  const terms = [
+    { term: { gene: "AKT1", name: "AKT1", type: "geneExpression" }, q: { mode: "continuous" } },
+    { term: { gene: "TP53", name: "TP53", type: "geneExpression" }, q: { mode: "continuous" } },
+    { term: { id: "agedx", name: "agedx", type: "float" }, q: { mode: "continuous" } }
+  ];
+  let rejected = false;
+  try {
+    const { app, hc } = await getHierClusterApp({ terms, dataType: "geneExpression" });
+    rejected = hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size() === 0;
+    if (app) app.destroy();
+  } catch (e) {
+    rejected = true;
+  }
+  test.ok(rejected, "should reject a cluster mixing geneExpression and float terms");
+  test.end();
+});
+async function getHierClusterApp(_opts = {}) {
+  const holder = select_default("body").append("div");
+  const defaults = {
+    debug: true,
+    holder,
+    genome: "hg38-test",
+    state: {
+      genome: "hg38-test",
+      dslabel: "TermdbTest",
+      termfilter: { filter0: _opts.filter0 },
+      plots: [
+        {
+          chartType: "hierCluster",
+          dataType: _opts.dataType || TermTypes.GENE_EXPRESSION,
+          settings: {
+            hierCluster: {
+              termGroupName: _opts.termGroupName || "Gene Expression (CGC genes only)"
+            },
+            matrix: {
+              // the matrix autocomputes the colw based on available screen width,
+              // need to set an exact screen width for consistent tests using getBBox()
+              availContentWidth: 1200
+            }
+          },
+          // force empty termgroups, genes since the instance requestData() will not have expression data,
+          // and will cause a non-trival error if using the actual requestData(), which will be mocked below
+          termgroups: [],
+          // _opts.termgroups || [],
+          // !!! there will be an initial load error since this is an empty geneset,
+          // !!! but will be ignored since it's not relevant to this test
+          terms: _opts.terms || [],
+          filter: _opts.filter
+        }
+      ]
+    },
+    app: {
+      features: ["recover"],
+      callbacks: _opts?.app?.callbacks || {}
+    },
+    recover: {
+      undoHtml: "Undo",
+      redoHtml: "Redo",
+      resetHtml: "Restore",
+      adjustTrackedState(state) {
+        const s = structuredClone(state);
+        delete s.termfilter.filter0;
+        return s;
+      }
+    },
+    hierCluster: _opts?.hierCluster || {}
+  };
+  const opts = Object.assign(defaults, _opts);
+  const app = await appInit(opts);
+  holder.select(".sja_errorbar").node()?.lastChild?.click?.();
+  const hc = Object.values(app.Inner.components.plots).find(
+    (p) => p.type == "hierCluster" || p.chartType == "hierCluster"
+  ).Inner;
+  return { app, hc };
+}
+function getGenes() {
+  return [
+    { gene: "AKT1", type: "geneExpression" },
+    { gene: "TP53", type: "geneExpression" },
+    { gene: "BCR", type: "geneExpression" },
+    { gene: "KRAS", type: "geneExpression" }
+  ];
+}
+//# sourceMappingURL=hierCluster.integration.spec-OL4FLSBS.js.map

package/dist/hierCluster.integration.spec-OL4FLSBS.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/test/hierCluster.integration.spec.js"],
+  "sourcesContent": ["import tape from 'tape'\nimport * as helpers from '#test/front.helpers.js'\nimport { sleep, detectOne, detectGte, detectLst, detectAttr } from '#test/test.helpers.js'\nimport { select } from 'd3-selection'\nimport { appInit } from '#plots/plot.app.js'\nimport { fillTermWrapper } from '#termsetting'\nimport { TermTypes } from '#shared/terms.js'\n/**************\n test sections\n\nbasic render\nfilter\navoid race condition\ndendrogram click\n\n***************/\n\ntape('\\n', function (test) {\n\ttest.comment('-***- plots/hierCluster.js -***-')\n\ttest.end()\n})\n\ntape('basic render', async test => {\n\ttest.timeoutAfter(4000)\n\tconst { app, hc } = await getHierClusterApp({ terms: getGenes() })\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 4, 'should render 4 gene rows')\n\ttest.equal(hc.dom.sampleLabelG.selectAll('.sjpp-matrix-label').size(), 60, 'should render 60 sample columns') // update \"60\" when data changes\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('filter', async test => {\n\ttest.timeoutAfter(4000)\n\tconst { app, hc } = await getHierClusterApp({\n\t\tterms: getGenes(),\n\t\tfilter: {\n\t\t\ttype: 'tvslst',\n\t\t\tjoin: '',\n\t\t\tin: true,\n\t\t\tlst: [{ type: 'tvs', tvs: { term: { id: 'diaggrp' }, values: [{ key: 'Acute lymphoblastic leukemia' }] } }]\n\t\t}\n\t})\n\ttest.equal(hc.dom.sampleLabelG.selectAll('.sjpp-matrix-label').size(), 36, 'should render 36 sample columns') // update \"36\" when data changes\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('avoid race condition - specified gene list', async test => {\n\t// !!!\n\t// to allow an app or chart code to fail due to race condition,\n\t// hardcode a constant value or comment out the ++ for the sequenceID\n\t// in rx/src/StoreApi.write()\n\t// !!!\n\ttest.timeoutAfter(4000)\n\ttest.plan(4)\n\tconst { app, hc } = await getHierClusterApp({ terms: getGenes() })\n\tconst termgroups = structuredClone(hc.config.termgroups)\n\tconst lst = await Promise.all([\n\t\tfillTermWrapper({ term: { gene: 'KRAS', name: 'KRAS', type: 'geneExpression' } }, app.vocabApi),\n\t\tfillTermWrapper({ term: { gene: 'AKT1', name: 'AKT1', type: 'geneExpression' } }, app.vocabApi),\n\t\tfillTermWrapper({ term: { gene: 'TP53', name: 'TP53', type: 'geneExpression' } }, app.vocabApi),\n\t\tfillTermWrapper({ term: { gene: 'BCR', name: 'BCR', type: 'geneExpression' } }, app.vocabApi)\n\t])\n\ttermgroups[0].lst = lst\n\tconst responseDelay = 250\n\thc.origRequestData = hc.requestData\n\thc.requestData = async () => {\n\t\tconst lst = hc.config.termgroups[0].lst\n\t\tconst data = await hc.origRequestData({})\n\t\tif (lst.length === 3) return data\n\t\t// artificially delay response to first request, to simulate a race condition\n\t\t// do this after the network request, so that this.api.getAbortSignal() in hc.requestData()\n\t\t// will generate the correct signal based on the order of dispatch/sequenceId\n\t\tawait sleep(250)\n\t\treturn data\n\t}\n\n\tconst prom = {}\n\tconst postRenderTest = new Promise(resolve => {\n\t\tprom.resolve = resolve\n\t})\n\tapp.on('postRender.test1', () => {\n\t\tapp.on('postRender.test1', null)\n\t\tprom.resolve()\n\t})\n\n\tawait Promise.all([\n\t\tapp.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: hc.id,\n\t\t\tconfig: { termgroups }\n\t\t}),\n\t\t(async () => {\n\t\t\tawait sleep(0)\n\t\t\tconst termgroups = structuredClone(hc.config.termgroups)\n\t\t\ttermgroups[0].lst = lst.slice(0, 3)\n\t\t\tawait app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: hc.id,\n\t\t\t\tconfig: { termgroups }\n\t\t\t})\n\t\t})()\n\t])\n\n\tawait postRenderTest\n\tawait sleep(responseDelay + 500)\n\t// run tests after the delayed response, as part of simulating the race condition\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 3, 'should render 3 gene rows')\n\tconst rects = hc.dom.seriesesG.selectAll('.sjpp-mass-series-g rect')\n\tconst hits = rects.filter(d => d.key !== 'BCR' && d.value.class != 'WT' && d.value.class != 'Blank')\n\ttest.equal(\n\t\trects.size(),\n\t\t180,\n\t\t'should have the expected total number of matrix cell rects, inlcuding WT and not tested'\n\t)\n\ttest.equal(hits.size(), 180, 'should have the expected number of matrix cell rects with hits')\n\ttest.equal(\n\t\tapp.Inner.dom.holder\n\t\t\t.selectAll('.sja_errorbar')\n\t\t\t.filter(function () {\n\t\t\t\treturn this.style.display != 'none'\n\t\t\t})\n\t\t\t.size(),\n\t\t0,\n\t\t'should not display errors'\n\t)\n\tif (test._ok) app.destroy()\n})\n\ntape('avoid race condition - reused fetch response cache', async test => {\n\t// !!!\n\t// to allow an app or chart code to fail due to race condition,\n\t// hardcode a constant value or comment out the ++ for the sequenceID\n\t// in rx/src/StoreApi.write()\n\t// !!!\n\ttest.timeoutAfter(4000)\n\ttest.plan(4)\n\t// the same terms lst as the previous tape() test above will trigger the reuse of cached fetch response\n\tconst { app, hc } = await getHierClusterApp({ terms: getGenes() })\n\tconst termgroups = structuredClone(hc.config.termgroups)\n\tconst responseDelay = 250\n\thc.origRequestData = hc.requestData\n\thc.requestData = async () => {\n\t\tconst lst = hc.config.termgroups[0].lst\n\t\tconst data = await hc.origRequestData({})\n\t\tif (lst.length === 3) return data\n\t\treturn data\n\t\t// artificially delay response to first request, to simulate a race condition\n\t\tawait sleep(responseDelay)\n\t\treturn data\n\t}\n\n\tconst prom = {}\n\tconst postRenderTest = new Promise(resolve => {\n\t\tprom.resolve = resolve\n\t})\n\tapp.on('postRender.test1', () => {\n\t\tapp.on('postRender.test1', null)\n\t\tprom.resolve()\n\t})\n\n\tawait Promise.all([\n\t\tapp.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: hc.id,\n\t\t\tconfig: { termgroups }\n\t\t}),\n\t\t(async () => {\n\t\t\t// sleep() >1 second will not cause an error when reusing a cached fetch response;\n\t\t\t// sleep(0) below is worst case for testing\n\t\t\tawait sleep(0)\n\t\t\tconst _termgroups = structuredClone(termgroups)\n\t\t\t_termgroups[0].lst = _termgroups[0].lst.slice(0, 3)\n\t\t\tawait app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: hc.id,\n\t\t\t\tconfig: { termgroups: _termgroups }\n\t\t\t})\n\t\t})()\n\t])\n\n\tawait postRenderTest\n\tawait sleep(responseDelay + 500)\n\t// run tests after the delayed response, as part of simulating the race condition\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 3, 'should render 3 gene rows')\n\tconst rects = hc.dom.seriesesG.selectAll('.sjpp-mass-series-g rect')\n\tconst hits = rects.filter(d => d.key !== 'BCR' && d.value.class != 'WT' && d.value.class != 'Blank')\n\ttest.equal(\n\t\trects.size(),\n\t\t180,\n\t\t'should have the expected total number of matrix cell rects, inlcuding WT and not tested'\n\t)\n\ttest.equal(hits.size(), 180, 'should have the expected number of matrix cell rects with hits')\n\ttest.equal(\n\t\tapp.Inner.dom.holder\n\t\t\t.selectAll('.sja_errorbar')\n\t\t\t.filter(function () {\n\t\t\t\treturn this.style.display != 'none'\n\t\t\t})\n\t\t\t.size(),\n\t\t0,\n\t\t'should not display errors'\n\t)\n\tif (test._ok) app.destroy()\n})\n\ntape('dendrogram click', async function (test) {\n\ttest.timeoutAfter(5000)\n\ttest.plan(3)\n\n\tlet numRenders = 0\n\tconst { app, hc } = await getHierClusterApp({ terms: getGenes() })\n\n\tconst img = await detectOne({ elem: hc.dom.topDendrogram.node(), selector: 'image' })\n\tconst svgBox = hc.dom.svg.node().getBoundingClientRect()\n\tconst imgBox = img.getBBox()\n\t// helper to see onscreen the x, y position of the click\n\t// select('body')\n\t// \t.append('div')\n\t// \t.style('position', 'absolute')\n\t// \t.style('top', svgBox.y + imgBox.y + imgBox.height/2)\n\t// \t.style('left', svgBox.x + hc.dimensions.xOffset + imgBox.x + imgBox.width/2)\n\t// \t.style('width', '5px').style('height', '5px')\n\t// \t.style('background-color', '#00f')\n\n\timg.dispatchEvent(\n\t\tnew MouseEvent('click', {\n\t\t\t//'view': window,\n\t\t\tbubbles: true,\n\t\t\tcancelable: true,\n\t\t\tclientX: svgBox.x + hc.dimensions.xOffset + imgBox.x + imgBox.width / 2,\n\t\t\tclientY: svgBox.y + imgBox.y + imgBox.height / 2\n\t\t})\n\t)\n\n\t// not able to nail down all the expected dataURI strings based on env\n\t// const dataUriEnd = hc.dom.topDendrogram.select('image')?.attr('href').slice(-60) || ''\n\t// const expectedUriEnd =\n\t// \twindow.devicePixelRatio === 1 && window.navigator.userAgent.includes('Electron')\n\t// \t\t? `VXLf89aL9WK9WC/DBawX62X4bDm168v/A9duR9df7eS8AAAAAElFTkSuQmCC`\n\t// \t\t: window.devicePixelRatio === 1\n\t// \t\t? `IyHnD+cP5w/nj/4CjhfHS/9qObXnl/8PkgA61yIPYtsAAAAASUVORK5CYII=`\n\t// \t\t: window.navigator.userAgent?.includes(`Electron`) // headless test\n\t// \t\t? `PgFeeOlp0S+88MJLnwAvvPS06Je9vfwCG6yWyx1uowQAAAAASUVORK5CYII=` // retina screen, headless\n\t// \t\t: `8NLTol944YWXPgFeeOlp0S+88HK+lx/PjoLLYOCCJQAAAABJRU5ErkJggg==` // retina screen\n\t//\n\t// test.equal(dataUriEnd, expectedUriEnd, `should rerender with the expected dataURI after a dendrogram click`)\n\n\ttest.deepEqual(\n\t\thc.clickedClusterIds,\n\t\t[\n\t\t\t46, 54, 37, 28, 27, 51, 53, 44, 49, 25, 34, 11, 20, 41, 45, 29, 33, 17, 15, 2, 38, 42, 30, 36, 22, 9, 14, 3, 4,\n\t\t\t31, 13, 26, 1, 16, 8, 10, 5, 6, 7, 23, 47, 48, 35, 43, 21, 32, 18, 24, 56\n\t\t],\n\t\t`should give the expected clickedClusterIds`\n\t)\n\n\ttest.deepEqual(\n\t\t['Zoom in', 'List 50 samples'],\n\t\t[...hc.dom.dendroClickMenu.d.node().querySelectorAll('.sja_menuoption')].map(elem => elem.__data__.label),\n\t\t'should show the expected menu options on dendrogram click'\n\t)\n\n\thc.dom.dendroClickMenu.d.node().querySelector('.sja_menuoption').parentNode.lastChild.click()\n\tawait sleep(5)\n\ttest.equal(\n\t\thc.dom.dendroClickMenu.d.node().querySelectorAll('.sjpp_row_wrapper').length,\n\t\t50,\n\t\t'should list the expected number of samples'\n\t)\n\tif (test._ok) {\n\t\thc.dom.dendroClickMenu.clear().hide()\n\t\tapp.destroy()\n\t}\n})\n\ntape('numeric dictionary terms (float)', async function (test) {\n\t// dictionary numeric terms cluster as their underlying type ('float'), not a synthetic dataType\n\t// leave it here in case it's used later: bins:{ default:{\"type\": \"regular-bin\", \"startinclusive\": true, \"bin_size\": 0.1, \"first_bin\": { \"stop\": 0.1 }, \"last_bin\": { \"start\": 0.7 }} }\n\tconst terms = [\n\t\t{\n\t\t\tid: 'aaclassic_5', // tw.id must be provided\n\t\t\tterm: { id: 'aaclassic_5', name: 'a1', type: 'float' }, // requires {id,name,type}; term.name doesn't need to be real, unique name works\n\t\t\tq: { mode: 'continuous' } // set to continuous to avoid validating tw.term.bins\n\t\t},\n\t\t{ id: 'hrtavg', term: { id: 'hrtavg', name: 'a2', type: 'float' }, q: { mode: 'continuous' } },\n\t\t{ id: 'agedx', term: { id: 'agedx', name: 'a3', type: 'float' }, q: { mode: 'continuous' } }\n\t]\n\tconst { app, hc } = await getHierClusterApp({ terms, dataType: 'float', termGroupName: 'Numeric Dictionary Terms' })\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 3, 'should render 3 rows')\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('isoform expression cluster', async function (test) {\n\ttest.timeoutAfter(4000)\n\tconst terms = [\n\t\t{\n\t\t\tterm: { isoform: 'ENST00000370314', name: 'ENST00000370314', type: 'isoformExpression' }\n\t\t},\n\t\t{\n\t\t\tterm: { isoform: 'ENST00000361510', name: 'ENST00000361510', type: 'isoformExpression' }\n\t\t},\n\t\t{\n\t\t\tterm: { isoform: 'ENST00000229281', name: 'ENST00000229281', type: 'isoformExpression' }\n\t\t}\n\t]\n\tconst { app, hc } = await getHierClusterApp({\n\t\tterms,\n\t\tdataType: 'isoformExpression',\n\t\ttermGroupName: 'Isoform Expression'\n\t})\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 3, 'should render 3 isoform rows')\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('ssGSEA cluster', async function (test) {\n\ttest.timeoutAfter(4000)\n\tconst terms = [\n\t\t{ term: { id: 'HALLMARK_ADIPOGENESIS', name: 'HALLMARK_ADIPOGENESIS', type: 'ssGSEA' } },\n\t\t{\n\t\t\tterm: { id: 'HALLMARK_ALLOGRAFT_REJECTION', name: 'HALLMARK_ALLOGRAFT_REJECTION', type: 'ssGSEA' }\n\t\t},\n\t\t{\n\t\t\tterm: { id: 'HALLMARK_ANDROGEN_RESPONSE', name: 'HALLMARK_ANDROGEN_RESPONSE', type: 'ssGSEA' }\n\t\t}\n\t]\n\tconst { app, hc } = await getHierClusterApp({\n\t\tterms,\n\t\tdataType: 'ssGSEA',\n\t\ttermGroupName: 'Gene Set Enrichment (ssGSEA)'\n\t})\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 3, 'should render 3 ssGSEA rows')\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('dnaMethylation cluster', async function (test) {\n\ttest.timeoutAfter(4000)\n\tconst terms = [\n\t\t{\n\t\t\tterm: { type: 'dnaMethylation', chr: 'chr17', start: 7673484, stop: 7681953, genomicFeatureType: 'gene' }\n\t\t},\n\t\t{\n\t\t\tterm: { type: 'dnaMethylation', chr: 'chr17', start: 7663195, stop: 7671664, genomicFeatureType: 'gene' }\n\t\t},\n\t\t{\n\t\t\tterm: { type: 'dnaMethylation', chr: 'chr17', start: 7673484, stop: 7681953, genomicFeatureType: 'promoter' }\n\t\t}\n\t]\n\tconst { app, hc } = await getHierClusterApp({ terms, dataType: 'dnaMethylation', termGroupName: 'DNA Methylation' })\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 3, 'should render 3 methylation rows')\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('cluster rejects a non-continuous term mode', async function (test) {\n\ttest.timeoutAfter(4000)\n\t// the client does not gate q.mode, so a discrete-mode term reaches the cluster route, which rejects\n\t// the whole request; the plot then renders no rows. (an incompatible term TYPE is instead caught\n\t// client-side by canTermBeInHierGrp before any request, so it can't be exercised through this path.)\n\tconst terms = [\n\t\t{ term: { gene: 'AKT1', name: 'AKT1', type: 'geneExpression' }, q: { mode: 'discrete' } },\n\t\t{ term: { gene: 'TP53', name: 'TP53', type: 'geneExpression' }, q: { mode: 'continuous' } },\n\t\t{ term: { gene: 'BCR', name: 'BCR', type: 'geneExpression' }, q: { mode: 'continuous' } }\n\t]\n\tconst { app, hc } = await getHierClusterApp({ terms, dataType: 'geneExpression' })\n\ttest.equal(\n\t\thc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(),\n\t\t0,\n\t\t'should render no rows when a term is not in continuous mode'\n\t)\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('cluster rejects incompatible numeric types', async function (test) {\n\ttest.timeoutAfter(4000)\n\t// geneExpression and a float dictionary term are both numeric but cannot be clustered together;\n\t// canTermBeInHierGrp throws in getPlotConfig (client-side) before any server request is made\n\tconst terms = [\n\t\t{ term: { gene: 'AKT1', name: 'AKT1', type: 'geneExpression' }, q: { mode: 'continuous' } },\n\t\t{ term: { gene: 'TP53', name: 'TP53', type: 'geneExpression' }, q: { mode: 'continuous' } },\n\t\t{ term: { id: 'agedx', name: 'agedx', type: 'float' }, q: { mode: 'continuous' } }\n\t]\n\tlet rejected = false\n\ttry {\n\t\tconst { app, hc } = await getHierClusterApp({ terms, dataType: 'geneExpression' })\n\t\t// if it didn't throw, the incompatible mix must have prevented any rows from rendering\n\t\trejected = hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size() === 0\n\t\tif (app) app.destroy()\n\t} catch (e) {\n\t\trejected = true\n\t}\n\ttest.ok(rejected, 'should reject a cluster mixing geneExpression and float terms')\n\ttest.end()\n})\n\n/*************************\n reusable helper functions\n**************************/\n\nasync function getHierClusterApp(_opts = {}) {\n\tconst holder = select('body').append('div')\n\tconst defaults = {\n\t\tdebug: true,\n\t\tholder,\n\t\tgenome: 'hg38-test',\n\t\tstate: {\n\t\t\tgenome: 'hg38-test',\n\t\t\tdslabel: 'TermdbTest',\n\t\t\ttermfilter: { filter0: _opts.filter0 },\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tdataType: _opts.dataType || TermTypes.GENE_EXPRESSION,\n\t\t\t\t\tsettings: {\n\t\t\t\t\t\thierCluster: {\n\t\t\t\t\t\t\ttermGroupName: _opts.termGroupName || 'Gene Expression (CGC genes only)'\n\t\t\t\t\t\t},\n\t\t\t\t\t\tmatrix: {\n\t\t\t\t\t\t\t// the matrix autocomputes the colw based on available screen width,\n\t\t\t\t\t\t\t// need to set an exact screen width for consistent tests using getBBox()\n\t\t\t\t\t\t\tavailContentWidth: 1200\n\t\t\t\t\t\t}\n\t\t\t\t\t},\n\t\t\t\t\t// force empty termgroups, genes since the instance requestData() will not have expression data,\n\t\t\t\t\t// and will cause a non-trival error if using the actual requestData(), which will be mocked below\n\t\t\t\t\ttermgroups: [], // _opts.termgroups || [],\n\t\t\t\t\t// !!! there will be an initial load error since this is an empty geneset,\n\t\t\t\t\t// !!! but will be ignored since it's not relevant to this test\n\t\t\t\t\tterms: _opts.terms || [],\n\t\t\t\t\tfilter: _opts.filter\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tapp: {\n\t\t\tfeatures: ['recover'],\n\t\t\tcallbacks: _opts?.app?.callbacks || {}\n\t\t},\n\t\trecover: {\n\t\t\tundoHtml: 'Undo',\n\t\t\tredoHtml: 'Redo',\n\t\t\tresetHtml: 'Restore',\n\t\t\tadjustTrackedState(state) {\n\t\t\t\tconst s = structuredClone(state)\n\t\t\t\tdelete s.termfilter.filter0\n\t\t\t\treturn s\n\t\t\t}\n\t\t},\n\t\thierCluster: _opts?.hierCluster || {}\n\t}\n\n\tconst opts = Object.assign(defaults, _opts)\n\tconst app = await appInit(opts)\n\t// dismiss the benign initial load error if present; guard the call since some error bars end in a\n\t// text node (no .click), e.g. the server error from the non-continuous-mode / no-data cluster tests\n\tholder.select('.sja_errorbar').node()?.lastChild?.click?.()\n\tconst hc = Object.values(app.Inner.components.plots).find(\n\t\tp => p.type == 'hierCluster' || p.chartType == 'hierCluster'\n\t).Inner\n\treturn { app, hc }\n}\nfunction getGenes() {\n\t// return a copy for each test, to avoid unexpected changes in reusing scoped variables\n\treturn [\n\t\t{ gene: 'AKT1', type: 'geneExpression' },\n\t\t{ gene: 'TP53', type: 'geneExpression' },\n\t\t{ gene: 'BCR', type: 'geneExpression' },\n\t\t{ gene: 'KRAS', type: 'geneExpression' }\n\t]\n}\n"],
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+  "names": ["tape", "lst", "termgroups"]
+}

package/dist/hierCluster.interactivity-VEHJHBKY.js

@@ -0,0 +1,54 @@
+import {
+  addSelectedRowsOptions,
+  addSelectedSamplesOptions,
+  getAllChildrenClusterIds,
+  getClusterFromLeftDendrogram,
+  getClusterFromTopDendrogram,
+  setClusteringBtn,
+  showTable4selectedRows,
+  showTable4selectedSamples,
+  triggerZoomBranch
+} from "./chunk-UKABZJQ7.js";
+import "./chunk-LYULXXGR.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-CPMOBFFR.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-B4VBTVVQ.js";
+import "./chunk-IQTEW3SK.js";
+import "./chunk-MNPTPENH.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  addSelectedRowsOptions,
+  addSelectedSamplesOptions,
+  getAllChildrenClusterIds,
+  getClusterFromLeftDendrogram,
+  getClusterFromTopDendrogram,
+  setClusteringBtn,
+  showTable4selectedRows,
+  showTable4selectedSamples,
+  triggerZoomBranch
+};
+//# sourceMappingURL=hierCluster.interactivity-VEHJHBKY.js.map

package/dist/hierCluster.renderers-OEVSBUBK.js

@@ -0,0 +1,21 @@
+import {
+  maySetSandboxHeader,
+  plotDendrogramHclust,
+  renderImage
+} from "./chunk-42FSM477.js";
+import "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  maySetSandboxHeader,
+  plotDendrogramHclust,
+  renderImage
+};
+//# sourceMappingURL=hierCluster.renderers-OEVSBUBK.js.map