@sjcrh/proteinpaint-client 2.193.0 → 2.195.0

package/dist/hierCluster.integration.spec-YKMAT7UU.js

@@ -1,395 +0,0 @@
-import {
-  appInit
-} from "./chunk-LLX3NKB4.js";
-import "./chunk-BO47H3VP.js";
-import "./chunk-SKMFMGCD.js";
-import {
-  detectOne,
-  sleep
-} from "./chunk-DJQTUDJM.js";
-import "./chunk-JWHFMFF2.js";
-import {
-  require_tape
-} from "./chunk-QWOE5YTB.js";
-import "./chunk-4KY4XKJV.js";
-import "./chunk-VRLC7DAU.js";
-import "./chunk-Y45JIQ5Y.js";
-import "./chunk-PXCFA4ZQ.js";
-import "./chunk-FVX76DZS.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-OR43PGBV.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-WKNI3HRQ.js";
-import "./chunk-NLQQIVTC.js";
-import "./chunk-E6XLLQCG.js";
-import {
-  fillTermWrapper
-} from "./chunk-L7VDSIM7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-UXDVUCXU.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-KM4JBR26.js";
-import "./chunk-COYULNJF.js";
-import "./chunk-6G4YOMWW.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import {
-  NUMERIC_DICTIONARY_TERM,
-  TermTypes
-} from "./chunk-IVXCWCKS.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)("numericDictTerm", 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: NUMERIC_DICTIONARY_TERM });
-  test.equal(hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(), 3, "should render 3 rows");
-  if (test._ok) app.destroy();
-  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: "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-YKMAT7UU.js.map

package/dist/hierCluster.integration.spec-YKMAT7UU.js.map

@@ -1,7 +0,0 @@
-{
-  "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, NUMERIC_DICTIONARY_TERM } 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('numericDictTerm', async function (test) {\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: NUMERIC_DICTIONARY_TERM })\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\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: '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\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-LPTHVWHR.js

@@ -1,54 +0,0 @@
-import {
-  addSelectedRowsOptions,
-  addSelectedSamplesOptions,
-  getAllChildrenClusterIds,
-  getClusterFromLeftDendrogram,
-  getClusterFromTopDendrogram,
-  setClusteringBtn,
-  showTable4selectedRows,
-  showTable4selectedSamples,
-  triggerZoomBranch
-} from "./chunk-BOO4W7WD.js";
-import "./chunk-L7VDSIM7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-UXDVUCXU.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-KM4JBR26.js";
-import "./chunk-COYULNJF.js";
-import "./chunk-6G4YOMWW.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import "./chunk-IVXCWCKS.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-LPTHVWHR.js.map

package/dist/hierCluster.renderers-4XWKHCNW.js

@@ -1,21 +0,0 @@
-import {
-  maySetSandboxHeader,
-  plotDendrogramHclust,
-  renderImage
-} from "./chunk-T46LHXJW.js";
-import "./chunk-IVXCWCKS.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-4XWKHCNW.js.map

package/dist/imagePlot-3DF7ZH3U.js

@@ -1,163 +0,0 @@
-import {
-  PlotBase,
-  controlsInit
-} from "./chunk-L7VDSIM7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-UXDVUCXU.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-KM4JBR26.js";
-import "./chunk-COYULNJF.js";
-import {
-  dofetch3
-} from "./chunk-6G4YOMWW.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import "./chunk-IVXCWCKS.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";
-
-// plots/imagePlot.ts
-var ImagePlot = class _ImagePlot extends PlotBase {
-  static {
-    this.type = "imagePlot";
-  }
-  constructor(opts, api) {
-    super(opts, api);
-    this.opts = opts;
-    this.api = api;
-    this.type = _ImagePlot.type;
-    if (this.opts?.header) {
-      if (this.opts?.headerText)
-        this.opts.header.append("span").style("padding-right", "5px").text(this.opts.headerText);
-      this.opts.header.append("span").text("IMAGE PLOT").style("font-size", "0.7em").style("opacity", 0.6);
-    }
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      config,
-      termfilter: appState.termfilter,
-      vocab: appState.vocab
-    };
-  }
-  async init(appState) {
-    const config = this.getState(appState).config;
-    const holder = this.opts.holder.append("div").attr("data-testid", "sjpp-imagePlot-holder");
-    this.dom = {
-      holder,
-      controlsHolder: holder.append("div").attr("data-testid", "sjpp-imagePlot-controlsDiv").style("display", "inline-block"),
-      imageHolder: holder.append("div").attr("data-testid", "sjpp-imagePlot-imagesDiv").style("display", "inline-block")
-    };
-    const sampleId = config.sample?.sampleId || config.sample?.sID;
-    let images;
-    if (config?.imgDir) {
-      const img = await dofetch3(
-        `img?file=${config.imgDir.folder}${config.imgDir.folder.endsWith("/") ? "" : "/"}${sampleId}/${config.imgDir.fileName}`
-      );
-      if (!img || img?.error) throw new Error(img?.error || "Error fetching image");
-      images = [img];
-    } else {
-      const result = await this.app.vocabApi.getSampleImages(sampleId);
-      if (result.error) throw new Error(result.error);
-      images = result.images;
-    }
-    for (const img of images) {
-      this.dom.imageHolder.append("img").style("padding", "10px").attr("src", img.src).attr("width", config.settings.imagePlot.width).attr("height", config.settings.imagePlot.height);
-    }
-  }
-  async setControls() {
-    this.components = {
-      controls: await controlsInit({
-        app: this.app,
-        id: this.id,
-        holder: this.dom.controlsHolder,
-        inputs: [
-          {
-            label: "Image width",
-            type: "number",
-            chartType: this.type,
-            settingsKey: "width"
-          },
-          {
-            label: "Image height",
-            type: "number",
-            chartType: this.type,
-            settingsKey: "height"
-          }
-        ]
-      })
-    };
-  }
-  async main() {
-  }
-};
-async function getPlotConfig(opts) {
-  const settings = getDefaultImagePlotSettings();
-  if (opts.settings) copyMerge(settings, opts.settings);
-  const config = {
-    settings: {
-      controls: {
-        isOpen: false
-      },
-      imagePlot: settings
-    }
-  };
-  return copyMerge(config, opts);
-}
-function getDefaultImagePlotSettings() {
-  return {
-    width: 500,
-    height: 500
-  };
-}
-var imagePlotInit = getCompInit(ImagePlot);
-var componentInit = imagePlotInit;
-async function renderImagePlot(state, holder, sample) {
-  const opts = {
-    holder,
-    state: {
-      vocab: state.vocab,
-      plots: [
-        {
-          chartType: "imagePlot",
-          sample
-        }
-      ]
-    }
-  };
-  const plot = await import("./plot.app-WRCBLYGO.js");
-  await plot.appInit(opts);
-}
-export {
-  componentInit,
-  getDefaultImagePlotSettings,
-  getPlotConfig,
-  imagePlotInit,
-  renderImagePlot
-};
-//# sourceMappingURL=imagePlot-3DF7ZH3U.js.map