@sjcrh/proteinpaint-client 2.183.0 → 2.183.1

package/dist/scatter.integration.spec-6KRDNHHH.js

@@ -1,1194 +0,0 @@
-import {
-  getGeneVariantTw,
-  getGenesetMutTw,
-  getScctTw,
-  getScgeneexpTw,
-  getSsgseaTw
-} from "./chunk-BAY47D5E.js";
-import {
-  getRunPp,
-  rideInit
-} from "./chunk-E4NVHKWD.js";
-import {
-  detectAttr,
-  detectChildAttr,
-  detectChildStyle,
-  detectGte,
-  detectLst,
-  detectStyle,
-  sleep
-} from "./chunk-ZIBWLDQI.js";
-import {
-  require_tape
-} from "./chunk-QWOE5YTB.js";
-import "./chunk-I4IKRKYJ.js";
-import "./chunk-4RR4KPRJ.js";
-import "./chunk-V245THQC.js";
-import "./chunk-DGMK7SXX.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-YY4CKQJ6.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-OSM7YS23.js";
-import "./chunk-S5ZI6N2I.js";
-import "./chunk-AQ4OP4GR.js";
-import {
-  getSamplelstTW,
-  openPlot,
-  openSummaryPlot
-} from "./chunk-OXJ2TWDO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-V6DLLX4N.js";
-import "./chunk-7RN3L2BX.js";
-import "./chunk-A6TQGNDQ.js";
-import "./chunk-HYZG6OPC.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-SEQLC4AD.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-KQMEJUWI.js";
-import "./chunk-UJU3Q7QJ.js";
-import "./chunk-WGL6FIUE.js";
-import "./chunk-6ITDJ5UR.js";
-import {
-  mclass
-} from "./chunk-XYFDBYOY.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import {
-  rgb
-} from "./chunk-OMR2DT66.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// plots/scatter/test/scatter.integration.spec.js
-var import_tape = __toESM(require_tape(), 1);
-var runpp = getRunPp("mass", {
-  state: {
-    nav: { activeTab: 1 },
-    vocab: {
-      dslabel: "TermdbTest",
-      genome: "hg38-test"
-    }
-  },
-  debug: 1
-});
-var state = {
-  plots: [
-    {
-      chartType: "sampleScatter",
-      colorTW: { id: "diaggrp" },
-      name: "TermdbTest TSNE"
-    }
-  ]
-};
-var open_state = {
-  nav: { header_mode: "hide_search" },
-  plots: [
-    {
-      chartType: "sampleScatter",
-      colorTW: { id: "diaggrp" },
-      name: "TermdbTest TSNE"
-    }
-  ]
-};
-var state3D = {
-  plots: [
-    {
-      chartType: "sampleScatter",
-      colorTW: { id: "diaggrp" },
-      name: "TermdbTest TSNE",
-      term0: { id: "agedx", q: { mode: "continuous" } }
-    }
-  ]
-};
-var stateDynamicScatter = {
-  plots: [
-    {
-      chartType: "sampleScatter",
-      colorTW: { id: "diaggrp" },
-      term: { id: "agedx", q: { mode: "continuous" } },
-      term2: { id: "hrtavg", q: { mode: "continuous" } }
-    }
-  ]
-};
-var state2geneexp = {
-  plots: [
-    {
-      chartType: "sampleScatter",
-      colorTW: { id: "diaggrp" },
-      term: { term: { type: "geneExpression", gene: "AKT1" }, q: { mode: "continuous" } },
-      term2: { term: { type: "geneExpression", gene: "TP53" }, q: { mode: "continuous" } }
-    }
-  ]
-};
-var state2ssgsea = {
-  plots: [
-    {
-      chartType: "sampleScatter",
-      colorTW: { id: "diaggrp" },
-      term: { term: { type: "ssGSEA", id: "HALLMARK_ADIPOGENESIS" }, q: { mode: "continuous" } },
-      term2: { term: { type: "ssGSEA", id: "HALLMARK_ALLOGRAFT_REJECTION" }, q: { mode: "continuous" } }
-    }
-  ]
-};
-var state2dnameth = {
-  plots: [
-    {
-      chartType: "sampleScatter",
-      colorTW: { id: "diaggrp" },
-      term: {
-        term: { type: "dnaMethylation", chr: "chr17", start: 7673484, stop: 7681953, genomicFeatureType: "gene" },
-        q: { mode: "continuous" }
-      },
-      term2: {
-        term: { type: "dnaMethylation", chr: "chr17", start: 7663195, stop: 7671664, genomicFeatureType: "gene" },
-        q: { mode: "continuous" }
-      }
-    }
-  ]
-};
-var state2scgeneexp = {
-  plots: [
-    {
-      chartType: "sampleScatter",
-      term: getScgeneexpTw(),
-      term2: getScgeneexpTw("TP53")
-    }
-  ]
-};
-var state3DContour = {
-  plots: [
-    {
-      chartType: "sampleScatter",
-      colorTW: { id: "diaggrp" },
-      name: "TermdbTest TSNE",
-      term0: { id: "agedx", q: { mode: "continuous" } },
-      settings: { sampleScatter: { showContour: true } }
-    }
-  ]
-};
-var groups = [
-  {
-    name: "Test group 1",
-    items: [
-      {
-        sample: "2646",
-        x: -103.141543,
-        y: 73.31223702,
-        sampleId: 41,
-        category_info: {},
-        hidden: {
-          category: false
-        },
-        category: '"Acute lymphoblastic leukemia"',
-        shape: "Ref"
-      },
-      {
-        sample: "2800",
-        x: -99.20065673,
-        y: 73.64971694,
-        sampleId: 52,
-        category_info: {},
-        hidden: {
-          category: false
-        },
-        category: '"Acute lymphoblastic leukemia"',
-        shape: "Ref"
-      }
-    ],
-    index: 1
-  }
-];
-function getHolder() {
-  return select_default("body").append("div");
-}
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- plots/sampleScatter -***-");
-  test.end();
-});
-(0, import_tape.default)("Render TermdbTest scatter plot and open survival and summary", function(test) {
-  test.timeoutAfter(8e3);
-  test.plan(7);
-  const holder = getHolder();
-  runpp({
-    holder,
-    //Fix for test failing because survival & summary sandboxs are not destroyed.
-    state,
-    sampleScatter: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(scatter) {
-    const scatterDiv = scatter.Inner.model.charts[0].chartDiv;
-    testPlot();
-    testLegendTitle();
-    const group = await testCreateGroup();
-    const tw = getSamplelstTW([group]);
-    await testOpenSurvivalPlot();
-    await testOpenSummaryPlot();
-    if (test._ok) holder.remove();
-    test.end();
-    function testPlot() {
-      const serieG = scatterDiv.select(".sjpcb-scatter-series");
-      const numSymbols = serieG.selectAll("path").size();
-      test.equal(
-        numSymbols,
-        scatter.Inner.model.charts[0].data.samples.length,
-        `Should be ${scatter.Inner.model.charts[0].data.samples.length}. Rendered ${numSymbols} symbols.`
-      );
-    }
-    function testLegendTitle() {
-      const g = scatterDiv.select(".sjpcb-scatter-legend");
-      test.true(g != null, "Should have a legend");
-      const texts = g.selectAll('text[data-testid="legendTitle"]');
-      test.true(
-        texts._groups[0][0].innerHTML.startsWith(scatter.Inner.config.colorTW.term.name),
-        "colorTW legend title made"
-      );
-      test.true(
-        texts._groups[0][1].innerHTML.startsWith(scatter.Inner.config.shapeTW.term.name),
-        "shapeTW legend title made"
-      );
-    }
-    async function testCreateGroup() {
-      const samples = scatterDiv.select(".sjpcb-scatter-series").selectAll("path").nodes().filter((p) => p.__data__?.category === "Acute lymphoblastic leukemia").map((path) => path.__data__);
-      test.equal(samples.length, 36, `Group should have 36 symbols.`);
-      const self = scatter.Inner;
-      const group2 = {
-        name: `Group 1`,
-        items: samples,
-        index: 0
-      };
-      self.config.groups.push(group2);
-      return group2;
-    }
-    async function testOpenSurvivalPlot() {
-      const plots = scatter.Inner.app.getState().plots;
-      const elem = scatter.Inner.app.Inner.dom.plotDiv.node();
-      const preSandboxes = [...elem.querySelectorAll(".sjpp-sandbox")];
-      const sandboxes = await detectLst({
-        elem,
-        selector: ".sjpp-sandbox",
-        count: plots.length + 1,
-        async trigger() {
-          const survivalTerm = await scatter.Inner.app.vocabApi.getterm("efs");
-          await openPlot("survival", survivalTerm, tw, scatter.Inner.app);
-        }
-      });
-      const newSandbox = sandboxes.find((s) => !preSandboxes.includes(s));
-      test.equal(
-        [...newSandbox.querySelectorAll(".sja_errorbar")].filter((b) => b.style.display != "none").length,
-        0,
-        'Should render survival plot without errors".'
-      );
-    }
-    async function testOpenSummaryPlot() {
-      const plots = scatter.Inner.app.getState().plots;
-      const elem = scatter.Inner.app.Inner.dom.plotDiv.node();
-      const preSandboxes = [...elem.querySelectorAll(".sjpp-sandbox")];
-      const survivalTerm = await scatter.Inner.app.vocabApi.getterm("efs");
-      const sandboxes = await detectLst({
-        elem,
-        selector: ".sjpp-sandbox",
-        count: plots.length + 1,
-        async trigger() {
-          const genderTerm = await scatter.Inner.app.vocabApi.getterm("sex");
-          await openSummaryPlot(genderTerm, tw, scatter.Inner.app);
-        }
-      });
-      const newSandbox = sandboxes.find((s) => !preSandboxes.includes(s));
-      test.equal(
-        [...newSandbox.querySelectorAll(".sja_errorbar")].filter((b) => b.style.display != "none").length,
-        0,
-        'Should render summary plot without errors".'
-      );
-    }
-  }
-});
-(0, import_tape.default)("Render TermdbTest scatter plot adding age as Z to render a 3D plot", function(test) {
-  test.timeoutAfter(8e3);
-  test.plan(1);
-  const holder = getHolder();
-  runpp({
-    holder,
-    //Fix for test failing because survival & summary sandboxs are not destroyed.
-    state: state3D,
-    sampleScatter: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(scatter) {
-    const is3D = scatter.Inner.model.is3D;
-    const scatterDiv = scatter.Inner.model.charts[0].chartDiv;
-    test.true(is3D, "Should be a 3D scatter plot");
-    if (test._ok) holder.remove();
-    test.end();
-  }
-});
-(0, import_tape.default)("Render 3D plot with age as Z and showContour set to true to apply contour on 3D plot", function(test) {
-  test.timeoutAfter(8e3);
-  test.plan(1);
-  const holder = getHolder();
-  runpp({
-    holder,
-    //Fix for test failing because survival & summary sandboxs are not destroyed.
-    state: state3DContour,
-    sampleScatter: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(scatter) {
-    const chart = scatter.Inner.model.charts[0];
-    await sleep(1e3);
-    test.true(chart.plane != null, "Should have a plane with the contour map");
-    if (test._ok) holder.remove();
-    test.end();
-  }
-});
-(0, import_tape.default)("dynamic scatter of agedx & hrtavg", function(test) {
-  test.timeoutAfter(8e3);
-  test.plan(2);
-  const holder = getHolder();
-  runpp({
-    holder,
-    state: stateDynamicScatter,
-    sampleScatter: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    const chart = scatter.Inner.model.charts[0];
-    test.true(scatter.Inner.settings.showAxes, "Dynamic scatter should have axes");
-    scatter.Inner.settings.showContour = true;
-    await scatter.Inner.app.dispatch({
-      type: "plot_edit",
-      id: scatter.Inner.id,
-      config: { settings: { sampleScatter: scatter.Inner.settings } }
-    });
-    const contourG = scatter.Inner.model.charts[0].chartDiv.select('g[stroke-linejoin="round"]').node();
-    test.true(
-      contourG != null,
-      "Scatter should have contour showing the density of points after selecting show contour"
-    );
-    if (test._ok) holder.remove();
-    test.end();
-  }
-});
-(0, import_tape.default)("dynamic scatter of 2-gene expression", function(test) {
-  const holder = getHolder();
-  runpp({
-    holder,
-    state: state2geneexp,
-    sampleScatter: { callbacks: { "postRender.test": runTests } }
-  });
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    const chart = scatter.Inner.model.charts[0];
-    test.true(scatter.Inner.settings.showAxes, "Dynamic scatter should have axes");
-    if (test._ok) holder.remove();
-    test.end();
-  }
-});
-(0, import_tape.default)("dynamic scatter of 2-ssgsea", function(test) {
-  const holder = getHolder();
-  runpp({
-    holder,
-    state: state2ssgsea,
-    sampleScatter: { callbacks: { "postRender.test": runTests } }
-  });
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    const chart = scatter.Inner.model.charts[0];
-    test.true(scatter.Inner.settings.showAxes, "Dynamic scatter should have axes");
-    if (test._ok) holder.remove();
-    test.end();
-  }
-});
-(0, import_tape.default)("dynamic scatter of 2-dnameth", function(test) {
-  const holder = getHolder();
-  runpp({
-    holder,
-    state: state2dnameth,
-    sampleScatter: { callbacks: { "postRender.test": runTests } }
-  });
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    const chart = scatter.Inner.model.charts[0];
-    test.true(scatter.Inner.settings.showAxes, "Dynamic scatter should have axes");
-    if (test._ok) holder.remove();
-    test.end();
-  }
-});
-(0, import_tape.default)("Show tooltip for sample", function(test) {
-  test.timeoutAfter(8e3);
-  test.plan(2);
-  const holder = getHolder();
-  runpp({
-    holder,
-    //Fix for test failing because survival & summary sandboxs are not destroyed.
-    state,
-    sampleScatter: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    const chart = scatter.Inner.model.charts[0];
-    const sample = groups[0].items[0];
-    scatter.Inner.vm.scatterTooltip.showSampleTooltip(sample, 100, 100, chart);
-    const tooltipDiv = scatter.Inner.view.dom.tooltip.d.node();
-    const tree = scatter.Inner.vm.scatterTooltip.tree;
-    const parentNode = tree.find((n) => n.id == "Acute lymphoblastic leukemia" && n.samples.length == 3);
-    test.true(parentNode != null, "Tooltip should have 3 samples for Acute lymphoblastic leukemia");
-    test.true(tooltipDiv != null, "Tooltip should be shown");
-    scatter.Inner.view.dom.tooltip.hide();
-    if (test._ok) holder.remove();
-    test.end();
-  }
-});
-(0, import_tape.default)("Test scale dot", function(test) {
-  test.timeoutAfter(8e3);
-  test.plan(2);
-  const holder = getHolder();
-  const state2 = {
-    plots: [
-      {
-        chartType: "sampleScatter",
-        scaleDotTW: { id: "agedx", q: { mode: "continuous" } },
-        name: "TermdbTest TSNE"
-      }
-    ]
-  };
-  runpp({
-    holder,
-    //Fix for test failing because survival & summary sandboxs are not destroyed.
-    state: state2,
-    sampleScatter: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    const self = scatter.Inner;
-    const chart = scatter.Inner.model.charts[0];
-    const dots = self.view.dom.mainDiv.selectAll(".sjpcb-scatter-series > path").nodes();
-    const minSize = self.settings.minShapeSize * self.zoom / 3;
-    const maxSize = self.settings.maxShapeSize * self.zoom / 3;
-    test.true(
-      dots.find((dot) => dot.getAttribute("transform").includes(`scale(${minSize})`)) != null,
-      `Dots with the minimum size should be found`
-    );
-    test.true(
-      dots.find((dot) => dot.getAttribute("transform").includes(`scale(${maxSize})`)) != null,
-      `Dots with the maximum size should be found`
-    );
-    if (test._ok) holder.remove();
-    test.end();
-  }
-});
-(0, import_tape.default)("Test lasso menus options", function(test) {
-  test.timeoutAfter(8e3);
-  runpp({
-    state,
-    sampleScatter: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    await triggerLassoMenu(scatter);
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-  async function triggerLassoMenu(scatter) {
-    const group = groups[0];
-    scatter.Inner.vm.scatterLasso.showLassoMenu(new PointerEvent("click"), group.items);
-    const groupsMenu = scatter.Inner.view.dom.tip.d.selectAll("div.sja_menuoption").nodes();
-    const options = ["List 2 samples", "Add to a group", "Add to a group and filter", "Open sample view"];
-    for (const [i, node] of Object.entries(groupsMenu)) {
-      const option = node.innerText;
-      test.equal(option, options[i], `Should display ${option} in the menu`);
-    }
-    scatter.Inner.vm.scatterLasso.showTable(group, 0, 0, false);
-    testSampleTable(scatter, group);
-    groupsMenu[1].click();
-    await sleep(1e3);
-    test.equal(scatter.Inner.state.groups.length, 1, `Should create a group in mass state`);
-    groupsMenu[2].click();
-    await sleep(1e3);
-    test.equal(scatter.Inner.state.groups.length, 2, `Should create another group in mass state`);
-    test.true(
-      scatter.Inner.state.termfilter?.filter?.lst[1]?.lst[0]?.tvs?.term.type == "samplelst",
-      `Should create a samplelst filter in mass state`
-    );
-  }
-  function testSampleTable(scatter, group) {
-    const samplesRendered = scatter.Inner.view.dom.tip.d.selectAll(".sjpp_row_wrapper > td:nth-child(3)").nodes();
-    const samples2Check = [];
-    for (const item of samplesRendered) {
-      samples2Check.push(item.innerHTML);
-    }
-    let foundSamples = 0;
-    for (const sampleData of group.items) {
-      if (samples2Check.some((d) => d == sampleData.sample)) ++foundSamples;
-      else test.fail(`Sample = ${sampleData.sample} is not displayed in sample table`);
-    }
-    test.equal(samples2Check.length, foundSamples, `Should render all samples for ${group.name}`);
-    scatter.Inner.view.dom.tip.hide();
-  }
-});
-(0, import_tape.default)("Invalid colorTW.id", async function(test) {
-  test.timeoutAfter(3e3);
-  const message = `Should display error for colorTW.id not found within dataset`;
-  const holder = getHolder();
-  const id = "Not real data";
-  try {
-    runpp({
-      holder,
-      state: {
-        plots: [
-          {
-            chartType: "sampleScatter",
-            colorTW: { id },
-            name: "TermdbTest TSNE"
-          }
-        ]
-      }
-    });
-    const errorbar = await detectGte({ elem: holder.node(), selector: ".sja_errorbar" });
-    test.equal(errorbar.length, 1, "Should display only one error message.");
-    test.ok(
-      errorbar[0].innerText.includes(`missing dictionary term for id=${id}`),
-      `Should display, "Error: no term found for ${id} [sampleScatter getPlotConfig()]".`
-    );
-  } catch (e) {
-    test.fail(message + ": " + e);
-  }
-  if (test._ok) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Invalid colorTW.term", async function(test) {
-  test.timeoutAfter(3e3);
-  const holder = getHolder();
-  const id = "Not real data";
-  try {
-    runpp({
-      holder,
-      state: {
-        plots: [
-          {
-            chartType: "sampleScatter",
-            colorTW: { term: { id } },
-            name: "TermdbTest TSNE"
-          }
-        ]
-      }
-    });
-    const errorbar = await detectGte({ elem: holder.node(), selector: ".sja_errorbar > div:nth-child(2)" });
-    const error = "Error: Error: Type is not defined [sampleScatter getPlotConfig()]";
-    test.true(errorbar[0].innerText.startsWith(error), `Should display, "${error}...".`);
-  } catch (e) {
-    test.fail(e);
-  }
-  if (test._ok) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Invalid plot name", async function(test) {
-  test.timeoutAfter(3e3);
-  const message = `Should display error for invalid plot name`;
-  const holder = getHolder();
-  try {
-    runpp({
-      holder,
-      state: {
-        plots: [
-          {
-            chartType: "sampleScatter",
-            colorTW: {
-              id: "diaggrp"
-            },
-            name: "Not real data"
-          }
-        ]
-      }
-    });
-    const errorbar = await detectGte({ elem: holder.node(), selector: ".sja_errorbar" });
-    test.equal(errorbar.length, 1, "Should display only one error message.");
-    test.ok(
-      errorbar[0].innerText.includes(`plot not found with plotName`),
-      'Should display, "Error: plot not found with plotName: Not real data".'
-    );
-  } catch (e) {
-    test.fail(message + ": " + e);
-  }
-  if (test._ok) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Test legend", function(test) {
-  test.timeoutAfter(6e3);
-  runpp({
-    state: structuredClone(state),
-    sampleScatter: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    const samples = scatter.Inner.model.charts[0].data.samples;
-    const scatterDiv = scatter.Inner.model.charts[0].chartDiv;
-    await testHideCategory(scatter, samples);
-    await testChangeColor(scatter, samples);
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-  async function testHideCategory(scatter, samples) {
-    const key = "Acute lymphoblastic leukemia";
-    const expectedNum = samples.filter((s) => s.category === key).length;
-    const matched = await detectChildStyle({
-      elem: scatter.Inner.view.dom.mainDiv.node(),
-      selector: ".sjpcb-scatter-series > path",
-      style: {
-        fillOpacity: "0"
-      },
-      count: expectedNum,
-      trigger: () => {
-        const chart = scatter.Inner.model.charts[0];
-        scatter.Inner.vm.legendvm.legendInteractivity.hideCategory(scatter.Inner.config.colorTW, key, true);
-        scatter.Inner.app.dispatch({
-          type: "plot_edit",
-          id: scatter.Inner.id,
-          config: { colorTW: scatter.Inner.config.colorTW }
-        });
-      }
-      /* example of a custom matcher, instead of opts.style
-               matcher(mutations, observer) {
-                   const hidden = mutations.filter(m => m.target.__data__.category == key && m.target.style.fillOpacity == '0')
-                   if (hidden.length >= expectedNum) return hidden.map(d => d.target)
-               }*/
-    });
-    test.equal(
-      matched.filter((t) => t.__data__.category == key).length,
-      expectedNum,
-      `Should remove all samples with category = ${key}`
-    );
-  }
-  async function testChangeColor(scatter, samples) {
-    const key = "Wilms tumor";
-    const color = "blue";
-    const expectedColor = rgb(color).toString();
-    const expectedNum = samples.filter((s) => s.category === key).length;
-    const targets = await detectChildAttr({
-      elem: scatter.Inner.view.dom.mainDiv.node(),
-      selector: ".sjpcb-scatter-series > path",
-      observe: {
-        attributeFilter: ["fill"]
-      },
-      /* example of opts.attr, instead of opts.matcher()
-               attr: {
-                   // key is name of attribute, value can be a string, number, or function
-                   fill: value => {
-                       return d3color.rgb(value).toString() === expectedColor
-                   }
-               },*/
-      count: expectedNum,
-      trigger: async () => {
-        scatter.Inner.vm.legendvm.legendInteractivity.changeColor(key, color);
-      },
-      // example of a custom matcher, instead of opts.attr{}
-      matcher(mutations) {
-        const targets2 = mutations.filter((m) => rgb(m.target.getAttribute("fill")) == expectedColor);
-        if (targets2.length >= expectedNum) return targets2.map((d) => d.target);
-      }
-    });
-    test.equal(targets.length, 2, `Should change the color of the category = ${key} to blue`);
-  }
-});
-(0, import_tape.default)("Render color groups", function(test) {
-  test.timeoutAfter(3e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "sampleScatter",
-          colorTW: {
-            id: "genetic_race",
-            q: {
-              customset: {
-                groups: [
-                  {
-                    name: "non-Asian Ancestry",
-                    type: "values",
-                    values: [
-                      { key: "European Ancestry", label: "European Ancestry" },
-                      { key: "African Ancestry", label: "African Ancestry" },
-                      { key: "Multi-Ancestry-Admixed", label: "Multi-Ancestry-Admixed" }
-                    ]
-                  },
-                  {
-                    name: "Asian Ancestry",
-                    type: "values",
-                    values: [{ key: "Asian Ancestry", label: "Asian Ancestry" }]
-                  }
-                ]
-              }
-            }
-          },
-          name: "TermdbTest TSNE"
-        }
-      ]
-    },
-    sampleScatter: {
-      callbacks: { "postRender.test": runTests }
-    }
-  });
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    await testColorLegend(scatter);
-    await changeColorGroups(scatter);
-    await testColorLegend(scatter);
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-  async function testColorLegend(scatter) {
-    const legendLabels = await detectGte({
-      elem: scatter.Inner.model.charts[0].chartDiv.node(),
-      selector: 'text[name="sjpp-scatter-legend-label"]'
-    });
-    const groups2 = [];
-    for (const group of legendLabels) {
-      const label = group.innerHTML.split(",");
-      groups2.push({
-        label: label[0],
-        samples: label[1].match(/[\d\.]+/g)
-      });
-    }
-    test.equal(
-      scatter.Inner.model.charts[0].colorLegend.size,
-      groups2.length + 1,
-      `Legend categories (# = ${groups2.length + 1}) should equal size of colorLegend (# = ${scatter.Inner.model.charts[0].colorLegend.size}) `
-    );
-    compareData2DOMLegend(scatter, groups2);
-  }
-  function compareData2DOMLegend(scatter, groups2) {
-    for (const group of groups2) {
-      const mapLeg = scatter.Inner.model.charts[0].colorLegend.get(group.label);
-      test.ok(mapLeg, `Should display group custom label = ${group.label} in legend`);
-      test.equal(
-        `${mapLeg.sampleCount}`,
-        group.samples[0],
-        `Should show matching n = ${group.samples[0]} for ${group.label}`
-      );
-    }
-  }
-  async function changeColorGroups(scatter) {
-    scatter.Inner.config.colorTW.q.customset = {
-      groups: [
-        {
-          name: "European Ancestryy",
-          type: "values",
-          values: [{ key: "European Ancestry", label: "European Ancestry" }]
-        },
-        {
-          name: "non-European Ancestry",
-          type: "values",
-          values: [
-            { key: "Asian Ancestry", label: "Asian Ancestry" },
-            { key: "African Ancestry", label: "African Ancestry" },
-            { key: "Multi-Ancestry-Admixed", label: "Multi-Ancestry-Admixed" }
-          ]
-        }
-      ]
-    };
-    await scatter.Inner.app.dispatch({
-      type: "plot_edit",
-      id: scatter.Inner.id,
-      config: scatter.Inner.config
-    });
-  }
-});
-(0, import_tape.default)("Change symbol and reference size from menu", function(test) {
-  test.timeoutAfter(1e4);
-  runpp({
-    state: structuredClone(open_state),
-    sampleScatter: {
-      callbacks: { "postRender.test": runTests }
-    }
-  });
-  const testSymSize = 300;
-  const testRefSize = 1;
-  async function runTests(scatter) {
-    rideInit({ arg: scatter, bus: scatter, eventType: "postRender.test" }).use(changeSymbolInput).to(testSymbolSize, { wait: 100 }).use(changeRefInput, { wait: 100 }).to(testRefDotSize, { wait: 300 }).done(test);
-  }
-  function changeSymbolInput(scatter) {
-    const sizeInput = scatter.Inner.view.dom.controlsHolder.selectAll("input").nodes().find((e) => e.value == scatter.Inner.settings.size);
-    sizeInput.value = testSymSize;
-    sizeInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter" }));
-  }
-  function testSymbolSize(scatter) {
-    test.equal(scatter.Inner.settings.size, testSymSize, `Should change symbol dot size to test value = ${testSymSize}`);
-  }
-  function changeRefInput(scatter) {
-    const refInput = scatter.Inner.view.dom.controlsHolder.selectAll("input").nodes().find((e) => e.value == scatter.Inner.settings.refSize);
-    refInput.value = testRefSize;
-    refInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter" }));
-  }
-  function testRefDotSize(scatter) {
-    test.equal(
-      scatter.Inner.settings.refSize,
-      testRefSize,
-      `Should change reference dot size to test value = ${testRefSize}`
-    );
-  }
-});
-(0, import_tape.default)("Change chart width and height from menu", function(test) {
-  test.timeoutAfter(1e3);
-  runpp({
-    state: structuredClone(open_state),
-    sampleScatter: {
-      callbacks: { "postRender.test": runTests }
-    }
-  });
-  const testWidth = 550;
-  const testHeight = 550;
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    await testChartSizeChange(scatter);
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-  async function testChartSizeChange(scatter) {
-    const widthInput = scatter.Inner.view.dom.controlsHolder.selectAll("input").nodes().find((e) => e.value == scatter.Inner.settings.svgw);
-    widthInput.value = testWidth;
-    const heightInput = scatter.Inner.view.dom.controlsHolder.selectAll("input").nodes().find((e) => e.value == scatter.Inner.settings.svgh);
-    heightInput.value = testHeight;
-    await detectAttr({
-      target: scatter.Inner.view.dom.mainDiv.select("svg").node(),
-      observe: {
-        attributeFilter: ["height", "width"]
-      },
-      // count: 1,
-      trigger() {
-        widthInput.dispatchEvent(new Event("change"));
-        heightInput.dispatchEvent(new Event("change"));
-      }
-      // matcher(mutations){
-      // 	let foundH, foundW = 0
-      // 	for (const mut of mutations) {
-      // 		if (mut.type == 'width') ++foundW
-      // 		if (mut.type == 'height') ++foundH
-      // 	}
-      // }
-    });
-    test.equal(
-      scatter.Inner.settings.svgw,
-      testWidth,
-      `Chart width = ${scatter.Inner.settings.svgw} should be equal to test width = ${testWidth}`
-    );
-    test.equal(
-      scatter.Inner.settings.svgh,
-      testHeight,
-      `Chart height = ${scatter.Inner.settings.svgh} should be equal to test height = ${testHeight}`
-    );
-  }
-});
-(0, import_tape.default)("Check/uncheck Show axes from menu", function(test) {
-  test.timeoutAfter(4e3);
-  runpp({
-    state: structuredClone(open_state),
-    sampleScatter: {
-      callbacks: { "postRender.test": runTests }
-    }
-  });
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    await showAxes(scatter, true);
-    await showAxes(scatter, false);
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-  async function showAxes(scatter, isvisible) {
-    const opacity = isvisible ? 1 : 0;
-    const axesDiv = await detectStyle({
-      target: scatter.Inner.view.dom.mainDiv.node().querySelector(".sjpcb-scatter-axis"),
-      style: {
-        opacity: `${opacity}`
-      },
-      trigger() {
-        const axesCheckbox = scatter.Inner.view.dom.controlsHolder.select('input[data-testid="showAxes"]');
-        axesCheckbox.property("checked", isvisible);
-        axesCheckbox.node().dispatchEvent(new Event("change"));
-      }
-    });
-    const axesStyle = getComputedStyle(axesDiv[0]);
-    test.equal(axesStyle.opacity, `${opacity}`, `Should ${isvisible ? "show" : "hide"} axes`);
-  }
-});
-(0, import_tape.default)("Click zoom in, zoom out, and reset buttons", function(test) {
-  test.timeoutAfter(1e4);
-  runpp({
-    state: structuredClone(state),
-    sampleScatter: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    await testZoomIn(scatter);
-    await testReset(scatter);
-    await testZoomOut(scatter);
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-  async function testZoomIn(scatter) {
-    const zoomin_bt = scatter.Inner.view.dom.toolsDiv.node().querySelector('div[name="sjpp-zoom-in-btn"]');
-    const m = await detectTransform(scatter, zoomin_bt, 1.2);
-    test.ok(m != null, `Plot should zoom in`);
-  }
-  async function testReset(scatter) {
-    const reset_bt = scatter.Inner.view.dom.toolsDiv.node().querySelector('div[name="sjpp-reset-btn"]');
-    const m = await detectTransform(scatter, reset_bt, 1);
-    test.ok(m != null, `Plot should reset`);
-  }
-  async function testZoomOut(scatter) {
-    const zoomout_bt = scatter.Inner.view.dom.toolsDiv.node().querySelector('div[name="sjpp-zoom-out-btn"]');
-    const m = await detectTransform(scatter, zoomout_bt, 0.8);
-    test.ok(m != null, `Plot should zoom out`);
-  }
-  async function detectTransform(scatter, btn, scale) {
-    const target = await detectAttr({
-      target: scatter.Inner.view.dom.mainDiv.node().querySelector(".sjpcb-scatter-series"),
-      observe: {
-        subtree: true,
-        characterData: true,
-        attributeFilter: ["transform"]
-      },
-      count: 1,
-      trigger() {
-        btn.click();
-      },
-      matcher(mutations) {
-        for (const m of mutations) {
-          if (m.attributeName == "transform" && m.target.attributes[1].value.includes(`scale(${scale})`)) return m;
-        }
-      }
-    });
-    return target;
-  }
-});
-(0, import_tape.default)("colorTW=geneVariant with no groupsetting", function(test) {
-  test.timeoutAfter(6e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "sampleScatter",
-          name: "TermdbTest TSNE",
-          colorTW: { term: { gene: "TP53", name: "TP53", type: "geneVariant" } }
-        }
-      ]
-    },
-    sampleScatter: { callbacks: { "postRender.test": runTests } }
-  });
-  async function runTests(scatter) {
-    const dots = scatter.Inner.view.dom.mainDiv.selectAll(".sjpcb-scatter-series > path").nodes();
-    test.true(
-      dots.find((dot) => dot.getAttribute("fill") == mclass["M"].color),
-      "At least a sample with MISSENSE color was expected"
-    );
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("colorTW=geneVariant with groupsetting", function(test) {
-  test.timeoutAfter(6e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "sampleScatter",
-          name: "TermdbTest TSNE",
-          colorTW: getGeneVariantTw()
-        }
-      ]
-    },
-    sampleScatter: { callbacks: { "postRender.test": runTests } }
-  });
-  async function runTests(scatter) {
-    const dots = scatter.Inner.view.dom.mainDiv.selectAll(".sjpcb-scatter-series > path").nodes();
-    const lab = "TP53 SNV/indel Mutated (somatic)";
-    test.true(
-      dots.find((d) => d.__data__.category == lab),
-      `A dot with category=${lab}`
-    );
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("colorTW=geneVariant with gene list", function(test) {
-  test.timeoutAfter(6e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "sampleScatter",
-          name: "TermdbTest TSNE",
-          colorTW: getGenesetMutTw()
-        }
-      ]
-    },
-    sampleScatter: { callbacks: { "postRender.test": runTests } }
-  });
-  async function runTests(scatter) {
-    const dots = scatter.Inner.view.dom.mainDiv.selectAll(".sjpcb-scatter-series > path").nodes();
-    const lab = "TP53, KRAS, AKT1, BCR SNV/indel Mutated (somatic)";
-    test.true(
-      dots.find((d) => d.__data__.category == lab),
-      `A dot with category=${lab}`
-    );
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("colorTW=ssgsea", function(test) {
-  test.timeoutAfter(6e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "sampleScatter",
-          name: "TermdbTest TSNE",
-          colorTW: getSsgseaTw()
-        }
-      ]
-    },
-    sampleScatter: { callbacks: { "postRender.test": runTests } }
-  });
-  async function runTests(scatter) {
-    const dots = scatter.Inner.view.dom.mainDiv.selectAll(".sjpcb-scatter-series > path").nodes();
-    test.true(
-      dots.find((d) => Number.isFinite(d.__data__.category)),
-      `A dot with category=number`
-    );
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("singlecell map", function(test) {
-  test.timeoutAfter(6e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "sampleScatter",
-          colorTW: getScctTw(),
-          singleCellPlot: { name: "scRNA", sample: { sID: "1_patient" } }
-        }
-      ]
-    },
-    sampleScatter: { callbacks: { "postRender.test": runTests } }
-  });
-  async function runTests(scatter) {
-    const dots = scatter.Inner.view.dom.mainDiv.selectAll(".sjpcb-scatter-series > path").nodes();
-    test.true(dots.length, "some dots are loaded from singlecell map");
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("singlecell geneexp", function(test) {
-  runpp({
-    state: state2scgeneexp,
-    sampleScatter: { callbacks: { "postRender.test": runTests } }
-  });
-  async function runTests(scatter) {
-    const dots = scatter.Inner.view.dom.mainDiv.selectAll(".sjpcb-scatter-series > path").nodes();
-    test.true(dots.length, "some dots are loaded from singlecell map");
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("Disco plot and lollipop", (test) => {
-  test.timeoutAfter(2e3);
-  const holder = getHolder();
-  runpp({
-    holder,
-    state: state2ssgsea,
-    sampleScatter: { callbacks: { "postRender.test": runTests } }
-  });
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    const sampleWithMutDataFile = scatter.Inner.dom.mainDiv.select(".sjpcb-scatter-series").selectAll("path").filter((d) => d.sample === "3416").node();
-    const box = sampleWithMutDataFile.getBoundingClientRect();
-    sampleWithMutDataFile.dispatchEvent(
-      new MouseEvent("click", {
-        bubbles: true,
-        clientX: box.x + box.width / 2,
-        clientY: box.y + box.height / 2
-      })
-    );
-    const chordTexts = await detectGte({
-      elem: holder.node(),
-      selector: ".chord-text",
-      count: 1,
-      trigger: () => {
-        scatter.Inner.dom.tooltip.d.selectAll("button").filter(function() {
-          return this.innerHTML == "Disco";
-        }).node().click();
-      }
-    });
-    const label = [...chordTexts].find((c) => c.__data__?.text === "TP53");
-    if (!label) {
-      test.failt("must have a TP53 gene label");
-    } else {
-      const trackLabelsG = await detectGte({
-        elem: holder.node(),
-        selector: '[data-testid="sja_sample_menu_opener"]',
-        count: 2,
-        trigger: () => {
-          label.dispatchEvent(new MouseEvent("click"));
-        }
-      });
-      await sleep(500);
-      const trackLabels = [...trackLabelsG[0].querySelectorAll("text")];
-      test.equal(
-        trackLabels.filter((t) => t.innerHTML.includes("unknown data source")).length,
-        0,
-        "must not have an error after clicking a Disco plot gene label to launch a genome browser track"
-      );
-      if (test._ok) holder.remove();
-      test.end();
-    }
-  }
-});
-//# sourceMappingURL=scatter.integration.spec-6KRDNHHH.js.map