@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

package/dist/violin.integration.spec-6NF5FDLQ.js

@@ -0,0 +1,1424 @@
+import {
+  getCategoryGroupsetting,
+  getGeneVariantTw,
+  getGenesetMutTw,
+  getSamplelstTw,
+  getScctTw,
+  getScgeneexpTw,
+  getSsgseaTw
+} from "./chunk-A4VLWLYF.js";
+import {
+  detectGte,
+  detectLst,
+  detectOne,
+  sleep,
+  whenVisible
+} from "./chunk-SSPDNHDW.js";
+import {
+  getRunPp
+} from "./chunk-4KPI7PB5.js";
+import {
+  require_tape
+} from "./chunk-QWOE5YTB.js";
+import "./chunk-37ARSZOI.js";
+import "./chunk-BMVLR3TM.js";
+import "./chunk-IKHIY6IZ.js";
+import "./chunk-IENFDUWD.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-ZEJB7CPC.js";
+import "./chunk-MKAF2BHB.js";
+import "./chunk-H4JIENLQ.js";
+import "./chunk-RQ2ZJ66W.js";
+import "./chunk-LO4NMQ7W.js";
+import {
+  fillTermWrapper,
+  filterJoin,
+  getFilterItemByTag
+} from "./chunk-2XPDA6NL.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-GHWHLSUX.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-AY4UBGLC.js";
+import "./chunk-2P6Z7JFC.js";
+import "./chunk-MYWJQRTD.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-B43MTEYB.js";
+import "./chunk-2T7VYQLY.js";
+import {
+  SINGLECELL_CELLTYPE
+} from "./chunk-FDK4UJMN.js";
+import "./chunk-X7GDCYND.js";
+import "./chunk-SJC2C77V.js";
+import "./chunk-C3SYSMNE.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-NMBIT4IK.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// plots/test/violin.integration.spec.js
+var import_tape = __toESM(require_tape(), 1);
+
+// plots/test/helpers.spec.ts
+async function testViolinByCount(test, div, count) {
+  const groups = await detectLst({ elem: div.node(), selector: "path.sjpp-vp-path", count: count * 2 });
+  test.ok(groups, `Detected ${count} violin <path class=sjpp-vp-path>`);
+}
+
+// plots/test/violin.integration.spec.js
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- plots/violin -***-");
+  test.end();
+});
+(0, import_tape.default)("agedx/sex, basic rendering", function(test) {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      plots: [open_state]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    violin.on("postRender.test", null);
+    const legendDiv = violin.Inner.dom.legendDiv;
+    const violinDiv = violin.Inner.dom.violinDiv;
+    const violinDivControls = violin.Inner.dom.controls;
+    const violinDivData = violin.Inner.data.charts;
+    await testViolinByCount(test, violinDiv, 2);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    testPlotTitle(violinDiv, violinDivControls);
+    testPvalue(violin, violinDiv, violinDivData);
+    testDescrStats(violin, legendDiv);
+    await testMedianRendering(violin, violinDiv);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+  function testPlotTitle(violinDiv, violinDivControls) {
+    const label = violinDiv.node().querySelector(".sjpp-numeric-term-label").innerHTML;
+    test.equal(
+      violinDivControls.node().querySelector(".ts_pill").innerHTML = label,
+      label,
+      "Plot title is same as ts-pill label"
+    );
+  }
+  function testPvalue(violin, violinDiv, violinDivData) {
+    const violinPvalueDiv = violinDiv.selectAll(".sjpp-tableHolder");
+    test.equal(violinPvalueDiv.size(), 1, "Should have 1 p-value table");
+    const pvalues = violinDivData[""].pvalues;
+    test.equal(
+      +pvalues[0][2].html,
+      +violinPvalueDiv.node().querySelectorAll(".sjpp_table_item")[5].innerHTML,
+      `Should render correct p-value of ${+violinPvalueDiv.node().querySelectorAll(".sjpp_table_item")[5].innerHTML}.`
+    );
+  }
+  function testDescrStats(violin, legendDiv) {
+    test.equal(
+      +legendDiv.node().querySelectorAll(".legend-row")[0].innerText.split(":")[1],
+      +violin.Inner.config.term.q.descrStats.total.value,
+      "Should render Total n values."
+    );
+    test.equal(
+      +legendDiv.node().querySelectorAll(".legend-row")[1].innerText.split(":")[1],
+      +violin.Inner.config.term.q.descrStats.min.value,
+      "Should render Minimum value."
+    );
+    test.equal(
+      +legendDiv.node().querySelectorAll(".legend-row")[2].innerText.split(":")[1],
+      +violin.Inner.config.term.q.descrStats.p25.value,
+      "Should render 1st quartile value."
+    );
+    test.equal(
+      +legendDiv.node().querySelectorAll(".legend-row")[3].innerText.split(":")[1],
+      +violin.Inner.config.term.q.descrStats.median.value,
+      "Should render Median value."
+    );
+    test.equal(
+      +legendDiv.node().querySelectorAll(".legend-row")[4].innerText.split(":")[1],
+      +violin.Inner.config.term.q.descrStats.p75.value,
+      "Should render 3rd quartile value."
+    );
+    test.equal(
+      +legendDiv.node().querySelectorAll(".legend-row")[5].innerText.split(":")[1],
+      +violin.Inner.config.term.q.descrStats.max.value,
+      "Should render Max value."
+    );
+    test.equal(
+      +legendDiv.node().querySelectorAll(".legend-row")[6].innerText.split(":")[1],
+      +violin.Inner.config.term.q.descrStats.mean.value,
+      "Should render Mean value."
+    );
+    test.equal(
+      +legendDiv.node().querySelectorAll(".legend-row")[7].innerText.split(":")[1],
+      +violin.Inner.config.term.q.descrStats.stdDev.value,
+      "Should render Standard deviation."
+    );
+  }
+  async function testMedianRendering(violin, violinDiv) {
+    const median = await detectGte({
+      elem: violinDiv.node(),
+      selector: ".sjpp-median-line",
+      count: 2
+    });
+    test.ok(median, "Should render median line(s)");
+    test.equal(median.length, violin.Inner.data.charts[""].plots.length, "Should render correct number of median lines");
+    const medianValues = median.map(({ __data__: { summaryStats } }) => {
+      const { value } = summaryStats.median;
+      return value;
+    });
+    const sumStatsValues = violin.Inner.data.charts[""].plots.map(({ summaryStats }) => {
+      const { value } = summaryStats.median;
+      return value;
+    });
+    test.equal(
+      medianValues[0],
+      sumStatsValues[0],
+      `Should render median correctly for plot ${violin.Inner.data.charts[""].plots[0].label}`
+    );
+    test.equal(
+      medianValues[1],
+      sumStatsValues[1],
+      `Should render median correctly for plot ${violin.Inner.data.charts[""].plots[1].label}`
+    );
+  }
+});
+(0, import_tape.default)("agedx/sex, basic controls", function(test) {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      plots: [open_state]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    violin.on("postRender.test", null);
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await changeSvgw(violin, violinDiv);
+    await changeMedianSize(violin, violinDiv);
+    await changeOrientation(violin, violinDiv);
+    await changeDataSymbol(violin, violinDiv);
+    await changeStrokeWidth(violin);
+    await changeSymbolSize(violin);
+    await changeScaleToLog(violin, violinDiv);
+    await changeOverlayTerm(violin, violinDiv);
+    await changeModeToDiscrete(violin);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+  async function changeSvgw(violin, violinDiv) {
+    const svgw = 333;
+    await violin.Inner.app.dispatch({
+      type: "plot_edit",
+      id: violin.Inner.id,
+      config: {
+        settings: {
+          violin: { svgw }
+        }
+      }
+    });
+    test.equal(violin.Inner.app.Inner.state.plots[0].settings.violin.svgw, svgw, "svgw changed in state");
+  }
+  async function changeMedianSize(violin, violinDiv) {
+    const testMedianLength = 10;
+    const testMedianThickness = 10;
+    const medianEle = await detectGte({
+      elem: violinDiv.node(),
+      selector: ".sjpp-median-line",
+      count: 1,
+      async trigger() {
+        await violin.Inner.app.dispatch({
+          type: "plot_edit",
+          id: violin.Inner.id,
+          config: {
+            settings: {
+              violin: {
+                medianLength: testMedianLength,
+                medianThickness: testMedianThickness
+              }
+            }
+          }
+        });
+      }
+    });
+    test.ok(medianEle, "Median exists");
+    test.equal(
+      violin.Inner.app.Inner.state.plots[0].settings.violin.medianLength,
+      testMedianLength,
+      "Should change Median length in state"
+    );
+    test.equal(
+      violin.Inner.app.Inner.state.plots[0].settings.violin.medianLength,
+      testMedianLength,
+      "Should change Median thickness in state"
+    );
+  }
+  async function changeOrientation(violin, violinDiv) {
+    await violin.Inner.app.dispatch({
+      type: "plot_edit",
+      id: violin.Inner.id,
+      config: {
+        settings: {
+          violin: {
+            orientation: "vertical"
+          }
+        }
+      }
+    });
+    test.equal(
+      violin.Inner.app.Inner.state.plots[0].settings.violin.orientation,
+      "vertical",
+      "Should change orientation to vertical in state"
+    );
+  }
+  async function changeDataSymbol(violin, violinDiv) {
+    await violin.Inner.app.dispatch({
+      type: "plot_edit",
+      id: violin.Inner.id,
+      config: {
+        settings: {
+          violin: {
+            datasymbol: "rug"
+          }
+        }
+      }
+    });
+    test.true(
+      violin.Inner.app.Inner.state.plots[0].settings.violin.datasymbol === "rug",
+      "Should change Data Symbol to Ticks"
+    );
+  }
+  async function changeStrokeWidth(violin) {
+    const testStrokeWidth = 1;
+    await violin.Inner.app.dispatch({
+      type: "plot_edit",
+      id: violin.Inner.id,
+      config: {
+        settings: {
+          violin: {
+            strokeWidth: testStrokeWidth
+          }
+        }
+      }
+    });
+    test.true(
+      violin.Inner.app.Inner.state.plots[0].settings.violin.strokeWidth === testStrokeWidth,
+      `Should change stroke width to ${testStrokeWidth}`
+    );
+  }
+  async function changeSymbolSize(violin) {
+    const testSymSize = 10;
+    await violin.Inner.app.dispatch({
+      type: "plot_edit",
+      id: violin.Inner.id,
+      config: {
+        settings: {
+          violin: {
+            radius: testSymSize
+          }
+        }
+      }
+    });
+    test.true(
+      violin.Inner.app.Inner.state.plots[0].settings.violin.radius === testSymSize,
+      `Symbol size changed to ${testSymSize}`
+    );
+  }
+  async function changeOverlayTerm(violin, violinDiv) {
+    const term2 = await fillTermWrapper({ id: "genetic_race" }, violin.Inner.app.vocabApi);
+    await violin.Inner.app.dispatch({
+      type: "plot_edit",
+      id: violin.Inner.id,
+      config: {
+        term2
+      }
+    });
+    test.true(violin.Inner.app.Inner.state.plots[0].term2.term.id === "genetic_race", "Overlay term changed");
+  }
+  async function changeScaleToLog(violin, violinDiv) {
+    const showLogScale = await detectOne({
+      elem: violinDiv.node(),
+      selector: ".sjpp-logscale",
+      async trigger() {
+        await violin.Inner.app.dispatch({
+          type: "plot_edit",
+          id: violin.Inner.id,
+          config: {
+            settings: {
+              violin: {
+                isLogScale: true,
+                plotThickness: 150
+              }
+            }
+          }
+        });
+      }
+    });
+    test.ok(showLogScale, "Log scale exists");
+    test.true(violin.Inner.app.Inner.state.plots[0].settings.violin.isLogScale, "Axis scale rendered in log");
+  }
+  async function changeModeToDiscrete(violin, violinDiv) {
+    violin.Inner.app.dispatch({
+      id: violin.Inner.id,
+      type: "plot_edit",
+      config: {
+        term: await fillTermWrapper({ id: "agedx", q: { mode: "discrete" } }, violin.Inner.app.vocabApi)
+      }
+    });
+    await sleep(20);
+    test.true(violin.Inner.app.Inner.state.plots[0].term.q.mode === "discrete", "q.mode changed to 'Discrete' ");
+  }
+});
+(0, import_tape.default)("test label clicking, filtering and hovering", function(test) {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      nav: {
+        header_mode: "hide_search"
+      },
+      plots: [open_state]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    violin.on("postRender.test", null);
+    const violinDiv = violin.Inner.dom.violinDiv;
+    const violinDivData = violin.Inner.data.charts[""].plots;
+    const violinSettings = violin.Inner.config.settings.violin;
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    await testFiltering(violin, violinSettings, violinDivData);
+    await testLabelHoverClick(test, violin, violinDiv, 1);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+  async function testFiltering(violin) {
+    const tvslst = {
+      type: "tvslst",
+      in: true,
+      join: "and",
+      lst: [
+        {
+          tvs: {
+            term: {
+              groupsetting: { disabled: true },
+              id: "sex",
+              isleaf: true,
+              name: "Sex",
+              type: "categorical",
+              values: {
+                1: { label: "Male" },
+                2: { label: "Female" }
+              }
+            },
+            values: [{ key: "2" }]
+          },
+          type: "tvs"
+        },
+        {
+          type: "tvs",
+          tvs: {
+            ranges: [
+              {
+                start: 12.289737495475805,
+                stop: 16.794964344698805
+              }
+            ],
+            term: {
+              id: "agedx",
+              isleaf: true,
+              name: "Age (years) at Cancer Diagnosis",
+              type: "float",
+              bins: {
+                default: {
+                  type: "regular-bin",
+                  bin_size: 5,
+                  startinclusive: true,
+                  first_bin: {
+                    startunbounded: true,
+                    stop: 5
+                  }
+                },
+                label_offset: 1
+              }
+            }
+          }
+        }
+      ]
+    };
+    const filterUiRoot = getFilterItemByTag(violin.Inner.state.termfilter.filter, "filterUiRoot");
+    const filter = filterJoin([filterUiRoot, tvslst]);
+    filter.tag = "filterUiRoot";
+    await violin.Inner.app.dispatch({
+      type: "filter_replace",
+      filter
+    });
+    test.ok(true, "Filtering works as expected upon given range(start, stop) of values");
+  }
+});
+(0, import_tape.default)("test hide option on label clicking", function(test) {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      nav: {
+        header_mode: "hide_search"
+      },
+      plots: [open_state]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    violin.on("postRender.test", null);
+    const legendDiv = violin.Inner.dom.legendDiv;
+    const violinDiv = violin.Inner.dom.violinDiv;
+    testHideOption(violin, legendDiv);
+    await testHiddenValues(violin, legendDiv, violinDiv);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+  function testHideOption(violin) {
+    const q = {
+      hiddenValues: { [violin.Inner.data.charts[""].plots[0].label]: 1 },
+      isAtomic: true,
+      type: "values"
+    };
+    violin.Inner.app.dispatch({
+      type: "plot_edit",
+      id: violin.Inner.id,
+      config: {
+        term2: {
+          isAtomic: true,
+          id: violin.Inner.config.term2.id,
+          term: violin.Inner.config.term2.term,
+          q
+        }
+      }
+    });
+    test.ok(true, "label Clicking and Hide option ok!");
+  }
+  async function testHiddenValues(violin, legendDiv, violinDiv) {
+    const htmlLegends = await detectGte({ elem: legendDiv.node(), selector: ".sjpp-htmlLegend" });
+    test.ok(htmlLegends, "Legend exists");
+    const hiddenKeys = Object.keys(violin.Inner.config.term2.q.hiddenValues);
+    test.equal(
+      Object.keys(violin.Inner.config.term2.q.hiddenValues)[0],
+      htmlLegends[8].innerHTML,
+      "q.hiddenValues match legend"
+    );
+    const unhideLegendValue = htmlLegends.filter((c) => hiddenKeys.find((k) => c.__data__.text === k));
+    unhideLegendValue[0].dispatchEvent(new Event("click"), { bubbles: true });
+    const hiddenValueRendered = await detectGte({
+      elem: violinDiv.node(),
+      selector: '[data-testid="sjpp-violin-label"]',
+      count: 2
+    });
+    test.ok(hiddenValueRendered, "hidden value rendered");
+    test.equal(
+      hiddenValueRendered[0].__data__.label,
+      unhideLegendValue[0].innerHTML,
+      "Clicking on hidden legend value renders the hidden plot"
+    );
+  }
+});
+(0, import_tape.default)("term1=categorical, term2=numeric", function(test) {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: { id: "diaggrp" },
+          term2: { id: "agedx", q: { mode: "continuous" } }
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testLabelHoverClick(test, violin, violinDiv, 7);
+    await testViolinByCount(test, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=numeric, term2=cat groupsetting", function(test) {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: { id: "agedx", q: { mode: "continuous" } },
+          term2: getCategoryGroupsetting()
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    await testViolinByCount(test, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=numeric, term2=survival", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: { id: "agedx", q: { mode: "continuous" } },
+          term2: { id: "efs" }
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 2);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=numeric, term2=geneVariant", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: { id: "agedx", q: { mode: "continuous" } },
+          term2: getGeneVariantTw()
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 1);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=numeric, term2=geneVariant geneset", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: { id: "agedx", q: { mode: "continuous" } },
+          term2: getGenesetMutTw()
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 1);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=numeric, term2=condition", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: { id: "agedx", q: { mode: "continuous" } },
+          term2: { id: "Hearing loss" }
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 1);
+    await testConditionTermOrder(violin, violinDiv);
+    await testLabelHoverClick(test, violin, violinDiv, 5);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+  async function testConditionTermOrder(violin, violinDiv) {
+    const groups = await detectGte({ elem: violinDiv.node(), selector: ".sjpp-vp-path", count: 1 });
+    test.ok(groups, "Condition groups exist");
+    test.deepEqual(
+      groups.filter((k, i) => i % 2 == 0).map((k) => k.__data__.label),
+      violin.Inner.data.charts[""].plots.filter((plot) => plot.plotValueCount > 5).map((k) => k.label),
+      "Order of conditional categories in term2 is accurate"
+    );
+  }
+});
+(0, import_tape.default)("term1=geneExp, term2=categorical", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: {
+            term: { gene: "TP53", name: "TP53", type: "geneExpression" },
+            q: { mode: "continuous" }
+          },
+          term2: { id: "diaggrp" }
+        }
+      ]
+    },
+    violin: { callbacks: { "postRender.test": runTests } }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 2);
+    await testLabelHoverClick(test, violin, violinDiv, 7);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=geneExp, term2=cat groupsetting", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: {
+            term: { gene: "TP53", name: "TP53", type: "geneExpression" },
+            q: { mode: "continuous" }
+          },
+          term2: getCategoryGroupsetting()
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 2);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=geneExp, term2=geneVariant", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: {
+            term: { gene: "TP53", name: "TP53", type: "geneExpression" },
+            q: { mode: "continuous" }
+          },
+          term2: getGeneVariantTw()
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 1);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=geneExp, term2=geneVariant geneset", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: {
+            term: { gene: "TP53", name: "TP53", type: "geneExpression" },
+            q: { mode: "continuous" }
+          },
+          term2: getGenesetMutTw()
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 1);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=ssgsea, term2=categorical", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: getSsgseaTw(),
+          term2: {
+            id: "diaggrp"
+          }
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 2);
+    await testLabelHoverClick(test, violin, violinDiv, 7);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=ssgsea, term2=cat groupsetting", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: getSsgseaTw(),
+          term2: getCategoryGroupsetting()
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 2);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=ssgsea, term2=geneVariant", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: getSsgseaTw(),
+          term2: getGeneVariantTw()
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 1);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=ssgsea, term2=geneVariant geneset", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: getSsgseaTw(),
+          term2: getGenesetMutTw()
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 1);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+import_tape.default.skip("term1=geneExp, term2=survival (SKIPPED)", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: {
+            term: { gene: "TP53", name: "TP53", type: "geneExpression" },
+            q: { mode: "continuous" }
+          },
+          term2: {
+            id: "efs"
+          }
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolin(violin, violinDiv);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+  async function testViolin(violin, violinDiv) {
+    const groups = await detectGte({ elem: violinDiv.node(), selector: ".sjpp-vp-path", count: 2 });
+    test.ok(groups, "survival groups exist");
+  }
+});
+(0, import_tape.default)("term1=numeric, term2=samplelst", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: { id: "agedx", q: { mode: "continuous" } },
+          term2: getSamplelstTw()
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 2);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=geneexp, term2=samplelst", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: {
+            term: { gene: "TP53", name: "TP53", type: "geneExpression" },
+            q: { mode: "continuous" }
+          },
+          term2: getSamplelstTw()
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 2);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=ssgsea, term2=samplelst", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: getSsgseaTw(),
+          term2: getSamplelstTw()
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 2);
+    await testLabelHoverClick(test, violin, violinDiv, 2);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term=agedx, term2=geneExp with regular bins", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: {
+            id: "agedx",
+            q: { mode: "continuous" }
+          },
+          term2: {
+            term: { gene: "TP53", name: "TP53", type: "geneExpression" },
+            q: {
+              type: "regular-bin",
+              startinclusive: true,
+              bin_size: 5,
+              first_bin: {
+                stop: 5
+              },
+              last_bin: {
+                start: 35
+              },
+              mode: "discrete"
+            }
+          }
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 4);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term=agedx, term2=geneExp with custom bins", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: { id: "agedx", q: { mode: "continuous" } },
+          term2: {
+            term: { gene: "TP53", type: "geneExpression", bins: { type: "custom-bin" } },
+            q: {
+              type: "custom-bin",
+              mode: "discrete",
+              lst: [
+                {
+                  startunbounded: true,
+                  stop: 10,
+                  startinclusive: true,
+                  stopinclusive: false,
+                  label: "<10"
+                },
+                {
+                  start: 10,
+                  startinclusive: true,
+                  stopinclusive: false,
+                  stop: 15,
+                  label: "10 to <15"
+                },
+                {
+                  start: 15,
+                  startinclusive: true,
+                  stopinclusive: false,
+                  stopunbounded: true,
+                  label: "\u226515"
+                }
+              ],
+              startinclusive: true
+            }
+          }
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 3);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("term1=numeric, term0=categorical", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: {
+            id: "agedx",
+            q: { mode: "continuous" }
+          },
+          term0: {
+            id: "sex",
+            isAtomic: true
+          }
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolin(violin, violinDiv);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+  async function testViolin(violin, violinDiv) {
+    const chartDivs = await detectGte({ elem: violinDiv.node(), selector: ".sjpp-vp-chartDiv" });
+    test.equal(chartDivs.length, 2, "Should have 2 charts");
+    const violinPaths = await detectGte({ elem: violinDiv.node(), selector: ".sjpp-vp-path" });
+    test.equal(violinPaths.length, 4, "Should have 4 paths");
+  }
+});
+(0, import_tape.default)("term1=numeric, term2=numeric, term0=categorical", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: {
+            id: "agedx",
+            q: { mode: "continuous" }
+          },
+          term2: {
+            id: "aaclassic_5",
+            isAtomic: true
+          },
+          term0: {
+            id: "sex",
+            isAtomic: true
+          }
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolin(violin, violinDiv);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+  async function testViolin(violin, violinDiv) {
+    const chartDivs = await detectGte({ elem: violinDiv.node(), selector: ".sjpp-vp-chartDiv" });
+    test.equal(chartDivs.length, 2, "Should have 2 charts");
+    const violinPaths = await detectGte({ elem: violinDiv.node(), selector: ".sjpp-vp-path" });
+    test.equal(violinPaths.length, 6, "Should have 6 paths");
+  }
+});
+(0, import_tape.default)("test uncomputable categories legend", function(test) {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      nav: {
+        header_mode: "hide_search"
+      },
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: {
+            id: "aaclassic_5",
+            isAtomic: true,
+            q: {
+              mode: "continuous"
+            }
+          }
+        }
+      ]
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    const legendDiv = violin.Inner.dom.legendDiv;
+    violin.on("postRender.test", null);
+    await testUncomputableCategories(violin, legendDiv);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+  async function testUncomputableCategories(violin, legendDiv) {
+    const keys = Object.keys(violin.Inner.data.uncomputableValues);
+    const categories = await detectGte({ elem: legendDiv.node(), selector: ".legend-row", count: 9 });
+    test.ok(categories, "Uncomputable categories exist");
+    const uncomputableLegend = categories.filter((c) => keys.find((k) => c.__data__.text.startsWith(k)));
+    test.equal(keys.length, uncomputableLegend.length, "should have the correct number of uncomputable legend entries");
+    test.equal(
+      uncomputableLegend.find((c) => c.__data__.text.startsWith(keys[0]))?.__data__.text.split(",").pop(),
+      " n = " + violin.Inner.data.uncomputableValues[keys[0]],
+      `Uncomputable category '${keys[0]}' rendered with the correct count`
+    );
+    test.equal(
+      uncomputableLegend.find((c) => c.__data__.text.startsWith(keys[1]))?.__data__.text.split(",").pop(),
+      " n = " + violin.Inner.data.uncomputableValues[keys[1]],
+      `Uncomputable category '${keys[1]}' rendered with the correct count`
+    );
+  }
+});
+(0, import_tape.default)("Load linear regression-violin UI", function(test) {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "regression",
+          hasUnsubmittedEdits: true,
+          regressionType: "linear",
+          outcome: {
+            id: "hrtavg",
+            isAtomic: true
+          }
+        }
+      ]
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(regression) {
+    regression.on("postRender.test", null);
+    await testViolinByCount(test, regression.Inner.inputs.outcome.dom.holder, 1);
+    if (test._ok) regression.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("Test violin render with term1=singleCellExpression, term2=singleCellCellType", function(test) {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          term: getScgeneexpTw(),
+          term2: getScctTw()
+        }
+      ],
+      vocab: {
+        genome: "hg38-test",
+        dslabel: "TermdbTest"
+      }
+    },
+    violin: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(violin) {
+    violin.on("postRender.test", null);
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 3);
+    await testLabelHoverClick(test, violin, violinDiv, 3);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("Test violin rendering with term1=dnameth, term2=geneExp", function(test) {
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "summary",
+          childType: "violin",
+          term: {
+            term: {
+              type: "dnaMethylation",
+              chr: "chr17",
+              start: 7673484,
+              stop: 7681953,
+              genomicFeatureType: "promoter"
+            },
+            q: { mode: "continuous" }
+          },
+          term2: { term: { gene: "TP53", name: "TP53", type: "geneExpression" } }
+        }
+      ]
+    },
+    violin: { callbacks: { "postRender.test": runTests } }
+  });
+  async function runTests(violin) {
+    const violinDiv = violin.Inner.dom.violinDiv;
+    await testViolinByCount(test, violinDiv, 4);
+    await testLabelHoverClick(test, violin, violinDiv, 8);
+    if (test._ok) violin.Inner.app.destroy();
+    test.end();
+  }
+});
+var runpp = getRunPp("mass", {
+  state: {
+    nav: { activeTab: 1 },
+    vocab: { dslabel: "TermdbTest", genome: "hg38-test" }
+  },
+  debug: 1
+});
+var open_state = {
+  chartType: "summary",
+  childType: "violin",
+  term: {
+    id: "agedx",
+    q: { mode: "continuous" }
+  },
+  term2: { id: "sex" }
+};
+async function testLabelHoverClick(test, violin, violinDiv, labelcount) {
+  const labs = await detectLst({
+    elem: violinDiv.node(),
+    selector: '[data-testid="sjpp-violin-label"]',
+    count: labelcount
+  });
+  test.ok(labs, `Detected ${labelcount} violin labels`);
+  for (let i = 0; i < labelcount; i++) {
+    const n = violin.Inner.data.charts[""].plots[i].values.length;
+    test.ok(labs[i].innerHTML.endsWith("n=" + n), `violin #${i} label text ends with "n=${n}"`);
+  }
+  labs[0].dispatchEvent(new Event("mouseover"), { bubbles: true });
+  {
+    const tip2 = violin.Inner.dom.hovertip;
+    await whenVisible(tip2.d);
+    const table = await detectOne({ elem: tip2.dnode, selector: '[data-testid="sja_simpletable"]' });
+    test.pass("summary stat table found in hover tooltip");
+    tip2.hide();
+  }
+  labs[0].dispatchEvent(new Event("click"), { bubbles: true });
+  const tip = violin.Inner.dom.clicktip;
+  if (!violin.Inner.state.config.term2 || violin.Inner.state.config.term2.term.type == SINGLECELL_CELLTYPE) {
+    test.equal(tip.d.style("display"), "none", "Clicked on first label and app.tip will not show");
+  } else {
+    await whenVisible(tip.d);
+    test.pass("Clicked on first label and app.tip will show");
+    await detectOne({ elem: tip.dnode, selector: '[data-testid="sjpp-violinLabOpt-addf"]' });
+    test.pass("Add filter option is in menu");
+    await detectOne({ elem: tip.dnode, selector: '[data-testid="sjpp-violinLabOpt-hide"]' });
+    test.pass("Hide option is in menu");
+    const lab = await detectOne({ elem: tip.dnode, selector: '[data-testid="sjpp-violinLabOpt-list"]' });
+    test.pass("List option is in menu");
+    await whenVisible(violin.Inner.dom.sampletabletip.d);
+    lab.dispatchEvent(new Event("click"));
+    await detectOne({ elem: violin.Inner.dom.sampletabletip.dnode, selector: '[data-testid="sjpp-listsampletable"]' });
+    test.pass('Tip with sample table displayed after clicking "List sample"');
+    violin.Inner.dom.sampletabletip.hide();
+    tip.hide();
+  }
+}
+//# sourceMappingURL=violin.integration.spec-6NF5FDLQ.js.map