@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/cuminc.integration.spec-UZA7BDTB.js

@@ -1,676 +0,0 @@
-import {
-  getRunPp
-} from "./chunk-ZVSXHCGP.js";
-import {
-  detectGte
-} from "./chunk-SSPDNHDW.js";
-import {
-  termjson
-} from "./chunk-HUA2EFQO.js";
-import {
-  require_tape
-} from "./chunk-QWOE5YTB.js";
-import "./chunk-EHXI36HJ.js";
-import "./chunk-FDOSJKDA.js";
-import "./chunk-OLUDD6EC.js";
-import "./chunk-65YTZS3R.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-LOMVTHAM.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-AQ4OP4GR.js";
-import "./chunk-MSW7OS2O.js";
-import "./chunk-ENP4FLOX.js";
-import "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// plots/test/cuminc.integration.spec.js
-var import_tape = __toESM(require_tape(), 1);
-var runpp = getRunPp("mass", {
-  state: {
-    nav: {
-      header_mode: "hide_search",
-      activeTab: 1
-    },
-    dslabel: "TermdbTest",
-    genome: "hg38-test"
-  },
-  debug: 1
-});
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- plots/cuminc -***-");
-  test.end();
-});
-(0, import_tape.default)("term1=Cardiac dysrhythmia", function(test) {
-  test.timeoutAfter(1e4);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "cuminc",
-          term: { id: "Cardiac dysrhythmia" },
-          settings: { cuminc: { minSampleSize: 1, minAtRisk: 0 } }
-        }
-      ]
-    },
-    cuminc: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(cuminc) {
-    const cumincDiv = cuminc.Inner.dom.chartsDiv;
-    test.equal(cumincDiv && cumincDiv.selectAll(".sjpcb-cuminc-series").size(), 1, "should render 1 cuminc series g");
-    test.equal(
-      cumincDiv && cumincDiv.selectAll(".sjpcb-cuminc-series path").size(),
-      2,
-      "should render 2 cuminc series paths for estimate line and 95% CI area"
-    );
-    test.equal(cumincDiv.selectAll(".sjpcb-cuminc-title").size(), 1, `Should render title above chart`);
-    test.equal(cumincDiv.selectAll(".sjpp-cuminc-atrisk").size(), 1, `Should render 'Number at risk' table below chart`);
-    if (test._ok) cuminc.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("term1=Cardiovascular System, filter=ALL", function(test) {
-  test.timeoutAfter(1e4);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "cuminc",
-          term: { id: "Cardiovascular System" },
-          settings: { cuminc: { minSampleSize: 1, minAtRisk: 0 } }
-        }
-      ],
-      termfilter: {
-        filter: {
-          type: "tvslst",
-          join: "",
-          in: true,
-          lst: [
-            {
-              type: "tvs",
-              tvs: {
-                term: { id: "diaggrp" },
-                values: [{ key: "Acute lymphoblastic leukemia", label: "Acute lymphoblastic leukemia" }]
-              }
-            }
-          ]
-        }
-      }
-    },
-    cuminc: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(plot) {
-    const div = plot.Inner.dom.chartsDiv;
-    test.equal(div.selectAll(".sjpcb-cuminc-series").size(), 1, "should render 1 cuminc series <g>");
-    test.equal(
-      div.selectAll(".sjpcb-cuminc-series path").size(),
-      2,
-      "should render 2 cuminc series paths for estimate line and 95% CI area"
-    );
-    if (test._ok) plot.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("term1=Cardiovascular System, term2=agedx", function(test) {
-  test.timeoutAfter(1e4);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "cuminc",
-          term: { id: "Cardiovascular System" },
-          term2: { id: "agedx" },
-          settings: { cuminc: { minSampleSize: 1, minAtRisk: 0 } }
-        }
-      ]
-    },
-    cuminc: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(cuminc) {
-    const div = cuminc.Inner.dom.chartsDiv;
-    test.equal(div.selectAll(".sjpcb-cuminc-series").size(), 2, "should render 2 cuminc series <g>");
-    test.equal(
-      div.selectAll(".sjpcb-cuminc-series path").size(),
-      4,
-      "should render 4 cuminc series paths for estimate line and 95% CI area"
-    );
-    const legend = div.selectAll(".pp-cuminc-chartLegends").node();
-    test.ok(legend, `Should render chart legend`);
-    const numRiskRowLabels = div.selectAll('[data-testid="sjpp-atrisk-seriesId"]').nodes();
-    for (const [i, d] of legend.__data__.visibleSerieses.entries()) {
-      if (cuminc.Inner.legendData[0].items[i].seriesId != d.seriesId)
-        test.fail(
-          `Missing or mismatched series found in legend, series = '${cuminc.Inner.legendData[0].items[i].seriesId}'`
-        );
-      else if (numRiskRowLabels[i].__data__.seriesId != d.seriesId)
-        test.fail(
-          `Missing or mismatched series found in 'Number at risk' table, series = '${numRiskRowLabels[i].__data__.seriesId}'`
-        );
-      else test.pass(`Should display series = '${d.seriesId}' in both legend and 'Number at risk' table`);
-    }
-    if (test._ok) cuminc.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("term1=Cardiovascular System, term0=sex", (test) => {
-  test.timeoutAfter(5e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "cuminc",
-          term: { id: "Cardiovascular System" },
-          term0: { id: "sex" },
-          settings: { cuminc: { minSampleSize: 1, minAtRisk: 0 } }
-        }
-      ]
-    },
-    cuminc: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(cuminc) {
-    cuminc.on("postRender.test", null);
-    const cumincDiv = cuminc.Inner.dom.chartsDiv;
-    const term0Values = cuminc.Inner.config.term0.term.values;
-    test.equal(
-      cumincDiv.selectAll(".pp-cuminc-chart").size(),
-      Object.keys(term0Values).length,
-      `Should render ${Object.keys(term0Values).length} cuminc charts`
-    );
-    test.equal(
-      cumincDiv.selectAll(".sjpp-cuminc-atrisk").size(),
-      Object.keys(term0Values).length,
-      `Should render 'Number at risk' tables below chart`
-    );
-    const titleNodes = cumincDiv.selectAll(".sjpcb-cuminc-title").nodes();
-    for (const v of Object.values(term0Values)) {
-      if (!titleNodes.some((d) => d.innerText == v.label)) test.fail(`Missing title for term0 value = ${v.label}`);
-    }
-    if (test._ok) cuminc.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("term1 = Cardiovascular System, term2 = agedx, numeric regular bins", (test) => {
-  test.timeoutAfter(1e4);
-  const testBinSize = 5;
-  const testStop = 5;
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "cuminc",
-          term: { id: "Cardiovascular System" },
-          term2: {
-            id: "agedx",
-            name: "Age (years) at Cancer Diagnosis",
-            type: "float",
-            bins: {
-              default: {
-                type: "regular-bin",
-                bin_size: testBinSize,
-                startinclusive: true,
-                first_bin: {
-                  startunbounded: true,
-                  stop: testStop
-                }
-              },
-              label_offset: 1
-            }
-          },
-          settings: {
-            cuminc: { minSampleSize: 1, minAtRisk: 0 }
-          }
-        }
-      ]
-    },
-    cuminc: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(cuminc) {
-    cuminc.on("postRender.test", null);
-    const div = cuminc.Inner.dom.chartsDiv;
-    test.equal(cuminc.Inner.config.term2.q.type, "regular-bin", `Should correctly pass 'regular-bin' to config`);
-    test.equal(
-      cuminc.Inner.config.term2.q.bin_size,
-      testBinSize,
-      `Should correctly pass q.bin_size = ${testBinSize} to config`
-    );
-    test.equal(
-      cuminc.Inner.config.term2.q.first_bin.stop,
-      testStop,
-      `Should correctly pass q.first_bin.stop = ${testStop} to config`
-    );
-    const config = structuredClone(cuminc.Inner.config);
-    const expectedCount = cuminc.Inner.uniqueSeriesIds.size;
-    const cumincCurves = await detectGte({
-      elem: div.node(),
-      selector: ".sjpcb-cuminc-series",
-      count: expectedCount,
-      async trigger() {
-        config.term2.q.bin_size = 3;
-        config.term2.q.first_bin.stop = 1;
-        await cuminc.Inner.app.dispatch({
-          type: "plot_edit",
-          id: cuminc.Inner.id,
-          config
-        });
-      },
-      matcher(mutations) {
-        const changedSeries = mutations.filter(
-          (m) => m.previousSibling != null && cuminc.Inner.uniqueSeriesIds.has(m.target.__data__.seriesId)
-        );
-        if (changedSeries.length >= expectedCount) return changedSeries.map((d) => d.target);
-      }
-    });
-    test.equal(cumincCurves.length, expectedCount, `Should update ${expectedCount} curves in plot`);
-    const numRiskRowLabels = div.selectAll('[data-testid="sjpp-atrisk-seriesId"]').nodes();
-    const foundNewLabels = numRiskRowLabels.filter((l) => cuminc.Inner.uniqueSeriesIds.has(l.__data__.seriesId));
-    test.equal(foundNewLabels.length, expectedCount, `Should update ${expectedCount} labels in Number at risk table`);
-    if (test._ok) cuminc.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("term1 = Cardiovascular System, term0 = agedx, numeric regular bins", (test) => {
-  test.timeoutAfter(5e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "cuminc",
-          term: { id: "Cardiovascular System" },
-          term0: {
-            id: "agedx",
-            term: {
-              type: "float",
-              bins: {
-                default: {
-                  type: "regular-bin",
-                  bin_size: 5,
-                  startinclusive: true,
-                  first_bin: {
-                    startunbounded: true,
-                    stop: 5
-                  },
-                  label_offset: 1
-                },
-                label_offset: 1
-              },
-              name: "Age (years) at Cancer Diagnosis",
-              id: "agedx"
-              // isleaf: true,
-              // values: {},
-              // included_types: [
-              // 	'float'
-              // ],
-              // child_types: []
-            },
-            q: {
-              isAtomic: true,
-              mode: "discrete",
-              type: "regular-bin"
-              // type: 'custom-bin',
-              // lst: [
-              // 	{
-              // 		startunbounded: true,
-              // 		stop: 8.164619357749999,
-              // 		stopinclusive: false,
-              // 		label: '<8.164619357749999'
-              // 	},
-              // 	{
-              // 		start: 8.164619357749999,
-              // 		startinclusive: true,
-              // 		stopunbounded: true,
-              // 		label: '≥8.164619357749999'
-              // 	}
-              // ],
-              // hiddenValues: {}
-            }
-          },
-          settings: {
-            cuminc: { minSampleSize: 1, minAtRisk: 0 },
-            controls: {
-              term0: { id: "agedx", term: termjson["agedx"] }
-            }
-          }
-        }
-      ]
-    },
-    cuminc: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(cuminc) {
-    cuminc.on("postRender.test", null);
-    test.end();
-  }
-});
-(0, import_tape.default)("term1 = Cardiovascular System, term2 = agedx, numeric custom bins", (test) => {
-  test.timeoutAfter(1e4);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "cuminc",
-          term: { id: "Cardiovascular System" },
-          term2: {
-            id: "agedx",
-            q: {
-              type: "custom-bin",
-              mode: "discrete",
-              lst: [
-                { startunbounded: true, stop: 7, stopinclusive: false, label: "<7" },
-                { startinclusive: true, stopinclusive: true, start: 7, stop: 12, label: "7 to 12" },
-                { start: 12, startinclusive: false, stopunbounded: true, label: ">12" }
-              ]
-            }
-          },
-          settings: {
-            cuminc: { minSampleSize: 1, minAtRisk: 0 }
-          }
-        }
-      ]
-    },
-    cuminc: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(cuminc) {
-    cuminc.on("postRender.test", null);
-    const inner = cuminc.Inner;
-    const div = inner.dom.chartsDiv;
-    test.equal(inner?.config.term2.q.type, "custom-bin", `Should correctly pass 'custom-bin' to config`);
-    const config = structuredClone(cuminc.Inner.config);
-    const expectedCount = cuminc.Inner.uniqueSeriesIds.size;
-    const cumincCurves = await detectGte({
-      elem: div.node(),
-      selector: ".sjpcb-cuminc-series",
-      count: expectedCount,
-      async trigger() {
-        config.term2.q.lst[2] = { startinclusive: true, stopinclusive: true, start: 12, stop: 15, label: "12 to 15" };
-        config.term2.q.lst.push({ start: 15, startinclusive: false, stopunbounded: true, label: ">15" });
-        await cuminc.Inner.app.dispatch({
-          type: "plot_edit",
-          id: inner.id,
-          config
-        });
-      },
-      matcher(mutations) {
-        const changedSeries = mutations.filter(
-          (m) => m.previousSibling != null && inner.uniqueSeriesIds.has(m.target.__data__.seriesId)
-        );
-        if (changedSeries.length >= expectedCount) return changedSeries.map((d) => d.target);
-      }
-    });
-    test.equal(cumincCurves.length, expectedCount, `Should update ${expectedCount} curves in plot`);
-    const numRiskRowLabels = div.selectAll('[data-testid="sjpp-atrisk-seriesId"]').nodes();
-    const foundNewLabels = numRiskRowLabels.filter((l) => inner.uniqueSeriesIds.has(l.__data__.seriesId));
-    test.equal(foundNewLabels.length, expectedCount, `Should update ${expectedCount} labels in Number at risk table`);
-    if (test._ok) inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("term1 = Cardiovascular System, term0 = agedx, numeric custom bins", (test) => {
-  test.timeoutAfter(1e4);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "cuminc",
-          term: { id: "Cardiovascular System" },
-          term0: {
-            id: "agedx",
-            term: {
-              type: "float",
-              bins: {
-                default: {
-                  type: "regular-bin",
-                  bin_size: 5,
-                  startinclusive: true,
-                  first_bin: {
-                    startunbounded: true,
-                    stop: 5
-                  },
-                  label_offset: 1
-                },
-                label_offset: 1
-              },
-              name: "Age (years) at Cancer Diagnosis",
-              id: "agedx"
-            },
-            q: {
-              isAtomic: true,
-              mode: "discrete",
-              type: "custom-bin",
-              lst: [
-                {
-                  startunbounded: true,
-                  stop: 12,
-                  stopinclusive: false,
-                  label: "<12"
-                },
-                {
-                  start: 12,
-                  startinclusive: true,
-                  stopunbounded: true,
-                  label: "\u226512"
-                }
-              ],
-              hiddenValues: {}
-            }
-          },
-          settings: {
-            cuminc: { minSampleSize: 1, minAtRisk: 0 }
-          }
-        }
-      ]
-    },
-    cuminc: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(cuminc) {
-    cuminc.on("postRender.test", null);
-    const inner = cuminc.Inner;
-    const div = cuminc.Inner.dom.chartsDiv;
-    test.equal(inner.config.term0.q.type, "custom-bin", `Should correctly pass 'custom-bin' to config`);
-    const config = structuredClone(inner.config);
-    const chartIds2Check = /* @__PURE__ */ new Set();
-    const cumincCurves = await detectGte({
-      target: div.node(),
-      selector: "g.sjpcb-cuminc-mainG",
-      async trigger() {
-        config.term0.q.lst[0] = { startunbounded: true, stop: 15, stopinclusive: false, label: "<15" };
-        config.term0.q.lst[1] = { start: 15, startinclusive: false, stopunbounded: true, label: ">15" };
-        config.term0.q.lst.forEach((d) => chartIds2Check.add(d.label));
-        await inner.app.dispatch({
-          type: "plot_edit",
-          id: inner.id,
-          config
-        });
-      },
-      matcher(mutations) {
-        const changedSeries = mutations.filter(
-          (m) => m.attributeName == "transform" && chartIds2Check.has(m.target.__data__.chartId)
-        );
-        if (changedSeries.length >= chartIds2Check.size) return changedSeries.map((d) => d.target);
-      }
-    });
-    test.equal(cumincCurves.length, chartIds2Check.size, `Should update ${chartIds2Check.size} plots`);
-    if (test._ok) inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("skipped series", function(test) {
-  test.timeoutAfter(1e4);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "cuminc",
-          term: { id: "Cardiovascular System" },
-          term2: { id: "genetic_race" },
-          settings: {
-            cuminc: { minSampleSize: 10, minAtRisk: 0 }
-          }
-        }
-      ]
-    },
-    cuminc: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(cuminc) {
-    const skippedDivs = cuminc.Inner.dom.chartsDiv.select(".pp-cuminc-chartLegends").selectAll(".pp-cuminc-chartLegends-skipped");
-    test.equal(skippedDivs && skippedDivs.size(), 1, "should render 1 skipped series");
-    if (test._ok) cuminc.Inner.app.destroy();
-    test.end();
-  }
-});
-import_tape.default.skip("term1 = Cardiovascular System, term2 = samplelst", function(test) {
-  test.timeoutAfter(5e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "cuminc",
-          term: { id: "Cardiovascular System" },
-          term2: {
-            term: {
-              name: "Samplelst term",
-              type: "samplelst",
-              values: {
-                "Group 1": {
-                  key: "Group 1",
-                  label: "Test 1",
-                  inuse: false,
-                  list: [
-                    { sampleId: 1, sample: 1 },
-                    { sampleId: 2, sample: 2 }
-                  ]
-                },
-                "Group 2": {
-                  key: "Group 2",
-                  label: "Test 2",
-                  inuse: false,
-                  list: [
-                    { sampleId: 3, sample: 3 },
-                    { sampleId: 4, sample: 4 },
-                    { sampleId: 5, sample: 5 }
-                  ]
-                },
-                "Group 3": { key: "Group 3", label: "Test 3", inuse: false, list: [{ sampleId: 6, sample: 6 }] }
-              }
-            },
-            q: {
-              groups: [
-                {
-                  name: "Group 1",
-                  in: false,
-                  values: [
-                    { sampleId: 1, sample: 1 },
-                    { sampleId: 2, sample: 2 }
-                  ]
-                },
-                {
-                  name: "Group 2",
-                  in: false,
-                  values: [
-                    { sampleId: 3, sample: 3 },
-                    { sampleId: 4, sample: 4 },
-                    { sampleId: 5, sample: 5 }
-                  ]
-                },
-                {
-                  name: "Group 3",
-                  in: false,
-                  values: [{ sampleId: 6, sample: 6 }]
-                }
-              ]
-            }
-          },
-          settings: {
-            cuminc: { minSampleSize: 1, minAtRisk: 0 }
-          }
-        }
-      ]
-    },
-    cuminc: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(cuminc) {
-    cuminc.on("postRender.test", null);
-    const valKeys = Object.keys(cuminc.Inner.config.term2.term.values);
-    const uniqueSeriesIds = Array.from(cuminc.Inner.uniqueSeriesIds);
-    test.equal(JSON.stringify(valKeys), JSON.stringify(uniqueSeriesIds), `Should create custom groups`);
-    let numGrpLabelFails = 0;
-    const numRiskRowLabels = cuminc.Inner.dom.chartsDiv.selectAll(".sjpp-cuminc-atrisk text").nodes().filter((d) => !d.__data__?.tickVal && d.className.animVal != "sjpp-atrisk-title");
-    for (const grp of Object.values(cuminc.Inner.config.term2.term.values)) {
-      const findGrpLabel = numRiskRowLabels.some((d) => d.__data__.seriesId == grp.key && d.innerHTML == grp.label);
-      if (!findGrpLabel) {
-        test.fail(`Missing group in 'Number at risk' table: group = ${grp.key}, label = ${grp.label}`);
-        ++numGrpLabelFails;
-      }
-    }
-    if (numGrpLabelFails == 0) test.pass(`All custom groups display`);
-    if (test._ok) cuminc.Inner.app.destroy();
-    test.end();
-  }
-});
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