@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/cuminc.integration.spec-IXS2UO2O.js

@@ -0,0 +1,676 @@
+import {
+  getRunPp
+} from "./chunk-62TF2MCH.js";
+import {
+  detectGte
+} from "./chunk-SSPDNHDW.js";
+import {
+  termjson
+} from "./chunk-HUA2EFQO.js";
+import {
+  require_tape
+} from "./chunk-QWOE5YTB.js";
+import "./chunk-GRG5MMPN.js";
+import "./chunk-YIMRBXQK.js";
+import "./chunk-L2HBHFTK.js";
+import "./chunk-ZGOOZK3I.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-ZH2VP6Q6.js";
+import "./chunk-MKAF2BHB.js";
+import "./chunk-AQ4OP4GR.js";
+import "./chunk-DGUTCYH2.js";
+import "./chunk-2UYBBUXK.js";
+import "./chunk-2YC6ZVE4.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-RYCOJY7M.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-I55NLUCQ.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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