@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/survival.integration.spec-FS7V4OXK.js

@@ -0,0 +1,800 @@
+import {
+  getRunPp
+} from "./chunk-62TF2MCH.js";
+import {
+  Locator,
+  detectGte,
+  sleep
+} from "./chunk-SSPDNHDW.js";
+import "./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/survival/test/survival.integration.spec.js
+var import_tape = __toESM(require_tape(), 1);
+var runpp = getRunPp("mass", {
+  state: {
+    nav: {
+      activeTab: 1
+    },
+    dslabel: "TermdbTest",
+    genome: "hg38-test"
+  },
+  debug: 1
+});
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- plots/survival -***-");
+  test.end();
+});
+(0, import_tape.default)("survival term as term1", function(test) {
+  test.timeoutAfter(1e4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  let survivalDiv;
+  async function runTests(survival) {
+    survivalDiv = survival.Inner.dom.chartsDiv;
+    test.equal(survivalDiv && survivalDiv.selectAll(".sjpp-survival-series").size(), 1, "should render 1 surv series g");
+    test.equal(
+      survivalDiv && survivalDiv.selectAll(".sjpp-survival-censored-x").size(),
+      10,
+      "should render 10 survival censored symbols"
+    );
+    if (test._ok) survival.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, with categorical overlay", function(test) {
+  test.timeoutAfter(1e4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          term2: {
+            id: "diaggrp"
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  let survivalDiv;
+  async function runTests(survival) {
+    survivalDiv = survival.Inner.dom.chartsDiv;
+    test.equal(survivalDiv && survivalDiv.selectAll(".sjpp-survival-series").size(), 7, "should render 7 surv series g");
+    test.equal(
+      survivalDiv && survivalDiv.selectAll(".sjpp-survival-censored-x").size(),
+      10,
+      "should render 9 survival censored symbols"
+    );
+    if (test._ok) survival.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, with numeric overlay", function(test) {
+  test.timeoutAfter(1e4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          term2: {
+            id: "agedx"
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  let survivalDiv;
+  async function runTests(survival) {
+    survivalDiv = survival.Inner.dom.chartsDiv;
+    test.equal(survivalDiv && survivalDiv.selectAll(".sjpp-survival-series").size(), 2, "should render 2 surv series g");
+    test.equal(
+      survivalDiv && survivalDiv.selectAll(".sjpp-survival-censored-x").size(),
+      10,
+      "should render 10 survival censored symbols"
+    );
+    if (test._ok) survival.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, with condition overlay (some samples have missing values)", function(test) {
+  test.timeoutAfter(1e4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          term2: {
+            id: "Auditory System"
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  let survivalDiv;
+  async function runTests(survival) {
+    survivalDiv = survival.Inner.dom.chartsDiv;
+    test.equal(survivalDiv && survivalDiv.selectAll(".sjpp-survival-series").size(), 5, "should render 5 surv series g");
+    test.equal(
+      survivalDiv && survivalDiv.selectAll(".sjpp-survival-censored-x").size(),
+      3,
+      "should render 3 survival censored symbols"
+    );
+    if (test._ok) survival.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as overlay", function(test) {
+  test.timeoutAfter(1e4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "diaggrp"
+          },
+          term2: {
+            id: "efs"
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  let survivalDiv;
+  async function runTests(survival) {
+    survivalDiv = survival.Inner.dom.chartsDiv;
+    test.equal(survivalDiv && survivalDiv.selectAll(".sjpp-survival-series").size(), 7, "should render 7 surv series g");
+    test.equal(
+      survivalDiv && survivalDiv.selectAll(".sjpp-survival-censored-x").size(),
+      10,
+      "should render 10 survival censored symbols"
+    );
+    if (test._ok) survival.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, with categorical divide by", function(test) {
+  test.timeoutAfter(1e4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          term0: {
+            id: "genetic_race"
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(survival) {
+    const inner = survival.Inner;
+    const survivalDiv = inner.dom.chartsDiv;
+    const term0Values = inner.state.config.term0.term.values;
+    test.equal(survivalDiv.selectAll(".pp-survival-chart").size(), 3, `Should render 3 survival charts`);
+    test.equal(
+      survivalDiv.selectAll(".sjpp-survival-atrisk").size(),
+      3,
+      `Should render 'Number at risk' tables below each chart`
+    );
+    const term0Labels = Object.values(term0Values).map((v) => v.label);
+    const titleNodes = survivalDiv.selectAll(".sjpp-survival-title").nodes();
+    for (const d of titleNodes) {
+      if (!term0Labels.includes(d.innerText)) test.fail(`Unexpected title: ${d.innerText}`);
+    }
+    if (test._ok) survival.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, with numeric divide by", function(test) {
+  test.timeoutAfter(1e4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          term0: {
+            id: "agedx"
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(survival) {
+    const inner = survival.Inner;
+    const survivalDiv = inner.dom.chartsDiv;
+    test.equal(survivalDiv.selectAll(".pp-survival-chart").size(), 2, `Should render 2 survival charts`);
+    test.equal(
+      survivalDiv.selectAll(".sjpp-survival-atrisk").size(),
+      2,
+      `Should render 'Number at risk' tables below each chart`
+    );
+    if (test._ok) survival.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, with condition divide by (some samples have missing values)", function(test) {
+  test.timeoutAfter(1e4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          term0: {
+            id: "Auditory System"
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(survival) {
+    const inner = survival.Inner;
+    const survivalDiv = inner.dom.chartsDiv;
+    const term0Values = inner.state.config.term0.term.values;
+    test.equal(survivalDiv.selectAll(".pp-survival-chart").size(), 5, `Should render 5 survival charts`);
+    test.equal(
+      survivalDiv.selectAll(".sjpp-survival-atrisk").size(),
+      5,
+      `Should render 'Number at risk' tables below each chart`
+    );
+    const term0Labels = Object.values(term0Values).map((v) => v.label);
+    const titleNodes = survivalDiv.selectAll(".sjpp-survival-title").nodes();
+    for (const d of titleNodes) {
+      if (!term0Labels.includes(d.innerText)) test.fail(`Unexpected title: ${d.innerText}`);
+    }
+    if (test._ok) survival.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, term2 = genetic_race, categorical groupsetting", function(test) {
+  test.timeoutAfter(3e3);
+  const 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" }]
+    }
+  ];
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          term2: {
+            id: "genetic_race",
+            q: {
+              customset: {
+                groups
+              }
+            }
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(survival) {
+    survival.on("postRender.test", null);
+    const inner = survival.Inner;
+    const config = inner.state.config;
+    test.equal(
+      JSON.stringify(config.term2.q.customset.groups),
+      JSON.stringify(groups),
+      `Should correctly pass customset groups for term2`
+    );
+    const numOfTerms = Object.keys(inner.term2toColor).length;
+    test.equal(
+      inner.dom.chartsDiv.selectAll(".sjpp-survival-series").size(),
+      numOfTerms,
+      `Should render ${numOfTerms} surv series g`
+    );
+    const censoredSym = inner.currData.filter((d) => d.ncensor);
+    test.equal(
+      inner.dom.chartsDiv.selectAll(".sjpp-survival-censored-x").size(),
+      censoredSym.length,
+      `should render ${censoredSym.length} survival censored symbols`
+    );
+    if (test._ok) survival.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, term0 = genetic_race, categorical groupsetting", function(test) {
+  test.timeoutAfter(1e4);
+  const 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" }]
+    }
+  ];
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          term0: {
+            id: "genetic_race",
+            q: {
+              customset: {
+                groups
+              }
+            }
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(survival) {
+    survival.on("postRender.test", null);
+    const inner = survival.Inner;
+    const config = inner.state.config;
+    const term0Values = config.term0.term.values;
+    test.equal(
+      JSON.stringify(config.term0.q.customset.groups),
+      JSON.stringify(groups),
+      `Should correctly pass customset groups for term0`
+    );
+    const termNum = inner.serverData.refs.orderedKeys.chart;
+    test.equal(
+      inner.dom.chartsDiv.selectAll(".pp-survival-chart").size(),
+      termNum.length,
+      `Should render ${termNum.length} survival charts`
+    );
+    test.equal(
+      inner.dom.chartsDiv.selectAll(".sjpp-survival-atrisk").size(),
+      termNum.length,
+      `Should render 'Number at risk' tables below each chart`
+    );
+    const titleNodes = inner.dom.chartsDiv.selectAll(".sjpp-survival-title").nodes();
+    termNum.forEach((v) => {
+      if (!titleNodes.some((d) => d.innerText == v)) test.fail(`Missing title for term0 value = ${v}`);
+    });
+    if (test._ok) survival.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, term2 = agedx, regular bins", function(test) {
+  test.timeoutAfter(1e4);
+  test.plan(4);
+  const testBinSize = 5;
+  const testStop = 5;
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          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
+            }
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(survival) {
+    survival.on("postRender.test", null);
+    test.equal(survival.Inner.state.config.term2.q.type, "regular-bin", `Should correctly pass 'regular-bin' to config`);
+    test.equal(
+      survival.Inner.state.config.term2.q.bin_size,
+      testBinSize,
+      `Should correctly pass q.bin_size = ${testBinSize} to config`
+    );
+    test.equal(
+      survival.Inner.state.config.term2.q.first_bin.stop,
+      testStop,
+      `Should correctly pass q.first_bin.stop = ${testStop} to config`
+    );
+    const newStop = 1;
+    const config = structuredClone(survival.Inner.state.config);
+    const expectedCount = 8;
+    const survCurves = await detectGte({
+      elem: survival.Inner.dom.chartsDiv.node(),
+      selector: ".sjpp-survival-series",
+      count: expectedCount,
+      async trigger() {
+        config.term2.q.bin_size = 3;
+        config.term2.q.first_bin.stop = newStop;
+        survival.Inner.app.dispatch({
+          type: "plot_edit",
+          id: survival.Inner.id,
+          config
+        });
+      }
+    });
+    test.equal(survCurves.length, expectedCount, `Should display the correct bin size = ${expectedCount}`);
+    if (test._ok) survival.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, term2 = agedx, custom bins", function(test) {
+  test.timeoutAfter(1e4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          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: {
+            survival: {}
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(survival) {
+    survival.on("postRender.test", null);
+    const inner = survival.Inner;
+    const config = inner.state.config;
+    test.equal(config.term2.q.type, "custom-bin", `Should correctly pass 'custom-bin' to config`);
+    const config2 = structuredClone(config);
+    const expectedCount = 3;
+    const survCurves = await detectGte({
+      elem: survival.Inner.dom.chartsDiv.node(),
+      selector: ".sjpp-survival-series",
+      count: expectedCount,
+      async trigger() {
+        config2.term2.q.lst[2] = { startinclusive: true, stopinclusive: true, start: 12, stop: 15, label: "12 to 15" };
+        config2.term2.q.lst.push({ start: 15, startinclusive: false, stopunbounded: true, label: ">15" });
+        inner.app.dispatch({
+          type: "plot_edit",
+          id: inner.id,
+          config: config2
+        });
+      }
+    });
+    test.equal(survCurves.length, expectedCount, `Should display the correct num of bins = ${expectedCount}`);
+    if (test._ok) inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, term0 = agedx, custom bins", function(test) {
+  test.timeoutAfter(2e4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          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: {}
+            }
+          }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(survival) {
+    survival.on("postRender.test", null);
+    const inner = survival.Inner;
+    const config = inner.state.config;
+    test.equal(config.term0.q.type, "custom-bin", `Should correctly pass 'custom-bin' to config`);
+    const config2 = structuredClone(config);
+    const expectedCount = 3;
+    const survCurves = await detectGte({
+      elem: survival.Inner.dom.chartsDiv.node(),
+      selector: ".sjpp-survival-series",
+      count: expectedCount,
+      async trigger() {
+        config2.term0.q.lst = [
+          { startunbounded: true, stop: 5, stopinclusive: false, label: "<5" },
+          { start: 5, stop: 8, startinclusive: true, stopinclusive: false, label: "5 to <8" },
+          { start: 8, startinclusive: true, stopunbounded: true, label: ">=8" }
+        ];
+        await inner.app.dispatch({
+          type: "plot_edit",
+          id: inner.id,
+          config: config2
+        });
+      }
+    });
+    test.equal(survCurves.length, expectedCount, `Should display the correct num of bins = ${expectedCount}`);
+    if (test._ok) inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, term2 = geneVariant", function(test) {
+  test.timeoutAfter(1e4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          term2: { term: { type: "geneVariant", gene: "TP53" } }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  let survivalDiv;
+  async function runTests(survival) {
+    survival.on("postRender.test", null);
+    const { chartsDiv, legendTip } = survival.Inner.dom;
+    survivalDiv = chartsDiv;
+    test.equal(survivalDiv && survivalDiv.selectAll(".sjpp-survival-series").size(), 2, "should render 2 surv series g");
+    test.equal(
+      survivalDiv && survivalDiv.selectAll(".sjpp-survival-censored-x").size(),
+      10,
+      "should render 10 survival censored symbols"
+    );
+    const atRiskLegend0 = await Locator.init(survivalDiv.node()).find(`[data-testid='sjpp-atrisk-seriesId']`).click(0);
+    const colorInput = await Locator.init(legendTip.d).shows('input[type="color"]').get(0);
+    colorInput.value = "#0000ff";
+    colorInput.dispatchEvent(new Event("change", { cancelable: true }));
+    await sleep(100);
+    test.equal(atRiskLegend0?.parentNode?.getAttribute("fill"), "rgb(0, 0, 255)", "should change the series color");
+    if (test._ok) {
+      survival.Inner.app.destroy();
+      legendTip.hide();
+    }
+    test.end();
+  }
+});
+(0, import_tape.default)("survival term as term1, term2 = geneExpression", function(test) {
+  test.timeoutAfter(1e4);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "survival",
+          term: {
+            id: "efs"
+          },
+          term2: { term: { type: "geneExpression", gene: "TP53" } }
+        }
+      ]
+    },
+    survival: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  let survivalDiv;
+  async function runTests(survival) {
+    survivalDiv = survival.Inner.dom.chartsDiv;
+    test.equal(survivalDiv && survivalDiv.selectAll(".sjpp-survival-series").size(), 2, "should render 2 surv series g");
+    test.equal(
+      survivalDiv && survivalDiv.selectAll(".sjpp-survival-censored-x").size(),
+      10,
+      "should render 10 survival censored symbols"
+    );
+    if (test._ok) survival.Inner.app.destroy();
+    test.end();
+  }
+});
+//# sourceMappingURL=survival.integration.spec-FS7V4OXK.js.map