@sjcrh/proteinpaint-client 2.166.0 → 2.167.0

package/dist/survival.integration.spec-AU7MCAQV.js

@@ -1,601 +0,0 @@
-import {
-  getRunPp
-} from "./chunk-XATIKUGU.js";
-import {
-  detectGte
-} from "./chunk-OQSP66C6.js";
-import "./chunk-AHBQHHH5.js";
-import {
-  require_tape
-} from "./chunk-EFPC6YYT.js";
-import "./chunk-JXHU2FIA.js";
-import "./chunk-CT3LPTWW.js";
-import "./chunk-AZ276Z7T.js";
-import "./chunk-KGSCQRQ5.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-47X254B7.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-RQUXELHE.js";
-import "./chunk-M7QVMSRW.js";
-import "./chunk-RS3G3HE7.js";
-import "./chunk-UT6W4ZZL.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-5TDKRZN5.js";
-import "./chunk-RYRCMHYR.js";
-import "./chunk-ECKWM4HB.js";
-import "./chunk-NXOWHUR4.js";
-import "./chunk-5MWX5HUZ.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-ICNJQHQZ.js";
-import "./chunk-FYTZCTJC.js";
-import "./chunk-7NTZWOJV.js";
-import "./chunk-OMO754MK.js";
-import "./chunk-RA5EXEHB.js";
-import "./chunk-PMZS3SHH.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-W2IWHXLL.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-UJUXE42U.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-NDWTN4U5.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 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 divide by", function(test) {
-  test.timeoutAfter(1e4);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "survival",
-          term: {
-            id: "efs"
-          },
-          term0: {
-            id: "sex"
-          }
-        }
-      ]
-    },
-    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;
-    const termNum = Object.keys(term0Values).length;
-    test.equal(survivalDiv.selectAll(".pp-survival-chart").size(), termNum, `Should render ${termNum} survival charts`);
-    test.equal(
-      survivalDiv.selectAll(".sjpp-survival-atrisk").size(),
-      termNum,
-      `Should render 'Number at risk' tables below chart`
-    );
-    const titleNodes = survivalDiv.selectAll(".sjpp-survival-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) 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, 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) {
-    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-AU7MCAQV.js.map