@sjcrh/proteinpaint-client 2.218.1-1 → 2.219.0

package/dist/survival-RAGOFPKJ.js

@@ -1,49 +0,0 @@
-import {
-  getPillNameDefault
-} from "./chunk-YQJ3E5QQ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-HW4CEUH4.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-YK2SIZOM.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-V3IGPIQS.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-I3IRPEFZ.js";
-import "./chunk-GHSHYM5E.js";
-import "./chunk-LENX7HXE.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// termsetting/handlers/survival.ts
-function getHandler(self) {
-  return {
-    async showEditMenu(div) {
-      if (!div) return;
-    },
-    getPillStatus() {
-    },
-    getPillName(d) {
-      return getPillNameDefault(self, d);
-    }
-  };
-}
-function fillTW(tw, vocabApi) {
-  if (tw) {
-  }
-  if (vocabApi) {
-  }
-}
-export {
-  fillTW,
-  getHandler
-};
-//# sourceMappingURL=survival-RAGOFPKJ.js.map

package/dist/survival.integration.spec-4J46YOSP.js

@@ -1,609 +0,0 @@
-import {
-  getRunPp
-} from "./chunk-LR7VWGLD.js";
-import {
-  detectGte,
-  sleep
-} from "./chunk-WA3C3A2M.js";
-import "./chunk-CWWE77DH.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-ZWIYP36K.js";
-import "./chunk-IUQNHN3O.js";
-import "./chunk-ZDQYDWQA.js";
-import "./chunk-FAKIIOCU.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-UVGYACXJ.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-4FTH4L3A.js";
-import "./chunk-WZXL6NM5.js";
-import "./chunk-MSEUZIN2.js";
-import "./chunk-YQJ3E5QQ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-HW4CEUH4.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-YK2SIZOM.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-V3IGPIQS.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-I3IRPEFZ.js";
-import "./chunk-GHSHYM5E.js";
-import "./chunk-LENX7HXE.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import {
-  __toESM
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/survival/test/survival.integration.spec.js
-var import_tape = __toESM(require_tape(), 1);
-
-// test/testdata/data.ts
-function getAgeCollectionFractionTw() {
-  return {
-    type: "TermCollectionTWFraction",
-    term: {
-      type: "termCollection",
-      termIds: ["agedx", "a_death", "a_ndi", "agelastvisit"],
-      name: "Fake Collection 1",
-      // NOTE this name must match with the termCollection entry in termdbtest
-      memberType: "numeric"
-    },
-    q: {
-      mode: "discrete",
-      numerators: ["a_death"],
-      denominators: ["agedx", "a_death"],
-      type: "custom-bin",
-      lst: [
-        { startunbounded: true, stop: 0.8, label: "<0.8" },
-        { stopunbounded: true, start: 0.8, label: ">0.8" }
-      ]
-    }
-  };
-}
-
-// plots/survival/test/survival.integration.spec.js
-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, 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`
-    );
-    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`
-    );
-    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
-        });
-      }
-    });
-    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
-        });
-      }
-    });
-    if (test._ok) inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("survival term as term1, term2 = geneVariant", function(test) {
-  test.timeoutAfter(5e3);
-  test.plan(1);
-  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;
-    await survival.Inner.app.dispatch({
-      type: "plot_edit",
-      id: survival.id,
-      config: {
-        settings: {
-          survival: {
-            atRiskVisible: false
-          }
-        }
-      }
-    });
-    await sleep(100);
-    test.equal(
-      survivalDiv.selectAll(".sjpp-atrisk-title").size(),
-      0,
-      "should hide at-risk legend when settings.survival.atRiskVisible is false"
-    );
-    if (test._ok) {
-      survival.Inner.app.destroy();
-      legendTip.hide();
-    }
-    test.end();
-  }
-});
-(0, import_tape.default)("survival term as term1, term2 = ssGSEA", function(test) {
-  test.timeoutAfter(8e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "survival",
-          term: { id: "efs" },
-          term2: { term: { type: "ssGSEA", id: "HALLMARK_ADIPOGENESIS" } }
-        }
-      ]
-    },
-    survival: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  let survivalDiv;
-  async function runTests(survival) {
-    survivalDiv = survival.Inner.dom.chartsDiv;
-    test.equal(survival.Inner.state.config.term2.q.mode, "discrete", "term2 ssGSEA should default to discrete mode");
-    test.equal(survival.Inner.state.config.term2.q.type, "custom-bin", "term2 ssGSEA should default to custom bins");
-    test.equal(survivalDiv && survivalDiv.selectAll(".sjpp-survival-series").size(), 2, "should render 2 surv series g");
-    if (test._ok) survival.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("survival term as term1, term2 = isoformExpression", function(test) {
-  test.timeoutAfter(8e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "survival",
-          term: { id: "efs" },
-          term2: {
-            term: { isoform: "ENST00000269305", gene: "TP53", name: "ENST00000269305 TPM", type: "isoformExpression" }
-          }
-        }
-      ]
-    },
-    survival: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  let survivalDiv;
-  async function runTests(survival) {
-    survivalDiv = survival.Inner.dom.chartsDiv;
-    test.equal(survival.Inner.state.config.term2.q.mode, "discrete", "term2 should default to discrete mode");
-    test.equal(survival.Inner.state.config.term2.q.type, "custom-bin", "term2 should default to custom bins");
-    test.equal(survivalDiv && survivalDiv.selectAll(".sjpp-survival-series").size(), 2, "should render 2 surv series g");
-    if (test._ok) survival.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("survival term as term1, term2 = dnaMethylation", function(test) {
-  test.timeoutAfter(8e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "survival",
-          term: { id: "efs" },
-          term2: {
-            term: {
-              chr: "chr17",
-              start: 7661778,
-              stop: 7687537,
-              type: "dnaMethylation",
-              unit: "Average Beta Value",
-              genomicFeatureType: "region",
-              name: "chr17:7661778-7687537 Average Beta Value"
-            }
-          }
-        }
-      ]
-    },
-    survival: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  let survivalDiv;
-  async function runTests(survival) {
-    survivalDiv = survival.Inner.dom.chartsDiv;
-    test.equal(survival.Inner.state.config.term2.q.mode, "discrete", "term2 should default to discrete mode");
-    test.equal(survival.Inner.state.config.term2.q.type, "custom-bin", "term2 should default to custom bins");
-    test.equal(survivalDiv && survivalDiv.selectAll(".sjpp-survival-series").size(), 2, "should render 2 surv series g");
-    if (test._ok) survival.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("survival term as term1, term2 = termCollection fraction", function(test) {
-  test.timeoutAfter(8e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "survival",
-          term: { id: "efs" },
-          term2: getAgeCollectionFractionTw()
-        }
-      ]
-    },
-    survival: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  let survivalDiv;
-  async function runTests(survival) {
-    survivalDiv = survival.Inner.dom.chartsDiv;
-    test.equal(
-      survival.Inner.state.config.term2.type,
-      "TermCollectionTWFraction",
-      "term2 should be a fraction termCollection tw"
-    );
-    test.equal(
-      survivalDiv && survivalDiv.selectAll(".sjpp-survival-series").size(),
-      2,
-      "should render 1 surv series g per fraction bin"
-    );
-    test.deepEqual(
-      survival.Inner.refs.orderedKeys.series,
-      ["<0.8", ">0.8"],
-      "should order the series by the fraction bins"
-    );
-    if (test._ok) survival.Inner.app.destroy();
-    test.end();
-  }
-});
-//# sourceMappingURL=survival.integration.spec-4J46YOSP.js.map