@sjcrh/proteinpaint-client 2.224.0 → 2.224.1

package/dist/survival-PRHRAD2T.js

@@ -0,0 +1,49 @@
+import {
+  getPillNameDefault
+} from "./chunk-3YQYWX4M.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-R3RD3VEX.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-KBTFT76L.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.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-PRHRAD2T.js.map

package/dist/survival.integration.spec-KH6GPVZ4.js

@@ -0,0 +1,609 @@
+import {
+  getRunPp
+} from "./chunk-QBGMD5UV.js";
+import {
+  detectGte,
+  sleep
+} from "./chunk-WA3C3A2M.js";
+import "./chunk-CWWE77DH.js";
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import "./chunk-AFEPQY5B.js";
+import "./chunk-Z6CMJQKG.js";
+import "./chunk-7TG44KO3.js";
+import "./chunk-MNN6NFZK.js";
+import "./chunk-O6T4SDC7.js";
+import "./chunk-JXVRNCAZ.js";
+import "./chunk-MKAF2BHB.js";
+import "./chunk-4FTH4L3A.js";
+import "./chunk-2GWAEK4R.js";
+import "./chunk-2VBU42YX.js";
+import "./chunk-3YQYWX4M.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-R3RD3VEX.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-KBTFT76L.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.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-KH6GPVZ4.js.map