@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/regression.spec-DU3UTDCJ.js

@@ -1,708 +0,0 @@
-import {
-  getRunPp
-} from "./chunk-M2G5R4WB.js";
-import {
-  require_tape
-} from "./chunk-TUMA63WX.js";
-import "./chunk-VJ6UFVGC.js";
-import "./chunk-QNHT74XC.js";
-import "./chunk-CTQ3IUCA.js";
-import "./chunk-PFRWS4CR.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-4IH7DORZ.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-WKNI3HRQ.js";
-import "./chunk-7OHRR2IE.js";
-import "./chunk-2GYWFQML.js";
-import "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// plots/test/regression.spec.js
-var import_tape = __toESM(require_tape(), 1);
-var raceGroupsetting = {
-  id: "genetic_race",
-  q: {
-    type: "custom-groupset",
-    customset: {
-      groups: [
-        {
-          name: "group 123",
-          type: "values",
-          values: [{ key: "European Ancestry" }, { key: "Multi-Ancestry-Admixed" }]
-        },
-        { name: "group 456", type: "values", values: [{ key: "African Ancestry" }, { key: "Asian Ancestry" }] }
-      ]
-    }
-  }
-};
-var diaggrpGroupsetting = {
-  id: "diaggrp",
-  q: {
-    type: "custom-groupset",
-    customset: {
-      groups: [
-        {
-          name: "Leukemia",
-          type: "values",
-          values: [
-            { key: "Acute lymphoblastic leukemia" },
-            { key: "Chronic myeloid leukemia" },
-            { key: "Other leukemia" },
-            { key: "Acute myeloid leukemia" }
-          ]
-        },
-        {
-          name: "Lymphoma",
-          type: "values",
-          values: [{ key: "Hodgkin lymphoma" }, { key: "Non-Hodgkin lymphoma" }]
-        },
-        {
-          name: "Solid",
-          type: "values",
-          values: [{ key: "Central nervous system (CNS)" }, { key: "Neuroblastoma" }]
-        }
-      ]
-    }
-  }
-};
-var pgsRegularBin = {
-  id: "prs_PGS000332",
-  q: {
-    type: "regular-bin",
-    startinclusive: true,
-    bin_size: 0.4,
-    first_bin: {
-      stop: -1,
-      startunbounded: true
-    },
-    rounding: ".1f"
-  },
-  refGrp: "-0.2 to <0.2"
-};
-var pgsCustomBin = {
-  id: "prs_PGS000332",
-  q: {
-    type: "custom-bin",
-    lst: [
-      {
-        startunbounded: true,
-        stop: -0.5,
-        stopinclusive: false,
-        label: "<0.5"
-      },
-      {
-        start: -0.5,
-        stop: 0,
-        stopinclusive: false,
-        label: "-0.5 to 0"
-      },
-      {
-        start: 0,
-        startinclusive: true,
-        stopunbounded: true,
-        label: "\u22650"
-      }
-    ]
-  }
-};
-var agedxCustomBin = {
-  id: "agedx",
-  q: {
-    type: "custom-bin",
-    lst: [
-      {
-        startunbounded: true,
-        stop: 1,
-        stopinclusive: false,
-        label: "Infants: <1"
-      },
-      {
-        start: 1,
-        stop: 4,
-        stopinclusive: false,
-        label: "Toddlers: 1-4"
-      },
-      {
-        start: 4,
-        startinclusive: true,
-        stopunbounded: true,
-        label: "\u22654"
-      }
-    ]
-  }
-};
-var snplst = {
-  term: {
-    type: "snplst",
-    id: "snplstTermId",
-    snps: [
-      { rsid: "rs1641548", effectAllele: "T" },
-      { rsid: "rs858528", effectAllele: "T" },
-      { rsid: "rs1642793", effectAllele: "C" },
-      { rsid: "rs1042522" },
-      { rsid: "rs1642782" },
-      { rsid: "rs6503048" }
-    ]
-  },
-  q: {
-    AFcutoff: 5,
-    alleleType: 0,
-    geneticModel: 0,
-    missingGenotype: 0,
-    restrictAncestry: {
-      name: "European ancestry",
-      tvs: {
-        term: {
-          id: "genetic_race",
-          type: "categorical",
-          name: "Genetically defined race"
-        },
-        values: [{ key: "European Ancestry", label: "European Ancestry" }]
-      }
-    }
-  }
-};
-var snplocus = {
-  term: {
-    type: "snplocus",
-    id: "snplocusTermId"
-  },
-  q: {
-    chr: "chr17",
-    start: 7674304,
-    stop: 7676849,
-    AFcutoff: 5,
-    alleleType: 0,
-    geneticModel: 0,
-    restrictAncestry: {
-      name: "European ancestry",
-      tvs: {
-        term: {
-          id: "genetic_race",
-          type: "categorical",
-          name: "Genetically defined race"
-        },
-        values: [{ key: "European Ancestry", label: "European Ancestry" }]
-      }
-    },
-    variant_filter: {
-      type: "tvslst",
-      join: "and",
-      in: true,
-      lst: [
-        /*
-        {
-        	type: 'tvs',
-        	tvs: {
-        		isnot: true,
-        		values: [{ label: 'Bad', key: 'Bad' }],
-        		term: {
-        			id: 'QC_sjlife',
-        			name: 'ABC classification',
-        			parent_id: null,
-        			isleaf: true,
-        			type: 'categorical',
-        			values: {
-        				SuperGood: { label: 'SuperGood', key: 'SuperGood' },
-        				Good: { label: 'Good', key: 'Good' },
-        				Ambiguous: { label: 'Ambiguous', key: 'Ambiguous' },
-        				Bad: { label: 'Bad', key: 'Bad' }
-        			}
-        		}
-        	}
-        },
-        */
-        /*
-        {
-        	type: 'tvs',
-        	tvs: {
-        		isnot: true,
-        		values: [{ label: 'Bad', key: 'Bad' }],
-        		term: {
-        			id: 'QC_ccss',
-        			name: 'XYZ classification',
-        			parent_id: null,
-        			isleaf: true,
-        			type: 'categorical',
-        			values: {
-        				SuperGood: { label: 'SuperGood', key: 'SuperGood' },
-        				Good: { label: 'Good', key: 'Good' },
-        				Ambiguous: { label: 'Ambiguous', key: 'Ambiguous' },
-        				Bad: { label: 'Bad', key: 'Bad' }
-        			}
-        		}
-        	}
-        },
-        */
-        {
-          type: "tvs",
-          tvs: {
-            ranges: [{ start: 0.95, startinclusive: true, stopunbounded: true }],
-            term: { id: "SJcontrol_CR", name: "ABC control call rate", parent_id: null, isleaf: true, type: "float" }
-          }
-        },
-        {
-          type: "tvs",
-          tvs: {
-            ranges: [{ start: 0.95, startinclusive: true, stopunbounded: true }],
-            term: { id: "CR", name: "Call rate, ABC+XYZ", parent_id: null, isleaf: true, type: "float" }
-          }
-        },
-        {
-          type: "tvs",
-          tvs: {
-            ranges: [{ start: 0.95, startinclusive: true, stopunbounded: true }],
-            term: { id: "CR_sjlife", name: "ABC call rate", parent_id: null, isleaf: true, type: "float" }
-          }
-        },
-        {
-          type: "tvs",
-          tvs: {
-            ranges: [{ start: 0.95, startinclusive: true, stopunbounded: true }],
-            term: { id: "CR_ccss", name: "XYZ call rate", parent_id: null, isleaf: true, type: "float" }
-          }
-        },
-        {
-          type: "tvs",
-          tvs: {
-            ranges: [{ start: 0.95, startinclusive: true, stopunbounded: true }],
-            term: { id: "gnomAD_CR", name: "gnmoAD call rate", parent_id: null, isleaf: true, type: "float" }
-          }
-        },
-        {
-          type: "tvs",
-          tvs: {
-            ranges: [{ start: 0.1, startinclusive: true, stopunbounded: true }],
-            term: {
-              id: "gnomAD_AF",
-              name: "gnomAD allele frequency",
-              parent_id: null,
-              isleaf: true,
-              type: "float",
-              min: 0,
-              max: 1,
-              values: {}
-            }
-          }
-        },
-        /*
-        {
-        	type: 'tvs',
-        	tvs: {
-        		isnot: true,
-        		values: [{ label: 'yes', key: '1' }],
-        		term: { id: 'BadBLAT', name: 'Paralog', parent_id: null, isleaf: true, type: 'categorical' }
-        	}
-        },
-        */
-        {
-          type: "tvs",
-          tvs: {
-            isnot: true,
-            values: [{ label: "yes", key: "1" }],
-            term: { id: "Polymer_region", name: "Polymer region", parent_id: null, isleaf: true, type: "categorical" }
-          }
-        }
-      ]
-    }
-  }
-};
-var testList = [
-  {
-    name: "sex race hrtavg",
-    // hrtavg is continuous
-    headingCount: 5,
-    independent: [{ id: "sex", refGrp: "1" }, { id: "genetic_race" }, { id: "hrtavg" }]
-  },
-  {
-    name: "sex*race hrtavg",
-    headingCount: 5,
-    independent: [
-      { id: "sex", refGrp: "1", interactions: ["genetic_race"] },
-      { id: "genetic_race", interactions: ["sex"] },
-      { id: "hrtavg" }
-    ]
-  },
-  {
-    name: "sex race*hrtavg",
-    headingCount: 5,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      { id: "genetic_race", interactions: ["hrtavg"] },
-      { id: "hrtavg", interactions: ["genetic_race"] }
-    ]
-  },
-  {
-    name: "sex hrtavg*agedx",
-    headingCount: 5,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      { id: "hrtavg", interactions: ["agedx"] },
-      { id: "agedx", interactions: ["hrtavg"] }
-    ]
-  },
-  {
-    name: "sex raceGroupsetting hrtavg",
-    // groupsetting, continuous
-    headingCount: 5,
-    independent: [{ id: "sex", refGrp: "1" }, raceGroupsetting, { id: "hrtavg" }]
-  },
-  {
-    name: "sex*raceGroupsetting hrtavg",
-    headingCount: 5,
-    independent: [
-      { id: "sex", refGrp: "1", interactions: ["genetic_race"] },
-      addInteraction(raceGroupsetting, "sex"),
-      { id: "hrtavg" }
-    ]
-  },
-  {
-    name: "sex raceGroupsetting*hrtavg",
-    headingCount: 5,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      addInteraction(raceGroupsetting, "hrtavg"),
-      { id: "hrtavg", interactions: ["genetic_race"] }
-    ]
-  },
-  {
-    name: "raceGroupsetting*diaggrpGroupsetting",
-    headingCount: 5,
-    independent: [addInteraction(raceGroupsetting, "diaggrp"), addInteraction(diaggrpGroupsetting, "genetic_race")]
-  },
-  {
-    name: "sex race pgsRegularBin",
-    headingCount: 5,
-    independent: [{ id: "sex", refGrp: "1" }, { id: "genetic_race" }, pgsRegularBin]
-  },
-  {
-    name: "sex race*pgsRegularBin",
-    headingCount: 5,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      { id: "genetic_race", interactions: ["prs_PGS000332"] },
-      addInteraction(pgsRegularBin, "genetic_race")
-    ]
-  },
-  {
-    name: "sex race pgsCustomBin",
-    headingCount: 5,
-    independent: [{ id: "sex", refGrp: "1" }, { id: "genetic_race" }, pgsCustomBin]
-  },
-  {
-    name: "sex race*pgsCustomBin",
-    headingCount: 5,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      { id: "genetic_race", interactions: ["prs_PGS000332"] },
-      addInteraction(pgsCustomBin, "genetic_race")
-    ]
-  },
-  {
-    name: "pgsRegularBin*agedxCustomBin",
-    headingCount: 5,
-    independent: [addInteraction(pgsRegularBin, "agedx"), addInteraction(agedxCustomBin, "prs_PGS000332")]
-  },
-  {
-    name: "raceGroupsetting*pgsRegularBin",
-    headingCount: 5,
-    independent: [addInteraction(raceGroupsetting, "prs_PGS000332"), addInteraction(pgsRegularBin, "genetic_race")]
-  },
-  {
-    name: "raceGroupsetting*pgsCustomBin",
-    headingCount: 5,
-    independent: [addInteraction(pgsCustomBin, "genetic_race"), addInteraction(raceGroupsetting, "prs_PGS000332")]
-  },
-  {
-    name: "sex hrtavgSpline",
-    headingCount: 6,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      { id: "hrtavg", q: { mode: "spline", knots: [{ value: 4 }, { value: 18 }, { value: 200 }] } }
-    ]
-  },
-  {
-    name: "sex hrtavgSpline ageSpline",
-    headingCount: 6,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      { id: "hrtavg", q: { mode: "spline", knots: [{ value: 4 }, { value: 18 }, { value: 200 }] } },
-      { id: "agedx", q: { mode: "spline", knots: [{ value: 0.5 }, { value: 3.5 }, { value: 10.5 }] } }
-    ]
-  },
-  {
-    name: "sex diaggrp agedx hrtavgSpline snplst",
-    headingCount: 6,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      { id: "diaggrp" },
-      { id: "agedx" },
-      snplst,
-      { id: "hrtavg", q: { mode: "spline", knots: [{ value: 4 }, { value: 18 }, { value: 200 }] } }
-    ]
-  },
-  {
-    // cannot use diaggrp to interact with snplst, it will timeout
-    name: "sex income*snplst",
-    headingCount: 5,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      { id: "homeinc", interactions: ["snplstTermId"] },
-      addInteraction(snplst, "homeinc")
-    ]
-  },
-  {
-    name: "sex hrtavg*snplst",
-    headingCount: 5,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      { id: "hrtavg", interactions: ["snplstTermId"] },
-      addInteraction(snplst, "hrtavg")
-    ]
-  },
-  {
-    name: "sex pgsRegularBin*snplst",
-    headingCount: 5,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      addInteraction(pgsRegularBin, "snplstTermId"),
-      addInteraction(snplst, "prs_PGS000332")
-    ]
-  },
-  {
-    name: "sex pgsCustomBin*snplst",
-    headingCount: 5,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      addInteraction(pgsCustomBin, "snplstTermId"),
-      addInteraction(snplst, "prs_PGS000332")
-    ]
-  },
-  {
-    name: "sex diaggrpGroupsetting*snplst",
-    headingCount: 5,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      addInteraction(diaggrpGroupsetting, "snplstTermId"),
-      addInteraction(snplst, "diaggrp")
-    ]
-  },
-  {
-    name: "sex diaggrp agedx hrtavgSpline snplocus",
-    headingCount: 0,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      { id: "diaggrp" },
-      { id: "agedx" },
-      snplocus,
-      { id: "hrtavg", q: { mode: "spline", knots: [{ value: 4 }, { value: 18 }, { value: 200 }] } }
-    ]
-  },
-  {
-    name: "sex income*snplocus",
-    headingCount: 0,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      { id: "homeinc", interactions: ["snplocusTermId"] },
-      addInteraction(snplocus, "homeinc")
-    ]
-  },
-  {
-    name: "sex hrtavg*snplocus",
-    headingCount: 0,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      { id: "hrtavg", interactions: ["snplocusTermId"] },
-      addInteraction(snplocus, "hrtavg")
-    ]
-  },
-  {
-    name: "sex pgsRegularBin*snplst",
-    headingCount: 0,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      addInteraction(pgsRegularBin, "snplocusTermId"),
-      addInteraction(snplocus, "prs_PGS000332")
-    ]
-  },
-  {
-    name: "sex pgsCustomBin*snplocus",
-    headingCount: 0,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      addInteraction(pgsCustomBin, "snplocusTermId"),
-      addInteraction(snplocus, "prs_PGS000332")
-    ]
-  },
-  {
-    name: "sex diaggrpGroupsetting*snplocus",
-    headingCount: 0,
-    independent: [
-      { id: "sex", refGrp: "1" },
-      addInteraction(diaggrpGroupsetting, "snplocusTermId"),
-      addInteraction(snplocus, "diaggrp")
-    ]
-  }
-];
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- mass/regression -***-");
-  test.end();
-});
-var activeTests = testList.filter((t) => t.runthis);
-for (const item of activeTests.length ? activeTests : testList) {
-  (0, import_tape.default)("(LINEAR) EF ~ " + item.name, (test) => {
-    test.timeoutAfter(5e4);
-    runpp(
-      {
-        regressionType: "linear",
-        outcome: { id: "LV_Ejection_Fraction_3D" },
-        independent: item.independent
-      },
-      async (reg) => {
-        reg.on("postRender.test", null);
-        test.equal(findResultHeadings(reg), item.headingCount, "result has " + item.headingCount + " headings");
-        mayDestroyDom(test, reg);
-        test.end();
-      },
-      test
-    );
-  });
-  (0, import_tape.default)("(LOGISTIC) EF ~ " + item.name, (test) => {
-    test.timeoutAfter(5e4);
-    runpp(
-      {
-        regressionType: "logistic",
-        outcome: { id: "LV_Ejection_Fraction_3D" },
-        independent: item.independent
-      },
-      async (reg) => {
-        reg.on("postRender.test", null);
-        test.equal(findResultHeadings(reg), item.headingCount, "result has " + item.headingCount + " headings");
-        mayDestroyDom(test, reg);
-        test.end();
-      },
-      test
-    );
-  });
-  (0, import_tape.default)("(LOGISTIC) Arrhythmias ~ " + item.name, (test) => {
-    test.timeoutAfter(5e4);
-    runpp(
-      {
-        regressionType: "logistic",
-        outcome: { id: "Arrhythmias" },
-        independent: item.independent
-      },
-      async (reg) => {
-        reg.on("postRender.test", null);
-        test.equal(findResultHeadings(reg), item.headingCount, "result has " + item.headingCount + " headings");
-        mayDestroyDom(test, reg);
-        test.end();
-      },
-      test
-    );
-  });
-  (0, import_tape.default)("(COX) Arrhythmias ~ " + item.name, (test) => {
-    test.timeoutAfter(5e4);
-    runpp(
-      {
-        regressionType: "cox",
-        outcome: { id: "Arrhythmias" },
-        independent: item.independent
-      },
-      async (reg) => {
-        reg.on("postRender.test", null);
-        test.equal(findResultHeadings(reg), item.headingCount, "result has " + item.headingCount + " headings");
-        mayDestroyDom(test, reg);
-        test.end();
-      },
-      test
-    );
-  });
-}
-function runpp(plot, runtest, test) {
-  plot.chartType = "regression";
-  getRunPp("mass", {
-    nav: {
-      activeTab: 1
-    },
-    state: {
-      genome: "hg38",
-      dslabel: "SJLife"
-    },
-    debug: 1
-  })({
-    state: { plots: [plot] },
-    app: {
-      callbacks: {
-        "postInit.test": (app, error = null) => {
-          if (!error) return;
-          test.fail("app.init() error: " + JSON.stringify(error));
-          test.end();
-        }
-      }
-    },
-    regression: {
-      callbacks: {
-        "postRender.test": runtest
-      }
-    }
-  });
-}
-function findResultHeadings(reg) {
-  if (reg.Inner.results.dom.err_div.style("display") == "block") {
-    return -1;
-  }
-  const spans = reg.Inner.results.dom.oneSetResultDiv.selectAll("span").nodes();
-  let foundNumber = 0;
-  foundNumber += spans.find((i) => i.innerText == "Sample size:") ? 1 : 0;
-  foundNumber += spans.find((i) => i.innerText == "Residuals") ? 1 : 0;
-  foundNumber += spans.find((i) => i.innerText == "Deviance residuals") ? 1 : 0;
-  foundNumber += spans.find((i) => i.innerText == "Cubic spline plots") ? 1 : 0;
-  foundNumber += spans.find((i) => i.innerText == "Coefficients") ? 1 : 0;
-  foundNumber += spans.find((i) => i.innerText == "Type III statistics") ? 1 : 0;
-  foundNumber += spans.find((i) => i.innerText == "Statistical tests") ? 1 : 0;
-  foundNumber += spans.find((i) => i.innerText == "Other summary statistics") ? 1 : 0;
-  return foundNumber;
-}
-function addInteraction(tw, interId) {
-  const a = JSON.parse(JSON.stringify(tw));
-  a.interactions = [interId];
-  return a;
-}
-function mayDestroyDom(test, component) {
-  if (!test._ok) return;
-  if (component.Inner.app) component.Inner.app.destroy();
-  else component.destroy();
-}
-//# sourceMappingURL=regression.spec-DU3UTDCJ.js.map