@sjcrh/proteinpaint-client 2.208.0 → 2.209.0

package/dist/genomeBrowser.spec-7PZCNBL3.js

@@ -1,276 +0,0 @@
-import {
-  getRunPp
-} from "./chunk-XOND7UIK.js";
-import {
-  detectGt,
-  detectOne
-} from "./chunk-FYXIK6Y6.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-HELEV3LT.js";
-import "./chunk-KZHF3MQX.js";
-import "./chunk-JEJV7V7M.js";
-import "./chunk-Z2FSHODI.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-TSI4W6XO.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-3GUVLDUS.js";
-import "./chunk-4FTH4L3A.js";
-import "./chunk-A7TXS6JR.js";
-import "./chunk-QJ3HYZH3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-DMWOK4DS.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-5IMFPVGT.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VMRO6DMC.js";
-import "./chunk-HKKTNIMX.js";
-import "./chunk-GMRIEUBW.js";
-import "./chunk-4EZLVENZ.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/gb/test/genomeBrowser.spec.js
-var import_tape = __toESM(require_tape(), 1);
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- plots/genomeBrowser -***-");
-  test.end();
-});
-(0, import_tape.default)("sjlife default setting", (test) => {
-  const holder = getHolder();
-  runpp({
-    holder,
-    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
-  });
-});
-(0, import_tape.default)("Sjlife default, with global mass filter", (test) => {
-  const holder = getHolder();
-  runpp({
-    holder,
-    state: {
-      termfilter: {
-        filter: {
-          type: "tvslst",
-          join: "and",
-          in: true,
-          lst: [
-            {
-              type: "tvs",
-              tvs: {
-                term: { id: "diaggrp_s" },
-                values: [{ key: "Acute lymphoblastic leukemia", label: "Acute lymphoblastic leukemia" }]
-              }
-            },
-            {
-              type: "tvs",
-              tvs: {
-                term: { id: "agedx_s", name: "agedx", type: "float" },
-                ranges: [{ startunbounded: true, stop: 10, stopinclusive: true }]
-              }
-            }
-          ]
-        }
-      }
-    },
-    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
-  });
-});
-(0, import_tape.default)("Two groups: filter + population", (test) => {
-  const holder = getHolder();
-  const p = getPlot([groupFilterAML, groupPopulation1]);
-  runpp({
-    holder,
-    state: { plots: [p] },
-    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
-  });
-});
-(0, import_tape.default)("Two groups: filter + info", (test) => {
-  const holder = getHolder();
-  const p = getPlot([groupFilterAML, groupInfo1]);
-  runpp({
-    holder,
-    state: { plots: [p] },
-    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
-  });
-});
-(0, import_tape.default)("Two groups: filter + filter", (test) => {
-  const holder = getHolder();
-  const p = getPlot([groupFilterAML, groupFilterALLmale]);
-  runpp({
-    holder,
-    state: { plots: [p] },
-    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
-  });
-});
-(0, import_tape.default)("Two groups: info + info", (test) => {
-  const holder = getHolder();
-  const p = getPlot([groupInfo1, groupInfo2]);
-  runpp({
-    holder,
-    state: { plots: [p] },
-    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
-  });
-});
-(0, import_tape.default)("Two groups: info + poulation", (test) => {
-  const holder = getHolder();
-  const p = getPlot([groupInfo1, groupPopulation1]);
-  runpp({
-    holder,
-    state: { plots: [p] },
-    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
-  });
-});
-(0, import_tape.default)("Two groups: population + poulation", (test) => {
-  const holder = getHolder();
-  const p = getPlot([groupPopulation1, groupPopulation2]);
-  runpp({
-    holder,
-    state: { plots: [p] },
-    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
-  });
-});
-(0, import_tape.default)("Single group: population", (test) => {
-  const holder = getHolder();
-  const p = getPlot([groupPopulation1]);
-  runpp({
-    holder,
-    state: { plots: [p] },
-    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
-  });
-});
-(0, import_tape.default)("Single group: filter", (test) => {
-  const holder = getHolder();
-  const p = getPlot([groupFilterALLmale]);
-  runpp({
-    holder,
-    state: { plots: [p] },
-    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
-  });
-});
-(0, import_tape.default)("Single group: info", (test) => {
-  const holder = getHolder();
-  const p = getPlot([groupInfo1]);
-  runpp({
-    holder,
-    state: { plots: [p] },
-    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
-  });
-});
-function getHolder() {
-  return select_default("body").append("div").style("border", "1px solid #aaa").style("padding", "5px").style("margin", "5px");
-}
-function getPlot(groups) {
-  const p = {
-    chartType: "genomeBrowser",
-    geneSearchResult: { chr: "chr10", start: 61901683, stop: 62096944 }
-  };
-  if (groups) {
-    p.snvindel = {
-      details: {
-        groups,
-        groupTestMethods: [
-          { name: "Allele frequency difference" },
-          { name: "Fisher's exact test", axisLabel: "-log10(pvalue)" }
-        ],
-        groupTestMethodsIdx: 1
-      }
-    };
-  }
-  return p;
-}
-var runpp = getRunPp("mass", {
-  state: {
-    nav: { activeTab: 1 },
-    vocab: { dslabel: "SJLife", genome: "hg38" },
-    plots: [getPlot()]
-  },
-  debug: 1
-});
-function runTests(test, holder) {
-  return async (gb) => {
-    const div = gb.Inner.dom.holder;
-    const blockDiv = await detectOne({ elem: div.node(), selector: ".sja_Block_div" });
-    test.ok(blockDiv, "Block div is rendered");
-    const tklst = blockDiv.querySelectorAll('[data-testid="sja_sample_menu_opener"]');
-    test.equal(tklst.length, 2, "Block has 2 tracks");
-    const variantTk = tklst[0];
-    const variants = await detectGt({ elem: variantTk, selector: ".sja_aa_discg" });
-    test.ok(variants.length > 0, "Should render variants in variants track");
-    if (test._ok) holder.remove();
-    test.end();
-  };
-}
-var groupFilterAML = {
-  type: "filter",
-  filter: {
-    type: "tvslst",
-    in: true,
-    join: "",
-    lst: [
-      {
-        type: "tvs",
-        tvs: {
-          term: { id: "diaggrp_s", name: "Diagnosis Group", type: "categorical" },
-          values: [{ key: "Acute myeloid leukemia", label: "Acute myeloid leukemia" }]
-        }
-      }
-    ]
-  }
-};
-var groupFilterALLmale = {
-  type: "filter",
-  filter: {
-    type: "tvslst",
-    in: true,
-    join: "and",
-    lst: [
-      {
-        type: "tvs",
-        tvs: {
-          term: { id: "diaggrp_s", name: "Diagnosis Group", type: "categorical" },
-          values: [{ key: "Acute lymphoblastic leukemia", label: "Acute lymphoblastic leukemia" }]
-        }
-      },
-      {
-        type: "tvs",
-        tvs: { term: { id: "sex_s", name: "Sex", type: "categorical" }, values: [{ key: "1", label: "Male" }] }
-      }
-    ]
-  }
-};
-var groupPopulation1 = {
-  type: "population",
-  key: "gnomAD",
-  label: "gnomAD",
-  allowto_adjust_race: true,
-  adjust_race: true
-};
-var groupPopulation2 = {
-  type: "population",
-  key: "TOPMed",
-  label: "TOPMed",
-  allowto_adjust_race: true,
-  adjust_race: true
-};
-var groupInfo1 = { type: "info", infoKey: "AF_sjlife" };
-var groupInfo2 = { type: "info", infoKey: "gnomAD_AF" };
-//# sourceMappingURL=genomeBrowser.spec-7PZCNBL3.js.map

package/dist/grin2-EUBCNH4Q.js

@@ -1,70 +0,0 @@
-import {
-  appInit
-} from "./chunk-CPIPN5F6.js";
-import "./chunk-MSSPT5YM.js";
-import "./chunk-X46YA4CB.js";
-import "./chunk-SKMFMGCD.js";
-import {
-  vocabInit
-} from "./chunk-QJ3HYZH3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-DMWOK4DS.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-5IMFPVGT.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VMRO6DMC.js";
-import "./chunk-HKKTNIMX.js";
-import "./chunk-GMRIEUBW.js";
-import "./chunk-4EZLVENZ.js";
-import {
-  copyMerge
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// gdc/grin2.ts
-async function gdcGRIN2ui(arg, _holder, genomes) {
-  const toolGenome = arg.genome || "hg38";
-  const toolDslabel = arg.dslabel || "GDC";
-  const genome = genomes[toolGenome];
-  if (!genome) throw toolGenome + " missing";
-  if (arg.filter0 && typeof arg.filter0 != "object") throw "arg.filter0 not object";
-  const vocabApi = await vocabInit({
-    state: { vocab: { genome: toolGenome, dslabel: toolDslabel } }
-  });
-  vocabApi.getTermdbConfig();
-  const plotAppApi = await appInit({
-    holder: select_default(arg.holder).select(".sja_root_holder"),
-    genome,
-    state: copyMerge(
-      {
-        genome: toolGenome,
-        dslabel: toolDslabel,
-        termfilter: { filter0: arg.filter0 },
-        plots: [{ chartType: "grin2" }]
-      },
-      arg.state || {}
-    ),
-    app: arg.opts?.app || {}
-  });
-  return plotAppApi;
-}
-export {
-  gdcGRIN2ui
-};
-//# sourceMappingURL=grin2-EUBCNH4Q.js.map