@sjcrh/proteinpaint-client 2.220.0 → 2.222.0

package/dist/genomeBrowser.spec-BFTGLRHG.js

@@ -0,0 +1,272 @@
+import {
+  getRunPp
+} from "./chunk-OPMEDR4F.js";
+import {
+  detectGt,
+  detectOne
+} from "./chunk-WA3C3A2M.js";
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import "./chunk-QI4EZK7S.js";
+import "./chunk-ZD6AIFTS.js";
+import "./chunk-LXSBSJUL.js";
+import "./chunk-34AGCF72.js";
+import "./chunk-O6T4SDC7.js";
+import "./chunk-3KKI63GB.js";
+import "./chunk-MKAF2BHB.js";
+import "./chunk-4FTH4L3A.js";
+import "./chunk-VLIOMJDR.js";
+import "./chunk-FRLAPBYW.js";
+import "./chunk-4ASBDE27.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-OF6FDDKV.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.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 {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.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-BFTGLRHG.js.map

package/dist/grin2-4AXUYJIL.js

@@ -0,0 +1,66 @@
+import {
+  appInit
+} from "./chunk-7TRD7A2U.js";
+import "./chunk-LHM4UVYZ.js";
+import "./chunk-4E2F26CC.js";
+import "./chunk-FE5TCBIT.js";
+import {
+  vocabInit
+} from "./chunk-4ASBDE27.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-OF6FDDKV.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.js";
+import {
+  copyMerge
+} from "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.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=grin2-4AXUYJIL.js.map