@sjcrh/proteinpaint-client 2.181.0 → 2.182.1

package/dist/dictionary-D4E2VEJT.js

@@ -0,0 +1,109 @@
+import {
+  appInit
+} from "./chunk-NVB7MQLH.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-4JON7TLI.js";
+import "./chunk-7RN3L2BX.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/dictionary.js
+var MassDict = class _MassDict {
+  static type = "tree";
+  constructor(opts) {
+    this.type = _MassDict.type;
+    this.dom = {
+      holder: opts.holder.style("padding", "20px"),
+      header: opts.header
+    };
+  }
+  async init(appState) {
+    const config = appState.plots.find((p) => p.id === this.id) || {};
+    const opts = {
+      vocabApi: this.app.vocabApi,
+      holder: this.dom.holder,
+      state: this.getState(appState),
+      tree: {
+        click_term: (_term) => {
+          const term = _term.term || _term;
+          const _config = Object.assign({}, config?.spawnConfig, {
+            chartType: term.type == "survival" ? "survival" : "summary",
+            term: _term.term ? _term : { term }
+          });
+          this.app.dispatch({
+            type: "plot_create",
+            config: _config
+          });
+          this.app.dispatch({
+            type: "plot_delete",
+            id: this.id
+          });
+        }
+      }
+    };
+    if (config?.tree?.usecase) {
+      opts.tree.usecase = config.tree.usecase;
+    }
+    this.tree = await appInit(opts);
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id) || {};
+    const tree = { usecase: { target: "dictionary" } };
+    if (config?.tree?.usecase?.specialCase) {
+      tree.usecase.specialCase = config.tree.usecase.specialCase;
+    }
+    return {
+      tree,
+      vocab: appState.vocab,
+      activeCohort: appState.activeCohort,
+      termfilter: appState.termfilter,
+      selectdTerms: appState.selectedTerms,
+      customTerms: appState.customTerms
+    };
+  }
+  main() {
+    if (this.dom.header) this.dom.header.text("Data Variables");
+    this.tree.dispatch({
+      type: "app_refresh",
+      state: this.state
+    });
+  }
+};
+var dictInit = getCompInit(MassDict);
+var componentInit = dictInit;
+function getPlotConfig(opts, app) {
+  const config = { hidePlotFilter: true };
+  return copyMerge(config, opts);
+}
+export {
+  componentInit,
+  dictInit,
+  getPlotConfig
+};
+//# sourceMappingURL=dictionary-D4E2VEJT.js.map

package/dist/dictionary-D4E2VEJT.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/dictionary.js"],
+  "sourcesContent": ["import { getCompInit, copyMerge } from '#rx'\nimport { appInit } from '#termdb/app'\n\n/**\n * The dictionary spawns either the survival or summary plot, depending on the term selected. \n * \n * .spawnConfig:{}\n\t\tproperties to pass on to the spawning plot (e.g. survival or summary), as needed\n\t\te.g. chartType: 'dictionary',\n\t\t\t\tspawnConfig: {\n\t\t\t\tparentId: this.id,\n\t\t\t}\n\t\tIn this example, the parentId is passed to the spawned survival or summary plot. \n */\n\nclass MassDict {\n\tstatic type = 'tree'\n\n\tconstructor(opts) {\n\t\tthis.type = MassDict.type\n\t\tthis.dom = {\n\t\t\tholder: opts.holder.style('padding', '20px'),\n\t\t\theader: opts.header\n\t\t}\n\t}\n\n\tasync init(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id) || {}\n\t\tconst opts = {\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tholder: this.dom.holder,\n\t\t\tstate: this.getState(appState),\n\t\t\ttree: {\n\t\t\t\tclick_term: _term => {\n\t\t\t\t\tconst term = _term.term || _term\n\t\t\t\t\tconst _config = Object.assign({}, config?.spawnConfig, {\n\t\t\t\t\t\tchartType: term.type == 'survival' ? 'survival' : 'summary',\n\t\t\t\t\t\tterm: _term.term ? _term : { term }\n\t\t\t\t\t})\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tconfig: _config\n\t\t\t\t\t})\n\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_delete',\n\t\t\t\t\t\tid: this.id\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (config?.tree?.usecase) {\n\t\t\topts.tree.usecase = config.tree.usecase\n\t\t}\n\t\tthis.tree = await appInit(opts)\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id) || {}\n\t\tconst tree = { usecase: { target: 'dictionary' } }\n\t\tif (config?.tree?.usecase?.specialCase) {\n\t\t\ttree.usecase.specialCase = config.tree.usecase.specialCase\n\t\t}\n\t\treturn {\n\t\t\ttree,\n\t\t\tvocab: appState.vocab,\n\t\t\tactiveCohort: appState.activeCohort,\n\t\t\ttermfilter: appState.termfilter,\n\t\t\tselectdTerms: appState.selectedTerms,\n\t\t\tcustomTerms: appState.customTerms\n\t\t}\n\t}\n\n\tmain() {\n\t\tif (this.dom.header) this.dom.header.text('Data Variables')\n\t\tthis.tree.dispatch({\n\t\t\ttype: 'app_refresh',\n\t\t\tstate: this.state\n\t\t})\n\t}\n}\n\nexport const dictInit = getCompInit(MassDict)\nexport const componentInit = dictInit\n\nexport function getPlotConfig(opts, app) {\n\t// currently, there are no configurations options for\n\t// the dictionary tree; may add appearance, styling options later\n\tconst config = { hidePlotFilter: true }\n\t// may apply overrides to the default configuration\n\treturn copyMerge(config, opts)\n}\n"],
+  "mappings": ";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAeA,IAAM,WAAN,MAAM,UAAS;AAAA,EACd,OAAO,OAAO;AAAA,EAEd,YAAY,MAAM;AACjB,SAAK,OAAO,UAAS;AACrB,SAAK,MAAM;AAAA,MACV,QAAQ,KAAK,OAAO,MAAM,WAAW,MAAM;AAAA,MAC3C,QAAQ,KAAK;AAAA,IACd;AAAA,EACD;AAAA,EAEA,MAAM,KAAK,UAAU;AACpB,UAAM,SAAS,SAAS,MAAM,KAAK,OAAK,EAAE,OAAO,KAAK,EAAE,KAAK,CAAC;AAC9D,UAAM,OAAO;AAAA,MACZ,UAAU,KAAK,IAAI;AAAA,MACnB,QAAQ,KAAK,IAAI;AAAA,MACjB,OAAO,KAAK,SAAS,QAAQ;AAAA,MAC7B,MAAM;AAAA,QACL,YAAY,WAAS;AACpB,gBAAM,OAAO,MAAM,QAAQ;AAC3B,gBAAM,UAAU,OAAO,OAAO,CAAC,GAAG,QAAQ,aAAa;AAAA,YACtD,WAAW,KAAK,QAAQ,aAAa,aAAa;AAAA,YAClD,MAAM,MAAM,OAAO,QAAQ,EAAE,KAAK;AAAA,UACnC,CAAC;AACD,eAAK,IAAI,SAAS;AAAA,YACjB,MAAM;AAAA,YACN,QAAQ;AAAA,UACT,CAAC;AAED,eAAK,IAAI,SAAS;AAAA,YACjB,MAAM;AAAA,YACN,IAAI,KAAK;AAAA,UACV,CAAC;AAAA,QACF;AAAA,MACD;AAAA,IACD;AACA,QAAI,QAAQ,MAAM,SAAS;AAC1B,WAAK,KAAK,UAAU,OAAO,KAAK;AAAA,IACjC;AACA,SAAK,OAAO,MAAM,QAAQ,IAAI;AAAA,EAC/B;AAAA,EAEA,SAAS,UAAU;AAClB,UAAM,SAAS,SAAS,MAAM,KAAK,OAAK,EAAE,OAAO,KAAK,EAAE,KAAK,CAAC;AAC9D,UAAM,OAAO,EAAE,SAAS,EAAE,QAAQ,aAAa,EAAE;AACjD,QAAI,QAAQ,MAAM,SAAS,aAAa;AACvC,WAAK,QAAQ,cAAc,OAAO,KAAK,QAAQ;AAAA,IAChD;AACA,WAAO;AAAA,MACN;AAAA,MACA,OAAO,SAAS;AAAA,MAChB,cAAc,SAAS;AAAA,MACvB,YAAY,SAAS;AAAA,MACrB,cAAc,SAAS;AAAA,MACvB,aAAa,SAAS;AAAA,IACvB;AAAA,EACD;AAAA,EAEA,OAAO;AACN,QAAI,KAAK,IAAI,OAAQ,MAAK,IAAI,OAAO,KAAK,gBAAgB;AAC1D,SAAK,KAAK,SAAS;AAAA,MAClB,MAAM;AAAA,MACN,OAAO,KAAK;AAAA,IACb,CAAC;AAAA,EACF;AACD;AAEO,IAAM,WAAW,YAAY,QAAQ;AACrC,IAAM,gBAAgB;AAEtB,SAAS,cAAc,MAAM,KAAK;AAGxC,QAAM,SAAS,EAAE,gBAAgB,KAAK;AAEtC,SAAO,UAAU,QAAQ,IAAI;AAC9B;",
+  "names": []
+}

package/dist/dnaMethylation-IFZWWBUG.js

@@ -0,0 +1,36 @@
+import {
+  SearchHandler
+} from "./chunk-KWFEGPZL.js";
+import "./chunk-NVB7MQLH.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-4JON7TLI.js";
+import "./chunk-7RN3L2BX.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  SearchHandler
+};
+//# sourceMappingURL=dnaMethylation-IFZWWBUG.js.map

package/dist/dnaMethylation.integration.spec-UKV4BSIO.js

@@ -0,0 +1,165 @@
+import {
+  hg38
+} from "./chunk-7VB2BKXW.js";
+import {
+  SearchHandler
+} from "./chunk-KWFEGPZL.js";
+import {
+  sleep
+} from "./chunk-SSPDNHDW.js";
+import {
+  require_tape
+} from "./chunk-QWOE5YTB.js";
+import {
+  vocabInit
+} from "./chunk-NVB7MQLH.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-4JON7TLI.js";
+import "./chunk-7RN3L2BX.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import {
+  TermTypes
+} from "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// termdb/handlers/test/dnaMethylation.integration.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+var vocabApi = await getVocabApi();
+var handler = new SearchHandler();
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- dnaMethylation search handler -***-");
+  test.end();
+});
+(0, import_tape.default)("Search handler layout", async (test) => {
+  const holder = getHolder();
+  await initializeSearchHandler({ holder });
+  const geneSearchInput = holder.select(".sja_genesearchinput").node();
+  test.ok(geneSearchInput, "should display gene search input");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Coordinate search", async (test) => {
+  let term;
+  const callback = (_term) => {
+    term = _term;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const geneSearchInput = holder.select(".sja_genesearchinput").node();
+  const chr = "chr17";
+  const start = 7661778;
+  const stop = 7687537;
+  const coord = `${chr}:${start}-${stop}`;
+  geneSearchInput.value = coord;
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(term.chr, chr, "term.chr should equal input chr");
+  test.equal(term.start, start, "term.start should equal input start");
+  test.equal(term.stop, stop, "term.stop should equal input stop");
+  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Gene search", async (test) => {
+  let term;
+  const callback = (_term) => {
+    term = _term;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const geneSearchInput = holder.select(".sja_genesearchinput").node();
+  const geneSymbol = "TP53";
+  geneSearchInput.value = geneSymbol;
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  const blockSvg = holder.select('[data-testid="sjpp_block_svg"]').node();
+  test.ok(blockSvg, "should render block svg");
+  const submitBtn = holder.select('[data-testid="sjpp-dnaMethylation-submitDiv"]').select("button").node();
+  submitBtn.click();
+  await sleep(100);
+  test.equal(term.chr, "chr17", "term.chr should be TP53 chr");
+  test.equal(term.start, 7661778, "term.start should be TP53 start");
+  test.equal(term.stop, 7687537, "term.stop should be TP53 stop");
+  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Gene search with navigation", async (test) => {
+  let term;
+  const callback = (_term) => {
+    term = _term;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const geneSearchInput = holder.select(".sja_genesearchinput").node();
+  const geneSymbol = "TP53";
+  geneSearchInput.value = geneSymbol;
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(1e3);
+  const blockCoordInput = holder.select(".sja_Block_div").select("input").node();
+  const chr = "chr17";
+  const start = 7682350;
+  const stop = 7684350;
+  const coord = `${chr}:${start}-${stop}`;
+  blockCoordInput.value = coord;
+  blockCoordInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(1e3);
+  const submitBtn = holder.select('[data-testid="sjpp-dnaMethylation-submitDiv"]').select("button").node();
+  submitBtn.click();
+  await sleep(100);
+  test.equal(term.chr, chr, "term.chr should equal input chr");
+  test.equal(term.start, 7682349, "term.start should equal input start");
+  test.equal(term.stop, 7684349, "term.stop should equal input stop");
+  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+async function getVocabApi() {
+  const vocabApi2 = vocabInit({ state: { vocab: { genome: "hg38-test", dslabel: "TermdbTest" } } });
+  if (!vocabApi2) throw "vocabApi is missing";
+  await vocabApi2.getTermdbConfig();
+  return vocabApi2;
+}
+function getHolder() {
+  const holder = select_default("body").append("div");
+  return holder;
+}
+async function initializeSearchHandler(opts) {
+  const callback = opts.callback || (() => {
+  });
+  const hg38_copy = structuredClone(hg38);
+  hg38_copy.hasSNP = false;
+  await handler.init({
+    holder: opts.holder,
+    app: { vocabApi },
+    genomeObj: hg38_copy,
+    callback
+  });
+}
+//# sourceMappingURL=dnaMethylation.integration.spec-UKV4BSIO.js.map

package/dist/dnaMethylation.integration.spec-UKV4BSIO.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termdb/handlers/test/dnaMethylation.integration.spec.ts"],
+  "sourcesContent": ["import tape from 'tape'\nimport * as d3s from 'd3-selection'\nimport { SearchHandler } from '../dnaMethylation.ts'\nimport { hg38 } from '../../../test/testdata/genomes'\nimport { sleep } from '../../../test/test.helpers.js'\nimport { vocabInit } from '../../vocabulary'\nimport { TermTypes } from '#shared/terms.js'\n\n/*\nTests:\n\tSearch handler layout\n\tCoordinate search\n\tGene search\n\tGene search with navigation\n*/\n\n/**************\n test sections\n***************/\n\nconst vocabApi: any = await getVocabApi()\nconst handler = new SearchHandler()\n\ntape('\\n', function (test) {\n\ttest.comment('-***- dnaMethylation search handler -***-')\n\ttest.end()\n})\n\ntape('Search handler layout', async test => {\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder })\n\tconst geneSearchInput = holder.select('.sja_genesearchinput').node()\n\ttest.ok(geneSearchInput, 'should display gene search input')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Coordinate search', async test => {\n\tlet term\n\tconst callback = _term => {\n\t\tterm = _term\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst geneSearchInput: any = holder.select('.sja_genesearchinput').node()\n\tconst chr = 'chr17'\n\tconst start = 7661778\n\tconst stop = 7687537\n\tconst coord = `${chr}:${start}-${stop}`\n\tgeneSearchInput.value = coord\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(term.chr, chr, 'term.chr should equal input chr')\n\ttest.equal(term.start, start, 'term.start should equal input start')\n\ttest.equal(term.stop, stop, 'term.stop should equal input stop')\n\t/** No longer necessary to pass the unit or name in the search handler.\n\t * Commenting out for now. Search handler may become more sophisticated and\n\t * require handling these properties in the future. */\n\t// test.equal(term.id, coord, 'term.id should equal input coord')\n\t// const unit = vocabApi.termdbConfig.queries.dnaMethylation.unit\n\t// const name = `${coord} ${unit}`\n\t// test.equal(term.name, name, 'term.name should be <coord> <unit>')\n\ttest.equal(term.type, TermTypes.DNA_METHYLATION, 'term.type should be dnaMethylation')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Gene search', async test => {\n\tlet term\n\tconst callback = _term => {\n\t\tterm = _term\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst geneSearchInput: any = holder.select('.sja_genesearchinput').node()\n\tconst geneSymbol = 'TP53'\n\tgeneSearchInput.value = geneSymbol\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\tconst blockSvg = holder.select('[data-testid=\"sjpp_block_svg\"]').node()\n\ttest.ok(blockSvg, 'should render block svg')\n\tconst submitBtn: any = holder.select('[data-testid=\"sjpp-dnaMethylation-submitDiv\"]').select('button').node()\n\tsubmitBtn.click()\n\tawait sleep(100)\n\ttest.equal(term.chr, 'chr17', 'term.chr should be TP53 chr')\n\ttest.equal(term.start, 7661778, 'term.start should be TP53 start')\n\ttest.equal(term.stop, 7687537, 'term.stop should be TP53 stop')\n\t// See note above\n\t// const coord = 'chr17:7661778-7687537'\n\t// test.equal(term.id, coord, 'term.id should equal input coord')\n\t// const unit = vocabApi.termdbConfig.queries.dnaMethylation.unit\n\t// const name = `${coord} ${unit}`\n\t// test.equal(term.name, name, 'term.name should be <coord> <unit>')\n\ttest.equal(term.type, TermTypes.DNA_METHYLATION, 'term.type should be dnaMethylation')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Gene search with navigation', async test => {\n\tlet term\n\tconst callback = _term => {\n\t\tterm = _term\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\t// search by gene symbol\n\tconst geneSearchInput: any = holder.select('.sja_genesearchinput').node()\n\tconst geneSymbol = 'TP53'\n\tgeneSearchInput.value = geneSymbol\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(1000)\n\t// then navigate to 2kb region within gene\n\tconst blockCoordInput: any = holder.select('.sja_Block_div').select('input').node()\n\tconst chr = 'chr17'\n\tconst start = 7682350\n\tconst stop = 7684350\n\tconst coord = `${chr}:${start}-${stop}`\n\tblockCoordInput.value = coord\n\tblockCoordInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(1000)\n\tconst submitBtn: any = holder.select('[data-testid=\"sjpp-dnaMethylation-submitDiv\"]').select('button').node()\n\tsubmitBtn.click()\n\tawait sleep(100)\n\t// term coordinate should equal coordinate of target region\n\t// TODO: term.start and term.stop are actually different by 1bp compared\n\t// to input start and input stop, respectively. This is different behavior\n\t// than when inputting a coordinate into the gene search box outside of block (see the \"Coordinate search\" test section above). Should resolve this discrepancy.\n\ttest.equal(term.chr, chr, 'term.chr should equal input chr')\n\ttest.equal(term.start, 7682349, 'term.start should equal input start')\n\ttest.equal(term.stop, 7684349, 'term.stop should equal input stop')\n\t// See note above\n\t// const new_coord = 'chr17:7682349-7684349'\n\t// test.equal(term.id, new_coord, 'term.id should equal input coord')\n\t// const unit = vocabApi.termdbConfig.queries.dnaMethylation.unit\n\t// const name = `${new_coord} ${unit}`\n\t// test.equal(term.name, name, 'term.name should be <coord> <unit>')\n\ttest.equal(term.type, TermTypes.DNA_METHYLATION, 'term.type should be dnaMethylation')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\n/*************************\n reusable helper functions\n**************************/\n\nasync function getVocabApi() {\n\tconst vocabApi = vocabInit({ state: { vocab: { genome: 'hg38-test', dslabel: 'TermdbTest' } } })\n\tif (!vocabApi) throw 'vocabApi is missing'\n\tawait vocabApi.getTermdbConfig()\n\treturn vocabApi\n}\n\nfunction getHolder() {\n\tconst holder = d3s.select('body').append('div')\n\treturn holder\n}\n\nasync function initializeSearchHandler(opts) {\n\tconst callback = opts.callback || (() => {})\n\tconst hg38_copy = structuredClone(hg38)\n\thg38_copy.hasSNP = false // to allow coordinate input\n\tawait handler.init({\n\t\tholder: opts.holder,\n\t\tapp: { vocabApi },\n\t\tgenomeObj: hg38_copy,\n\t\tcallback\n\t})\n}\n"],
+  "mappings": ";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kBAAiB;AAoBjB,IAAM,WAAgB,MAAM,YAAY;AACxC,IAAM,UAAU,IAAI,cAAc;AAAA,IAElC,YAAAA,SAAK,MAAM,SAAU,MAAM;AAC1B,OAAK,QAAQ,2CAA2C;AACxD,OAAK,IAAI;AACV,CAAC;AAAA,IAED,YAAAA,SAAK,yBAAyB,OAAM,SAAQ;AAC3C,QAAM,SAAS,UAAU;AACzB,QAAM,wBAAwB,EAAE,OAAO,CAAC;AACxC,QAAM,kBAAkB,OAAO,OAAO,sBAAsB,EAAE,KAAK;AACnE,OAAK,GAAG,iBAAiB,kCAAkC;AAC3D,MAAI,KAAK,KAAK,EAAG,QAAO,OAAO;AAC/B,OAAK,IAAI;AACV,CAAC;AAAA,IAED,YAAAA,SAAK,qBAAqB,OAAM,SAAQ;AACvC,MAAI;AACJ,QAAM,WAAW,WAAS;AACzB,WAAO;AAAA,EACR;AACA,QAAM,SAAS,UAAU;AACzB,QAAM,wBAAwB,EAAE,QAAQ,SAAS,CAAC;AAClD,QAAM,kBAAuB,OAAO,OAAO,sBAAsB,EAAE,KAAK;AACxE,QAAM,MAAM;AACZ,QAAM,QAAQ;AACd,QAAM,OAAO;AACb,QAAM,QAAQ,GAAG,GAAG,IAAI,KAAK,IAAI,IAAI;AACrC,kBAAgB,QAAQ;AACxB,kBAAgB,cAAc,IAAI,cAAc,SAAS,EAAE,KAAK,SAAS,MAAM,SAAS,SAAS,KAAK,CAAC,CAAC;AACxG,QAAM,MAAM,GAAG;AACf,OAAK,MAAM,KAAK,KAAK,KAAK,iCAAiC;AAC3D,OAAK,MAAM,KAAK,OAAO,OAAO,qCAAqC;AACnE,OAAK,MAAM,KAAK,MAAM,MAAM,mCAAmC;AAQ/D,OAAK,MAAM,KAAK,MAAM,UAAU,iBAAiB,oCAAoC;AACrF,MAAI,KAAK,KAAK,EAAG,QAAO,OAAO;AAC/B,OAAK,IAAI;AACV,CAAC;AAAA,IAED,YAAAA,SAAK,eAAe,OAAM,SAAQ;AACjC,MAAI;AACJ,QAAM,WAAW,WAAS;AACzB,WAAO;AAAA,EACR;AACA,QAAM,SAAS,UAAU;AACzB,QAAM,wBAAwB,EAAE,QAAQ,SAAS,CAAC;AAClD,QAAM,kBAAuB,OAAO,OAAO,sBAAsB,EAAE,KAAK;AACxE,QAAM,aAAa;AACnB,kBAAgB,QAAQ;AACxB,kBAAgB,cAAc,IAAI,cAAc,SAAS,EAAE,KAAK,SAAS,MAAM,SAAS,SAAS,KAAK,CAAC,CAAC;AACxG,QAAM,MAAM,GAAG;AACf,QAAM,WAAW,OAAO,OAAO,gCAAgC,EAAE,KAAK;AACtE,OAAK,GAAG,UAAU,yBAAyB;AAC3C,QAAM,YAAiB,OAAO,OAAO,+CAA+C,EAAE,OAAO,QAAQ,EAAE,KAAK;AAC5G,YAAU,MAAM;AAChB,QAAM,MAAM,GAAG;AACf,OAAK,MAAM,KAAK,KAAK,SAAS,6BAA6B;AAC3D,OAAK,MAAM,KAAK,OAAO,SAAS,iCAAiC;AACjE,OAAK,MAAM,KAAK,MAAM,SAAS,+BAA+B;AAO9D,OAAK,MAAM,KAAK,MAAM,UAAU,iBAAiB,oCAAoC;AACrF,MAAI,KAAK,KAAK,EAAG,QAAO,OAAO;AAC/B,OAAK,IAAI;AACV,CAAC;AAAA,IAED,YAAAA,SAAK,+BAA+B,OAAM,SAAQ;AACjD,MAAI;AACJ,QAAM,WAAW,WAAS;AACzB,WAAO;AAAA,EACR;AACA,QAAM,SAAS,UAAU;AACzB,QAAM,wBAAwB,EAAE,QAAQ,SAAS,CAAC;AAElD,QAAM,kBAAuB,OAAO,OAAO,sBAAsB,EAAE,KAAK;AACxE,QAAM,aAAa;AACnB,kBAAgB,QAAQ;AACxB,kBAAgB,cAAc,IAAI,cAAc,SAAS,EAAE,KAAK,SAAS,MAAM,SAAS,SAAS,KAAK,CAAC,CAAC;AACxG,QAAM,MAAM,GAAI;AAEhB,QAAM,kBAAuB,OAAO,OAAO,gBAAgB,EAAE,OAAO,OAAO,EAAE,KAAK;AAClF,QAAM,MAAM;AACZ,QAAM,QAAQ;AACd,QAAM,OAAO;AACb,QAAM,QAAQ,GAAG,GAAG,IAAI,KAAK,IAAI,IAAI;AACrC,kBAAgB,QAAQ;AACxB,kBAAgB,cAAc,IAAI,cAAc,SAAS,EAAE,KAAK,SAAS,MAAM,SAAS,SAAS,KAAK,CAAC,CAAC;AACxG,QAAM,MAAM,GAAI;AAChB,QAAM,YAAiB,OAAO,OAAO,+CAA+C,EAAE,OAAO,QAAQ,EAAE,KAAK;AAC5G,YAAU,MAAM;AAChB,QAAM,MAAM,GAAG;AAKf,OAAK,MAAM,KAAK,KAAK,KAAK,iCAAiC;AAC3D,OAAK,MAAM,KAAK,OAAO,SAAS,qCAAqC;AACrE,OAAK,MAAM,KAAK,MAAM,SAAS,mCAAmC;AAOlE,OAAK,MAAM,KAAK,MAAM,UAAU,iBAAiB,oCAAoC;AACrF,MAAI,KAAK,KAAK,EAAG,QAAO,OAAO;AAC/B,OAAK,IAAI;AACV,CAAC;AAMD,eAAe,cAAc;AAC5B,QAAMC,YAAW,UAAU,EAAE,OAAO,EAAE,OAAO,EAAE,QAAQ,aAAa,SAAS,aAAa,EAAE,EAAE,CAAC;AAC/F,MAAI,CAACA,UAAU,OAAM;AACrB,QAAMA,UAAS,gBAAgB;AAC/B,SAAOA;AACR;AAEA,SAAS,YAAY;AACpB,QAAM,SAAa,eAAO,MAAM,EAAE,OAAO,KAAK;AAC9C,SAAO;AACR;AAEA,eAAe,wBAAwB,MAAM;AAC5C,QAAM,WAAW,KAAK,aAAa,MAAM;AAAA,EAAC;AAC1C,QAAM,YAAY,gBAAgB,IAAI;AACtC,YAAU,SAAS;AACnB,QAAM,QAAQ,KAAK;AAAA,IAClB,QAAQ,KAAK;AAAA,IACb,KAAK,EAAE,SAAS;AAAA,IAChB,WAAW;AAAA,IACX;AAAA,EACD,CAAC;AACF;",
+  "names": ["tape", "vocabApi"]
+}