@sjcrh/proteinpaint-client 2.225.0 → 2.227.0

package/dist/junction.unit.spec-7EJK4HML.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termdb/handlers/test/junction.unit.spec.ts"],
+  "sourcesContent": ["import tape from 'tape'\nimport * as d3s from 'd3-selection'\nimport type { JunctionTerm } from '#types'\nimport { SearchHandler } from '../junction.ts'\nimport { makeJunctionCustomTerm } from '../junction.customTerm.ts'\n\nfunction makeJunction(id: string): JunctionTerm {\n\treturn {\n\t\ttype: 'junction',\n\t\tid,\n\t\tname: `Name ${id}`,\n\t\tchr: 'chr1',\n\t\tstart: 100,\n\t\tstop: 200,\n\t\tstrand: '+',\n\t\tinfo: {}\n\t} as JunctionTerm\n}\n\nfunction getOpts(\n\tholder,\n\tdslabel: string,\n\tcustomTerms: any[] = [],\n\tcallback = (_term: any) => {},\n\ttermCollectionSelectionMode?: 'fraction'\n) {\n\tconst state = { customTerms }\n\treturn {\n\t\tholder,\n\t\tcallback,\n\t\ttermCollectionSelectionMode,\n\t\tgenomeObj: { name: 'hg38' },\n\t\tapp: {\n\t\t\tvocabApi: {\n\t\t\t\tvocab: { dslabel },\n\t\t\t\tstate,\n\t\t\t\tasync deleteCustomTermById(id: string) {\n\t\t\t\t\tconst index = state.customTerms.findIndex(term => term.id === id)\n\t\t\t\t\tif (index !== -1) state.customTerms.splice(index, 1)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\ntape('\\n', test => {\n\ttest.comment('-***- termdb/handlers/junction -***-')\n\ttest.end()\n})\n\ntape('init() shows the empty-state message', async test => {\n\tconst holder = d3s.select('body').append('div')\n\tconst handler = new SearchHandler()\n\tawait handler.init(getOpts(holder, 'junction-handler-empty'))\n\n\ttest.ok(holder.text().includes('Junctions selected from genome browser'), 'shows the empty-state instructions')\n\n\tholder.remove()\n\ttest.end()\n})\n\ntape('ungrouped junctions render as selectable pills and can be deleted', async test => {\n\tconst holder = d3s.select('body').append('div')\n\tconst handler = new SearchHandler()\n\tlet selected: any\n\tconst dslabel = 'junction-handler-ungrouped'\n\tconst customTerms = [makeJunctionCustomTerm([makeJunction('junction-1')])]\n\tawait handler.init(\n\t\tgetOpts(holder, dslabel, customTerms, term => {\n\t\t\tselected = term\n\t\t})\n\t)\n\n\tconst pill = holder.select('.ts_pill')\n\ttest.equal(pill.text(), 'Name junction-1', 'renders the junction name in a pill')\n\t;(pill.node() as HTMLElement).click()\n\ttest.equal(selected?.id, 'junction-1', 'selects the individual junction')\n\t;(holder.select('[data-testid=\"sjpp-junction-delete\"]').node() as HTMLButtonElement).click()\n\tawait new Promise(resolve => setTimeout(resolve, 0))\n\ttest.equal(holder.selectAll('.ts_pill').size(), 0, 'removes the deleted junction pill')\n\ttest.ok(holder.text().includes('Junctions selected from genome browser'), 'restores the empty state')\n\n\tholder.remove()\n\ttest.end()\n})\n\ntape('event junctions render as one pill that selects and deletes the term collection', async test => {\n\tconst holder = d3s.select('body').append('div')\n\tconst handler = new SearchHandler()\n\tlet selected: any\n\tconst dslabel = 'junction-handler-event'\n\tconst customTerms = [makeJunctionCustomTerm([makeJunction('junction-1'), makeJunction('junction-2')], 'Event A')]\n\tawait handler.init(\n\t\tgetOpts(holder, dslabel, customTerms, term => {\n\t\t\tselected = term\n\t\t})\n\t)\n\n\tconst pills = holder.selectAll('.ts_pill')\n\ttest.equal(pills.size(), 1, 'renders one pill for the event and no member junction pills')\n\ttest.equal(pills.text(), 'Event A', 'uses the event label as the pill text')\n\ttest.ok(holder.text().includes('junction-1'), 'lists the first junction ID')\n\ttest.ok(holder.text().includes('junction-2'), 'lists the second junction ID')\n\t;(pills.node() as HTMLElement).click()\n\ttest.equal(selected?.type, 'termCollection', 'selects a term collection')\n\ttest.equal(selected?.memberType, 'numeric', 'creates a numeric collection')\n\ttest.equal(selected?.name, 'Event A', 'uses the event label as the collection name')\n\ttest.deepEqual(selected?.termIds, ['junction-1', 'junction-2'], 'includes all event junction IDs')\n\ttest.ok(selected?.propsByTermId['junction-1'].color, 'assigns the first junction a color')\n\ttest.ok(selected?.propsByTermId['junction-2'].color, 'assigns the second junction a color')\n\ttest.notEqual(\n\t\tselected?.propsByTermId['junction-1'].color,\n\t\tselected?.propsByTermId['junction-2'].color,\n\t\t'assigns distinct member colors'\n\t)\n\t;(holder.select('[data-testid=\"sjpp-junction-delete\"]').node() as HTMLButtonElement).click()\n\tawait new Promise(resolve => setTimeout(resolve, 0))\n\ttest.equal(holder.selectAll('.ts_pill').size(), 0, 'removes the complete event choice')\n\n\tholder.remove()\n\ttest.end()\n})\n\ntape('init() only shows state-backed junction custom terms', async test => {\n\tconst holder = d3s.select('body').append('div')\n\tconst handler = new SearchHandler()\n\tconst customTerms = [\n\t\tmakeJunctionCustomTerm([makeJunction('active-junction')]),\n\t\t{ id: 'other-custom-term', name: 'Other', tw: { term: { type: 'float', id: 'other', name: 'Other' } } }\n\t]\n\n\tawait handler.init(getOpts(holder, 'active', customTerms))\n\n\ttest.equal(holder.selectAll('.ts_pill').size(), 1, 'renders only one matching junction term')\n\ttest.equal(holder.select('.ts_pill').text(), 'Name active-junction', 'renders the state-backed junction')\n\n\tholder.remove()\n\ttest.end()\n})\n\ntape('event junction renders fraction choices when requested', async test => {\n\tconst holder = d3s.select('body').append('div')\n\tconst handler = new SearchHandler()\n\tlet selected: any\n\tconst customTerms = [makeJunctionCustomTerm([makeJunction('junction-1'), makeJunction('junction-2')], 'Event A')]\n\tawait handler.init(\n\t\tgetOpts(\n\t\t\tholder,\n\t\t\t'junction-handler-fraction',\n\t\t\tcustomTerms,\n\t\t\tterm => {\n\t\t\t\tselected = term\n\t\t\t},\n\t\t\t'fraction'\n\t\t)\n\t)\n\t;(holder.select('.ts_pill').node() as HTMLElement).click()\n\ttest.ok(holder.text().includes('Denominator'), 'renders denominator choices for the event collection')\n\t;(holder.select('[data-testid=\"sjpp-term-collection-fraction-select\"]').node() as HTMLButtonElement).click()\n\ttest.equal(selected?.type, 'TermCollectionTWFraction', 'returns a fraction wrapper')\n\ttest.deepEqual(selected?.q.denominators, ['junction-1', 'junction-2'], 'defaults both junctions as denominators')\n\ttest.deepEqual(selected?.q.numerators, ['junction-1'], 'defaults only the first junction as numerator')\n\ttest.equal(selected?.term.termlst.length, 2, 'retains both junction members')\n\n\tholder.remove()\n\ttest.end()\n})\n\ntape('the sample type row sets the chosen sample types on the picked junction and event', async test => {\n\tconst holder = d3s.select('body').append('div')\n\tconst handler = new SearchHandler()\n\tlet selected: any\n\tconst customTerms = [\n\t\tmakeJunctionCustomTerm([makeJunction('junction-1')]),\n\t\tmakeJunctionCustomTerm([makeJunction('junction-2'), makeJunction('junction-3')], 'Event A')\n\t]\n\tconst opts: any = getOpts(holder, 'junction-handler-sampletypes', customTerms, term => {\n\t\tselected = term\n\t})\n\topts.app.vocabApi.termdbConfig = {\n\t\tqueries: { junction: { sampleTypes: [2, 3] } },\n\t\tsampleTypes: {\n\t\t\t1: { name: 'patient', plural_name: 'patients', parent_id: null },\n\t\t\t2: { name: 'diagnosis sample', plural_name: 'diagnosis samples', parent_id: 1 },\n\t\t\t3: { name: 'relapse sample', plural_name: 'relapse samples', parent_id: 1 }\n\t\t}\n\t}\n\tawait handler.init(opts)\n\n\tconst pills = () => holder.selectAll('.ts_pill').nodes() as HTMLElement[]\n\tconst boxes = () => holder.selectAll('input[type=checkbox]').nodes() as HTMLInputElement[]\n\ttest.equal(boxes().length, 2, 'renders a checkbox for each sample type of the junction file')\n\n\tpills()[0].click()\n\ttest.equal(selected.name, 'Name junction-1', 'keeps the name when every sample type is checked')\n\ttest.notOk('sampleTypes' in selected, 'reads every sample, as before the selector, when every type is checked')\n\n\tboxes()[1].click()\n\tpills()[0].click()\n\ttest.deepEqual(selected.sampleTypes, [2], 'sets the checked sample types on the junction term')\n\ttest.equal(selected.name, 'Name junction-1 (diagnosis samples)', 'names the sample types')\n\ttest.equal(selected.id, 'junction-1', 'keeps the junction id')\n\ttest.notOk(customTerms[0].tw.term.sampleTypes, 'leaves the stored custom term unchanged')\n\n\tpills()[1].click()\n\ttest.deepEqual(selected.sampleTypes, [2], 'sets the sample types on the event collection')\n\ttest.ok(\n\t\tselected.termlst.every(m => m.sampleTypes?.[0] == 2),\n\t\t'sets them on each member junction, which the server reads on its own'\n\t)\n\n\t// a delete draws the list again, which must keep the choice and not apply the sample types twice\n\t;(holder.select('[data-testid=\"sjpp-junction-delete\"]').node() as HTMLButtonElement).click()\n\tawait new Promise(resolve => setTimeout(resolve, 0))\n\ttest.equal(boxes()[1].checked, false, 'keeps the sample type choice after a delete')\n\tpills()[0].click()\n\ttest.equal(selected.name, 'Event A (diagnosis samples)', 'names the sample types once after the list is redrawn')\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n"],
+  "mappings": 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+  "names": ["tape"]
+}

package/dist/launch.adhoc-ONCSL65L.js

@@ -0,0 +1,33 @@
+import {
+  launch
+} from "./chunk-PVJ6IIFA.js";
+import "./chunk-R6O3FLKW.js";
+import "./chunk-GKA6USKV.js";
+import "./chunk-4E2F26CC.js";
+import "./chunk-7NVFEGCE.js";
+import "./chunk-YBXQBSFY.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-QKVKQD6S.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-VVWZ4BOI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-2IAELUCN.js";
+import "./chunk-CFYWQJ7F.js";
+import "./chunk-2N345NXD.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";
+export {
+  launch
+};
+//# sourceMappingURL=launch.adhoc-ONCSL65L.js.map

package/dist/leftlabel.sample-H5G3U7AA.js

@@ -0,0 +1,260 @@
+import {
+  displaySampleTable,
+  getFilterName,
+  makelabel
+} from "./chunk-ZO7KUAIF.js";
+import "./chunk-7NVFEGCE.js";
+import "./chunk-LVFWXUUX.js";
+import "./chunk-46GCGTHJ.js";
+import "./chunk-72FUMSAN.js";
+import "./chunk-V2OJLJSK.js";
+import "./chunk-4FTH4L3A.js";
+import "./chunk-6UHSGC6G.js";
+import {
+  Tabs,
+  fillbar,
+  filterInit,
+  getNormalRoot,
+  renderTable,
+  violinRenderer
+} from "./chunk-YBXQBSFY.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-QKVKQD6S.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-VVWZ4BOI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-2IAELUCN.js";
+import "./chunk-CFYWQJ7F.js";
+import "./chunk-2N345NXD.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";
+
+// mds3/leftlabel.sample.js
+function makeSampleLabel(data, tk, block, laby) {
+  if (!tk.leftlabels.doms.samples) {
+    tk.leftlabels.doms.samples = makelabel(tk, block, laby);
+  }
+  if (data.sampleTotalNumber) {
+    tk.leftlabels.doms.samples.attr("class", "sja_clbtext2").style("opacity", 1).text(`${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? "s" : ""}`).attr("data-testid", "sjpp-mds3tk-samples-label").on("click", async (event) => {
+      tk.menutip.clear().showunder(event.target);
+      await mayShowSummary(tk, block);
+      const buttonrow = tk.menutip.d.append("div").style("margin", "10px");
+      menu_listSamples(buttonrow, data, tk, block);
+    });
+  } else {
+    tk.leftlabels.doms.samples.text("No samples").attr("class", "").style("opacity", 0.5).on("click", null);
+  }
+}
+function makeSampleFilterLabel(data, tk, block, laby) {
+  if (!tk.leftlabels.doms.filterObj) {
+    tk.leftlabels.doms.filterObj = makelabel(tk, block, laby);
+    tk.leftlabels.doms.filterObj.attr("data-testid", "sjpp-mds3tk-leftlabel-samplefilter");
+  }
+  tk.leftlabels.doms.filterObj.text(getFilterName(tk.filterObj)).on("click", async (event) => {
+    tk.menutip.clear().showunder(event.target);
+    const arg = {
+      holder: tk.menutip.d.append("div").style("margin", "10px"),
+      vocabApi: tk.mds.termdb.vocabApi,
+      callback: (f) => {
+        tk.filterObj = f;
+        tk.load();
+      }
+    };
+    mayAddGetCategoryArgs(arg, block);
+    filterInit(arg).main(tk.filterObj);
+  });
+}
+function mayAddGetCategoryArgs(arg, block) {
+  if (block.usegm) {
+    arg.getCategoriesArguments = { currentGeneNames: [block.usegm.name] };
+  } else {
+    arg.getCategoriesArguments = { rglst: structuredClone(block.rglst) };
+  }
+}
+async function mayShowSummary(tk, block) {
+  if (!tk.mds.variant2samples.twLst) {
+    return;
+  }
+  const div = tk.menutip.d.append("div").style("margin", "10px");
+  const wait = div.append("div").text("Loading...");
+  try {
+    const { summary } = await tk.mds.getSamples({ isSummary: true });
+    tk.leftlabels.__samples_data = summary;
+    wait.remove();
+    await showSummary4terms(summary, div.append("div").attr("data-testid", "sjpp-mds3tk-samplesummarydiv"), tk, block);
+  } catch (e) {
+    wait.text(`Error: ${e.message || e}`);
+    if (e.stack) console.log(e.stack);
+  }
+}
+async function showSummary4terms(data, div, tk, block) {
+  const tabs = [];
+  for (const { termid, numbycategory } of data) {
+    tabs.push({
+      label: tk.mds.variant2samples.twLst.find((i) => i.term.id == termid).term.name + (numbycategory ? `<span style="font-size:.8em;float:right;margin-left: 5px;">n=${numbycategory.length}</span>` : ""),
+      keydownCallback: function(event) {
+        setTimeout(() => {
+          const tr = this.contentHolder.select("tbody").select("tr").node();
+          if (!tr) return;
+          tr.focus();
+        }, 100);
+      }
+    });
+  }
+  new Tabs({
+    holder: div,
+    tabsPosition: "vertical",
+    linePosition: "right",
+    tabs
+  }).main();
+  for (const [i, d] of data.entries()) {
+    const holder = tabs[i].contentHolder.style("padding-left", "20px");
+    if (d.numbycategory) {
+      holder.append("div").text("Click a category to create new track.").style("margin-bottom", "10px").style("font-size", ".8em").style("opacity", 0.5);
+      showSummary4oneTerm(d.termid, holder, d.numbycategory, tk, block);
+      continue;
+    }
+    if (d.density_data) {
+      if (!Number.isFinite(d.density_data.min) || !Number.isFinite(d.density_data.max)) {
+        holder.append("div").text("No data");
+        continue;
+      }
+      holder.append("div").text("Select a range to create new track.").style("margin-bottom", "10px").style("font-size", ".8em").style("opacity", 0.5);
+      showDensity4oneTerm(d.termid, holder, d, tk, block);
+      continue;
+    }
+    throw "unknown summary data";
+  }
+}
+function showSummary4oneTerm(termid, div, numbycategory, tk, block) {
+  const tw = tk.mds.variant2samples.twLst.find((i) => i.term.id == termid);
+  if (!tw) throw "showSummary4oneTerm(): tw not found from variant2samples.twLst";
+  const rows = [];
+  for (const [category_key, count, total] of numbycategory) {
+    const sk = category_key.replace(/\s/g, "-");
+    const row = Object.assign(
+      [
+        { value: tw.term.values?.[category_key]?.label || category_key },
+        { html: total == void 0 ? "" : fillbar(null, { f: count / total, v1: count, v2: total }) },
+        {
+          html: `<span data-testid="sjpp-mds3tk-samsumcatmutcount-${sk}">${count}</span>
+						${total ? ` <span style="font-size:.8em">/ <span data-testid="sjpp-mds3tk-samsumcattotalcount-${sk}">${total}</span></span>` : ""}`
+        }
+      ],
+      {
+        testId: `sjpp-mds3tk-samsumcatrow-${sk}`
+      }
+    );
+    rows.push(row);
+  }
+  renderTable({
+    div,
+    rows,
+    columns: [
+      {
+        nowrap: true
+        // to force all category values to show in one line without wrap. otherwise they wrap and column width appears fixed
+      },
+      {},
+      {}
+    ],
+    showHeader: false,
+    singleMode: true,
+    noRadioBtn: true,
+    noButtonCallback: (i) => {
+      clickCategory(numbycategory[i][0]);
+    }
+  });
+  async function clickCategory(category) {
+    tk.menutip.clear();
+    const term = await tk.mds.termdb.vocabApi.getterm(termid);
+    if (!term.values || Object.keys(term.values).length == 0) {
+      term.values = {};
+      for (const c of numbycategory) {
+        term.values[c[0]] = { label: c[0], samplecount: c[1] };
+      }
+    }
+    const tvs = {
+      type: "tvs",
+      tvs: { term, values: [{ key: category }] }
+    };
+    createSubTk(tk, block, tvs);
+  }
+}
+function getNewFilter(tk, tvs) {
+  if (tk.filterObj) {
+    return getNormalRoot({
+      type: "tvslst",
+      join: "and",
+      in: true,
+      lst: [tk.filterObj, tvs]
+    });
+  }
+  return {
+    type: "tvslst",
+    in: true,
+    join: "",
+    lst: [tvs]
+  };
+}
+async function showDensity4oneTerm(termid, div, data, tk, block) {
+  const term = await tk.mds.termdb.vocabApi.getterm(termid);
+  const callback = async (range) => {
+    tk.menutip.clear();
+    const tvs = {
+      type: "tvs",
+      tvs: { term, ranges: [{ start: range.range_start, stop: range.range_end }] }
+    };
+    createSubTk(tk, block, tvs);
+  };
+  const vr = new violinRenderer({
+    holder: div,
+    rd: data.density_data,
+    width: 400,
+    height: 100,
+    radius: 8,
+    callback,
+    scaleFactor: term.valueConversion ? term.valueConversion.scaleFactor : 1
+  });
+  vr.render();
+}
+function createSubTk(tk, block, tvs) {
+  const tk2 = block.block_addtk_template(tk.duplicateTk(getNewFilter(tk, tvs)));
+  tk2.subtk = true;
+  tk2.g.attr("class", "sjpp-mds3tk-subtk");
+  block.tk_load(tk2);
+}
+function menu_listSamples(buttonrow, data, tk, block) {
+  buttonrow.append("div").text(`List ${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? "s" : ""}`).attr("class", "sja_menuoption sja_mds3_slb_sampletablebtn").attr("data-testid", "sjpp-mds3tk-list-samples-option").on("click", async () => {
+    tk.menutip.clear();
+    const wait = tk.menutip.d.append("div").text("Loading...").style("margin", "15px");
+    try {
+      const { samples } = await tk.mds.getSamples();
+      await displaySampleTable(samples, {
+        div: tk.menutip.d,
+        tk,
+        block
+      });
+      wait.remove();
+    } catch (e) {
+      wait.text(e.message || e);
+      console.log(e);
+    }
+  });
+}
+export {
+  makeSampleFilterLabel,
+  makeSampleLabel
+};
+//# sourceMappingURL=leftlabel.sample-H5G3U7AA.js.map

package/dist/leftlabel.sample-H5G3U7AA.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../mds3/leftlabel.sample.js"],
+  "sourcesContent": ["import { makelabel } from './leftlabel'\nimport { Tabs, fillbar, renderTable, violinRenderer } from '#dom'\nimport { displaySampleTable } from './sampletable'\nimport { filterInit, getNormalRoot } from '../filter/filter'\nimport { getFilterName } from './filterName'\n\n/*\nmakeSampleLabel()\n\tmakes the \"# samples\" sub label on the left.\n\tclick label to view summaries about samples that have mutation data in the view range\n\nmakeSampleFilterLabel()\ncreateSubTk()\n*/\n\nexport function makeSampleLabel(data, tk, block, laby) {\n\tif (!tk.leftlabels.doms.samples) {\n\t\t// \"Samples\" label is missing. create\n\t\ttk.leftlabels.doms.samples = makelabel(tk, block, laby)\n\t}\n\n\tif (data.sampleTotalNumber) {\n\t\t// current data has samples, activate label\n\t\ttk.leftlabels.doms.samples\n\t\t\t.attr('class', 'sja_clbtext2')\n\t\t\t.style('opacity', 1)\n\t\t\t.text(`${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? 's' : ''}`)\n\t\t\t.attr('data-testid', 'sjpp-mds3tk-samples-label')\n\t\t\t.on('click', async event => {\n\t\t\t\ttk.menutip.clear().showunder(event.target)\n\n\t\t\t\tawait mayShowSummary(tk, block)\n\n\t\t\t\tconst buttonrow = tk.menutip.d.append('div').style('margin', '10px')\n\n\t\t\t\tmenu_listSamples(buttonrow, data, tk, block)\n\t\t\t\t// TODO new button \"Customize variables\", launch tree in submit_lst mode to update tk.mds.variant2samples.twLst\n\t\t\t})\n\t} else {\n\t\t// current data has no sample, disable label\n\t\ttk.leftlabels.doms.samples.text('No samples').attr('class', '').style('opacity', 0.5).on('click', null)\n\t}\n}\n\nexport function makeSampleFilterLabel(data, tk, block, laby) {\n\t// track has a modifiable sample filter. add a new label to access the filter UI\n\tif (!tk.leftlabels.doms.filterObj) {\n\t\ttk.leftlabels.doms.filterObj = makelabel(tk, block, laby)\n\t\ttk.leftlabels.doms.filterObj.attr('data-testid', 'sjpp-mds3tk-leftlabel-samplefilter')\n\t}\n\n\ttk.leftlabels.doms.filterObj.text(getFilterName(tk.filterObj)).on('click', async event => {\n\t\ttk.menutip.clear().showunder(event.target)\n\n\t\t// display filter UI\n\n\t\tconst arg = {\n\t\t\tholder: tk.menutip.d.append('div').style('margin', '10px'),\n\t\t\tvocabApi: tk.mds.termdb.vocabApi,\n\t\t\tcallback: f => {\n\t\t\t\ttk.filterObj = f\n\t\t\t\ttk.load()\n\t\t\t}\n\t\t}\n\t\tmayAddGetCategoryArgs(arg, block)\n\t\tfilterInit(arg).main(tk.filterObj)\n\t})\n}\n\nfunction mayAddGetCategoryArgs(arg, block) {\n\tif (block.usegm) {\n\t\t/////////////////////////////////////\n\t\t//\n\t\t// GDC specific logic\n\t\t// in gene mode, supply the current gene name as a new parameter\n\t\t// for the vocabApi getCategories() query, so it can pull the number of mutated samples for a term\n\t\t// this parameter is used by some sneaky gdc-specific logic in termdb.matrix.js getData()\n\t\t// should not impact non-gdc datasets\n\t\t//\n\t\t/////////////////////////////////////\n\t\targ.getCategoriesArguments = { currentGeneNames: [block.usegm.name] }\n\t\t// TODO {name: block.usegm.name, isoform, q:{allowedDt}}\n\t} else {\n\t\t/////////////////////////////////////\n\t\t//\n\t\t// GDC specific logic\n\t\t// in genomic mode, pass rglst for pulling cases mutated in this region, handled in the same way as currentGeneNames\n\t\t//\n\t\t/////////////////////////////////////\n\t\targ.getCategoriesArguments = { rglst: structuredClone(block.rglst) }\n\t}\n}\n\nasync function mayShowSummary(tk, block) {\n\tif (!tk.mds.variant2samples.twLst) {\n\t\t// no terms to summarize for\n\t\treturn\n\t}\n\n\tconst div = tk.menutip.d.append('div').style('margin', '10px')\n\n\tconst wait = div.append('div').text('Loading...')\n\n\ttry {\n\t\tconst { summary } = await tk.mds.getSamples({ isSummary: true })\n\t\ttk.leftlabels.__samples_data = summary // for testing\n\t\twait.remove()\n\t\tawait showSummary4terms(summary, div.append('div').attr('data-testid', 'sjpp-mds3tk-samplesummarydiv'), tk, block)\n\t} catch (e) {\n\t\twait.text(`Error: ${e.message || e}`)\n\t\tif (e.stack) console.log(e.stack)\n\t}\n}\n\n/* show summaries over a list of terms\ndata is array, each ele: {termid, numbycategory}\n*/\nasync function showSummary4terms(data, div, tk, block) {\n\tconst tabs = []\n\tfor (const { termid, numbycategory } of data) {\n\t\ttabs.push({\n\t\t\tlabel:\n\t\t\t\ttk.mds.variant2samples.twLst.find(i => i.term.id == termid).term.name +\n\t\t\t\t(numbycategory\n\t\t\t\t\t? `<span style=\"font-size:.8em;float:right;margin-left: 5px;\">n=${numbycategory.length}</span>`\n\t\t\t\t\t: ''),\n\t\t\tkeydownCallback: function (event) {\n\t\t\t\tsetTimeout(() => {\n\t\t\t\t\tconst tr = this.contentHolder.select('tbody').select('tr').node()\n\t\t\t\t\tif (!tr) return\n\t\t\t\t\t// to support keyboard navigation, automatically highlight the first table row\n\t\t\t\t\t// after this tab/button is clicked, use setTimeout() to ensure the table has\n\t\t\t\t\t// finished rendering\n\t\t\t\t\t//\n\t\t\t\t\t// TODO: support violin plot range selection, which does not use table rows,\n\t\t\t\t\t//       should use start-stop input there\n\t\t\t\t\t//\n\t\t\t\t\ttr.focus()\n\t\t\t\t}, 100)\n\t\t\t}\n\t\t})\n\t}\n\n\tnew Tabs({\n\t\tholder: div,\n\t\ttabsPosition: 'vertical',\n\t\tlinePosition: 'right',\n\t\ttabs\n\t}).main()\n\n\tfor (const [i, d] of data.entries()) {\n\t\tconst holder = tabs[i].contentHolder.style('padding-left', '20px')\n\t\tif (d.numbycategory) {\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.text('Click a category to create new track.')\n\t\t\t\t.style('margin-bottom', '10px')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('opacity', 0.5)\n\t\t\tshowSummary4oneTerm(d.termid, holder, d.numbycategory, tk, block)\n\t\t\tcontinue\n\t\t}\n\t\tif (d.density_data) {\n\t\t\tif (!Number.isFinite(d.density_data.min) || !Number.isFinite(d.density_data.max)) {\n\t\t\t\tholder.append('div').text('No data')\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.text('Select a range to create new track.')\n\t\t\t\t.style('margin-bottom', '10px')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('opacity', 0.5)\n\t\t\tshowDensity4oneTerm(d.termid, holder, d, tk, block)\n\t\t\tcontinue\n\t\t}\n\t\tthrow 'unknown summary data'\n\t}\n}\n\n/*\nshow categories and #case for one term\nclick a category to launch subtrack\nnumbycategory = []\n\teach element is array of length 3 representing one category, from a categorical term\n\t[0] = category name\n\t[1] = number of cases mutated in current gene\n\t[2] = total number of cases from this category\n*/\nfunction showSummary4oneTerm(termid, div, numbycategory, tk, block) {\n\tconst tw = tk.mds.variant2samples.twLst.find(i => i.term.id == termid)\n\tif (!tw) throw 'showSummary4oneTerm(): tw not found from variant2samples.twLst'\n\n\tconst rows = []\n\tfor (const [category_key, count, total] of numbycategory) {\n\t\t// in future tw may be in groupsetting mode\n\t\tconst sk = category_key.replace(/\\s/g, '-') // safe key to avoid space\n\t\tconst row = Object.assign(\n\t\t\t[\n\t\t\t\t{ value: tw.term.values?.[category_key]?.label || category_key },\n\t\t\t\t{ html: total == undefined ? '' : fillbar(null, { f: count / total, v1: count, v2: total }) },\n\t\t\t\t{\n\t\t\t\t\thtml: `<span data-testid=\"sjpp-mds3tk-samsumcatmutcount-${sk}\">${count}</span>\n\t\t\t\t\t\t${\n\t\t\t\t\t\t\ttotal\n\t\t\t\t\t\t\t\t? ` <span style=\"font-size:.8em\">/ <span data-testid=\"sjpp-mds3tk-samsumcattotalcount-${sk}\">${total}</span></span>`\n\t\t\t\t\t\t\t\t: ''\n\t\t\t\t\t\t}`\n\t\t\t\t}\n\t\t\t],\n\t\t\t{\n\t\t\t\ttestId: `sjpp-mds3tk-samsumcatrow-${sk}`\n\t\t\t}\n\t\t)\n\t\trows.push(row)\n\t}\n\trenderTable({\n\t\tdiv,\n\t\trows,\n\t\tcolumns: [\n\t\t\t{\n\t\t\t\tnowrap: true // to force all category values to show in one line without wrap. otherwise they wrap and column width appears fixed\n\t\t\t},\n\t\t\t{},\n\t\t\t{}\n\t\t],\n\t\tshowHeader: false,\n\t\tsingleMode: true,\n\t\tnoRadioBtn: true,\n\t\tnoButtonCallback: i => {\n\t\t\tclickCategory(numbycategory[i][0])\n\t\t}\n\t})\n\n\tasync function clickCategory(category) {\n\t\t// for a selected category, launch subtrack\n\t\ttk.menutip.clear()\n\n\t\tconst term = await tk.mds.termdb.vocabApi.getterm(termid)\n\n\t\tif (!term.values || Object.keys(term.values).length == 0) {\n\t\t\t/////////////////////////////////////\n\t\t\t//\n\t\t\t// GDC specific logic:\n\t\t\t// a gdc term will have blank .values{}, fill in term.values{} so filter/tvs won't break\n\t\t\t//\n\t\t\t/////////////////////////////////////\n\t\t\tterm.values = {}\n\t\t\tfor (const c of numbycategory) {\n\t\t\t\tterm.values[c[0]] = { label: c[0], samplecount: c[1] }\n\t\t\t}\n\t\t}\n\n\t\tconst tvs = {\n\t\t\ttype: 'tvs',\n\t\t\ttvs: { term, values: [{ key: category }] }\n\t\t}\n\t\tcreateSubTk(tk, block, tvs)\n\t}\n}\n\nfunction getNewFilter(tk, tvs) {\n\tif (tk.filterObj) {\n\t\t// merge new tvs to current filter\n\t\treturn getNormalRoot({\n\t\t\ttype: 'tvslst',\n\t\t\tjoin: 'and',\n\t\t\tin: true,\n\t\t\tlst: [tk.filterObj, tvs]\n\t\t})\n\t}\n\t// create new filter\n\treturn {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin: '',\n\t\tlst: [tvs]\n\t}\n}\n\n// will be nice if the data computing and rendering can both be replaced by violin\nasync function showDensity4oneTerm(termid, div, data, tk, block) {\n\tconst term = await tk.mds.termdb.vocabApi.getterm(termid)\n\tconst callback = async range => {\n\t\t// a range is selected\n\t\ttk.menutip.clear()\n\t\tconst tvs = {\n\t\t\ttype: 'tvs',\n\t\t\ttvs: { term, ranges: [{ start: range.range_start, stop: range.range_end }] }\n\t\t}\n\t\tcreateSubTk(tk, block, tvs)\n\t}\n\tconst vr = new violinRenderer({\n\t\tholder: div,\n\t\trd: data.density_data,\n\t\twidth: 400,\n\t\theight: 100,\n\t\tradius: 8,\n\t\tcallback,\n\t\tscaleFactor: term.valueConversion ? term.valueConversion.scaleFactor : 1\n\t})\n\tvr.render()\n}\n\nfunction createSubTk(tk, block, tvs) {\n\tconst tk2 = block.block_addtk_template(tk.duplicateTk(getNewFilter(tk, tvs)))\n\ttk2.subtk = true\n\ttk2.g.attr('class', 'sjpp-mds3tk-subtk')\n\tblock.tk_load(tk2)\n}\n\nfunction menu_listSamples(buttonrow, data, tk, block) {\n\t// subject to change\n\n\tbuttonrow\n\t\t.append('div')\n\t\t.text(`List ${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? 's' : ''}`)\n\t\t.attr('class', 'sja_menuoption sja_mds3_slb_sampletablebtn')\n\t\t.attr('data-testid', 'sjpp-mds3tk-list-samples-option')\n\t\t.on('click', async () => {\n\t\t\ttk.menutip.clear()\n\t\t\tconst wait = tk.menutip.d.append('div').text('Loading...').style('margin', '15px')\n\t\t\ttry {\n\t\t\t\tconst { samples } = await tk.mds.getSamples()\n\t\t\t\tawait displaySampleTable(samples, {\n\t\t\t\t\tdiv: tk.menutip.d,\n\t\t\t\t\ttk,\n\t\t\t\t\tblock\n\t\t\t\t})\n\t\t\t\twait.remove()\n\t\t\t} catch (e) {\n\t\t\t\twait.text(e.message || e)\n\t\t\t\tconsole.log(e)\n\t\t\t}\n\t\t})\n}\n"],
+  "mappings": 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+  "names": []
+}

package/dist/lollipop-BWP4BG7Q.js

@@ -0,0 +1,162 @@
+import {
+  block_init_default
+} from "./chunk-HGIPR72Y.js";
+import {
+  addGeneSearchbox,
+  first_genetrack_tolist
+} from "./chunk-YBXQBSFY.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-QKVKQD6S.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import {
+  dofetch3
+} from "./chunk-VVWZ4BOI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-2IAELUCN.js";
+import "./chunk-CFYWQJ7F.js";
+import "./chunk-2N345NXD.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";
+
+// gdc/lollipop.js
+var tip = new Menu({ padding: "" });
+async function init(arg, holder, genomes) {
+  const useGenome = arg.genome || "hg38";
+  const useDslabel = arg.dslabel || "GDC";
+  const genome = genomes[useGenome];
+  if (!genome) throw useGenome + " missing";
+  if (arg.geneSearch4GDCmds3.onloadalltk_always && typeof arg.geneSearch4GDCmds3.onloadalltk_always != "function")
+    throw "arg.geneSearch4GDCmds3.onloadalltk_always not function";
+  if (arg.geneSearch4GDCmds3.postRender && typeof arg.geneSearch4GDCmds3.postRender != "function")
+    throw "arg.geneSearch4GDCmds3.postRender not function";
+  holder.selectAll(".sja_lollipop_holder").remove();
+  const mainDiv = holder.append("div").attr("class", "sja_lollipop_holder");
+  const geneInputDiv = mainDiv.append("div").style("margin-left", "20px");
+  geneInputDiv.append("div").text(
+    arg.geneSearch4GDCmds3.hardcodeCnvOnly ? `To view ${useDslabel} CNV segments over a gene or region, enter genomic position (chr11:108195437-108267444), dbSNP accesion, or gene name (MYC).` : `To view ${useDslabel} mutations on a gene, enter one of gene symbol (MYC), alias (c-Myc), GENCODE accession (ENSG00000136997, ENST00000621592), or RefSeq accession (NM_002467).`
+  );
+  const graphDiv = mainDiv.append("div").attr("class", "sja_geneSearch4GDCmds3_blockdiv");
+  const searchOpt = {
+    genome,
+    tip,
+    row: geneInputDiv,
+    callback: launchView,
+    geneSymbol: arg.geneSymbol,
+    triggerSearch: arg.geneSymbol && arg.geneSearch4GDCmds3?.hardcodeCnvOnly == true,
+    hideInputBeforeCallback: arg.geneSearch4GDCmds3?.hardcodeCnvOnly == true
+  };
+  if (!arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
+    searchOpt.searchOnly = "gene";
+  }
+  const coordInput = addGeneSearchbox(searchOpt);
+  let userSelection;
+  await arg.geneSearch4GDCmds3.postRender?.({ tip });
+  if (arg.state) {
+    if (arg.state.userSelection) launchView(false, arg.state.userSelection);
+    delete arg.state;
+  }
+  async function launchView(triggeredByInput = true, userSelection2) {
+    const pa = {
+      // param for instantiating block
+      genome,
+      holder: graphDiv,
+      gmmode: "exon only",
+      nobox: 1,
+      hide_dsHandles: arg.hide_dsHandles,
+      onloadalltk_always: arg.geneSearch4GDCmds3.onloadalltk_always
+    };
+    if (arg.tracks) {
+      pa.tklst = arg.tracks;
+    } else {
+      const tk = {
+        type: "mds3",
+        dslabel: useDslabel,
+        allow2selectSamples: arg.allow2selectSamples,
+        filter0: arg.filter0
+      };
+      pa.tklst = [tk];
+      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
+        tk.hardcodeCnvOnly = 1;
+        delete pa.gmmode;
+        first_genetrack_tolist(pa.genome, pa.tklst);
+      }
+      if (arg.geneSearch4GDCmds3.snvIndelOnly) {
+        tk.snvIndelOnly = 1;
+      }
+    }
+    if (userSelection2) {
+      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
+        if (typeof userSelection2 != "object") throw "userSelection not object when pa.block is true";
+        pa.chr = userSelection2.chr;
+        pa.start = userSelection2.start;
+        pa.stop = userSelection2.stop;
+        if (!pa.chr || !Number.isInteger(pa.start) || !Number.isInteger(pa.stop))
+          throw "userSelection not {chr,start,stop}";
+      } else {
+        if (typeof userSelection2 != "string") throw "userSelection should be string when pa.block is not true";
+        pa.query = userSelection2;
+      }
+    } else {
+      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
+        if (!coordInput.chr || !Number.isInteger(coordInput.start) || !Number.isInteger(coordInput.stop)) {
+          if (triggeredByInput) throw "coordInput.chr/start/stop missing";
+        }
+        pa.chr = coordInput.chr;
+        pa.start = coordInput.start;
+        pa.stop = coordInput.stop;
+      } else {
+        if (!coordInput.geneSymbol) {
+          if (triggeredByInput) throw "coordInput.geneSymbol missing";
+        }
+        const gmlst = (await dofetch3(`genelookup?deep=1&input=${coordInput.geneSymbol}&genome=${useGenome}`)).gmlst;
+        if (!Array.isArray(gmlst) || gmlst.length == 0) throw "gmlst is not non-empty array";
+        pa.query = getSelectedIsoform(coordInput, gmlst);
+        if (gmlst.some((i) => i.coding)) pa.gmmode = "protein";
+      }
+    }
+    graphDiv.selectAll("*").remove();
+    if (!arg.geneSearch4GDCmds3.hardcodeCnvOnly) return await block_init_default(pa);
+    const _ = await import("./block-AGX6Z4BR.js");
+    return new _.Block(pa);
+  }
+  const api = {
+    update: (_arg) => {
+      Object.assign(arg, _arg);
+      launchView(false);
+    },
+    getState: () => ({ userSelection })
+  };
+  return api;
+}
+function getSelectedIsoform(coordInput, gmlst) {
+  if (coordInput.fromWhat) {
+    if (gmlst.some((i) => i.isoform.toUpperCase() == coordInput.fromWhat.toUpperCase())) {
+      return coordInput.fromWhat;
+    }
+    if (coordInput.fromWhat.toUpperCase().startsWith("ENSG")) {
+      for (const i of gmlst) {
+        if (i.isdefault && i.isoform.startsWith("ENST")) return i.isoform;
+      }
+    }
+  }
+  const defaultIsoform = gmlst.find((i) => i.isdefault);
+  if (defaultIsoform) return defaultIsoform.isoform;
+  return gmlst[0].isoform;
+}
+export {
+  init
+};
+//# sourceMappingURL=lollipop-BWP4BG7Q.js.map