@sjcrh/proteinpaint-client 2.192.0 → 2.193.0

package/dist/isoformExpression.unit.spec-6FSMHT4K.js

@@ -1,208 +0,0 @@
-import {
-  SearchHandler,
-  filterIsoforms
-} from "./chunk-MP3DN6JK.js";
-import {
-  require_tape
-} from "./chunk-QWOE5YTB.js";
-import "./chunk-KUZPTJJO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-C4BCMAIK.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-LQJMCE7G.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-Z457XQSX.js";
-import "./chunk-AI2LUQS6.js";
-import "./chunk-2JR7RPB6.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-TLTS33EY.js";
-import {
-  ISOFORM_EXPRESSION
-} from "./chunk-2U2CP2Y2.js";
-import "./chunk-ZF6HNVYD.js";
-import "./chunk-BKPDYW5T.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-TJYRBEBK.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-SOTB4FRE.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";
-
-// termdb/handlers/test/isoformExpression.unit.spec.ts
-var import_tape = __toESM(require_tape(), 1);
-function mockGm(isoform) {
-  return { isoform, chr: "chr1", start: 0, stop: 100, exon: [[0, 100]] };
-}
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- termdb/handlers/isoformExpression -***-");
-  test.end();
-});
-(0, import_tape.default)("selectIsoform() should call callback with configured unit from termdbConfig", (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {
-          isoformExpression: { unit: "TPM" }
-        }
-      }
-    }
-  };
-  handler.selectIsoform("ENST00000269305", "TP53");
-  test.equal(selected?.isoform, "ENST00000269305", "Should pass selected isoform");
-  test.equal(selected?.gene, "TP53", "Should pass gene");
-  test.equal(selected?.name, "ENST00000269305 TPM", "Should include configured unit in term name");
-  test.equal(selected?.type, ISOFORM_EXPRESSION, "Should set type to isoformExpression");
-  test.end();
-});
-(0, import_tape.default)("selectIsoform() should use default unit when not configured", (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {}
-      }
-    }
-  };
-  handler.selectIsoform("ENST00000269305", "TP53");
-  test.equal(selected?.isoform, "ENST00000269305", "Should pass selected isoform");
-  test.equal(selected?.name, "ENST00000269305 TPM", "Should use default unit TPM");
-  test.equal(selected?.type, ISOFORM_EXPRESSION, "Should set type to isoformExpression");
-  test.end();
-});
-(0, import_tape.default)("selectCollection() should create a custom termCollection from multiple isoforms", (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {
-          isoformExpression: { unit: "TPM" }
-        }
-      }
-    }
-  };
-  handler.selectCollection([mockGm("ENST00000256078"), mockGm("ENST00000311936")], "KRAS");
-  test.equal(selected?.type, "termCollection", "Should set type to termCollection");
-  test.equal(selected?.isCustom, true, "Should set isCustom flag");
-  test.equal(selected?.memberType, "numeric", "Should set memberType to numeric");
-  test.equal(selected?.name, "KRAS Isoforms (TPM)", "Should include gene and unit in name");
-  test.equal(selected?.isleaf, true, "Should set isleaf");
-  test.deepEqual(selected?.propsByTermId, {}, "Should have empty propsByTermId");
-  test.equal(selected?.termlst?.length, 2, "Should have 2 member terms");
-  const mt = selected.termlst[0];
-  test.equal(mt.id, "ENST00000256078", "Member term id should be the isoform ID");
-  test.equal(mt.name, "ENST00000256078", "Member term name should be the isoform ID");
-  test.equal(mt.type, "isoformExpression", "Member term type should be isoformExpression");
-  test.equal(mt.isoform, "ENST00000256078", "Member term should carry isoform field");
-  test.end();
-});
-(0, import_tape.default)("selectCollection() should use default unit when not configured", (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {}
-      }
-    }
-  };
-  handler.selectCollection([mockGm("ENST00000256078"), mockGm("ENST00000311936")], "KRAS");
-  test.equal(selected?.name, "KRAS Isoforms (TPM)", "Should use default unit TPM");
-  test.end();
-});
-(0, import_tape.default)("showIsoforms multi-select: single isoform calls selectIsoform, multiple calls selectCollection", (test) => {
-  const handler = new SearchHandler();
-  const calls = [];
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {
-          isoformExpression: { unit: "TPM" }
-        }
-      }
-    }
-  };
-  handler.selectIsoform = (isoform, gene) => {
-    calls.push({ method: "selectIsoform", args: { isoform, gene } });
-  };
-  handler.selectCollection = (gms, gene) => {
-    calls.push({ method: "selectCollection", args: { gms, gene } });
-  };
-  const onMultiSelect1 = (selected) => {
-    if (selected.length === 1) handler.selectIsoform(selected[0].isoform, "TP53");
-    else handler.selectCollection(selected, "TP53");
-  };
-  onMultiSelect1([mockGm("ENST00000269305")]);
-  test.equal(calls.length, 1, "Should have one call");
-  test.equal(calls[0].method, "selectIsoform", "Single isoform should call selectIsoform");
-  const onMultiSelect2 = (selected) => {
-    if (selected.length === 1) handler.selectIsoform(selected[0].isoform, "KRAS");
-    else handler.selectCollection(selected, "KRAS");
-  };
-  onMultiSelect2([mockGm("ENST00000256078"), mockGm("ENST00000311936")]);
-  test.equal(calls.length, 2, "Should have two calls total");
-  test.equal(calls[1].method, "selectCollection", "Multiple isoforms should call selectCollection");
-  test.equal(calls[1].args.gms.length, 2, "Should pass both gene models");
-  test.end();
-});
-(0, import_tape.default)("filterIsoforms() should return only ENST isoforms present in availableItems", (test) => {
-  const gmlst = [mockGm("ENST00000269305"), mockGm("ENST00000413465"), mockGm("NM_000546"), mockGm("ENST00000359597")];
-  const availableItems = ["ENST00000269305", "ENST00000359597"];
-  const result = filterIsoforms(gmlst, availableItems);
-  test.equal(result.length, 2, "Should return 2 matching isoforms");
-  test.equal(result[0].isoform, "ENST00000269305", "First match correct");
-  test.equal(result[1].isoform, "ENST00000359597", "Second match correct");
-  test.end();
-});
-(0, import_tape.default)("filterIsoforms() should exclude non-ENST isoforms even if in availableItems", (test) => {
-  const gmlst = [mockGm("NM_000546"), mockGm("NR_176326"), mockGm("ENST00000269305")];
-  const availableItems = ["NM_000546", "ENST00000269305"];
-  const result = filterIsoforms(gmlst, availableItems);
-  test.equal(result.length, 1, "Should only return ENST isoform");
-  test.equal(result[0].isoform, "ENST00000269305", "Should be the ENST match");
-  test.end();
-});
-(0, import_tape.default)("filterIsoforms() should return all ENST isoforms when availableItems is empty", (test) => {
-  const gmlst = [mockGm("ENST00000269305"), mockGm("ENST00000413465"), mockGm("NM_000546")];
-  const result = filterIsoforms(gmlst, []);
-  test.equal(result.length, 2, "Should return all ENST isoforms when no filter");
-  test.equal(result[0].isoform, "ENST00000269305", "First ENST correct");
-  test.equal(result[1].isoform, "ENST00000413465", "Second ENST correct");
-  test.end();
-});
-(0, import_tape.default)("filterIsoforms() should return empty array when no ENST isoforms match", (test) => {
-  const gmlst = [mockGm("ENST00000269305"), mockGm("ENST00000413465")];
-  const availableItems = ["ENST00000999999"];
-  const result = filterIsoforms(gmlst, availableItems);
-  test.equal(result.length, 0, "Should return empty when no matches");
-  test.end();
-});
-//# sourceMappingURL=isoformExpression.unit.spec-6FSMHT4K.js.map

package/dist/launch.adhoc-ZYTIRVIC.js

@@ -1,42 +0,0 @@
-import {
-  launch
-} from "./chunk-3BBK6A4X.js";
-import "./chunk-JWBP4ZZB.js";
-import "./chunk-DMSX5PSO.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-4KY4XKJV.js";
-import "./chunk-KUZPTJJO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-C4BCMAIK.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-LQJMCE7G.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-Z457XQSX.js";
-import "./chunk-AI2LUQS6.js";
-import "./chunk-2JR7RPB6.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-TLTS33EY.js";
-import "./chunk-2U2CP2Y2.js";
-import "./chunk-ZF6HNVYD.js";
-import "./chunk-BKPDYW5T.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-TJYRBEBK.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-SOTB4FRE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  launch
-};
-//# sourceMappingURL=launch.adhoc-ZYTIRVIC.js.map

package/dist/leftlabel.sample-66U6MHPN.js

@@ -1,260 +0,0 @@
-import {
-  displaySampleTable,
-  getFilterName,
-  makelabel
-} from "./chunk-PDFCQ7AU.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-KVIH5JPC.js";
-import "./chunk-AJYJW4LX.js";
-import "./chunk-V2OJLJSK.js";
-import "./chunk-WKNI3HRQ.js";
-import "./chunk-A4Z3CI24.js";
-import {
-  fillbar,
-  filterInit,
-  getNormalRoot,
-  renderTable
-} from "./chunk-KUZPTJJO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-C4BCMAIK.js";
-import "./chunk-HYOEWQ5P.js";
-import {
-  Tabs
-} from "./chunk-HBW42TDT.js";
-import "./chunk-LQJMCE7G.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-Z457XQSX.js";
-import "./chunk-AI2LUQS6.js";
-import "./chunk-2JR7RPB6.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-TLTS33EY.js";
-import "./chunk-2U2CP2Y2.js";
-import "./chunk-ZF6HNVYD.js";
-import {
-  violinRenderer
-} from "./chunk-BKPDYW5T.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-TJYRBEBK.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-SOTB4FRE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.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", "sja_mds3samplesummarydiv"), 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 row = [
-      { value: tw.term.values?.[category_key]?.label || category_key },
-      { html: total == void 0 ? "" : fillbar(null, { f: count / total, v1: count, v2: total }) },
-      { html: count + (total ? ' <span style="font-size:.8em">/ ' + total + "</span>" : "") }
-    ];
-    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;
-  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-mds3-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-66U6MHPN.js.map

package/dist/leftlabel.sample-66U6MHPN.js.map

@@ -1,7 +0,0 @@
-{
-  "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', 'sja_mds3samplesummarydiv'), 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 row = [\n\t\t\t{ value: tw.term.values?.[category_key]?.label || category_key },\n\t\t\t{ html: total == undefined ? '' : fillbar(null, { f: count / total, v1: count, v2: total }) },\n\t\t\t{ html: count + (total ? ' <span style=\"font-size:.8em\">/ ' + total + '</span>' : '') }\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\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-mds3-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"],
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