@sjcrh/proteinpaint-client 2.201.0 → 2.202.0

package/dist/facet-74LKIPTA.js

@@ -1,521 +0,0 @@
-import {
-  PlotBase,
-  addNewGroup,
-  controlsInit,
-  fillTermWrapper,
-  getCombinedTermFilter,
-  getFilter,
-  getSamplelstTW,
-  getT0T2defaultQ,
-  select2Terms
-} from "./chunk-K6OVOHIZ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-XFAL46LZ.js";
-import "./chunk-HQAJVJCQ.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import "./chunk-6QCYT6G2.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-ZFJUVP2N.js";
-import "./chunk-R3ARQMM4.js";
-import "./chunk-4USLEUNR.js";
-import "./chunk-4WF3XDQP.js";
-import {
-  isNumericTerm
-} from "./chunk-X6VTVZY7.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-L44P5N4U.js";
-import "./chunk-GEQUQ3GG.js";
-import "./chunk-WPHUM5S5.js";
-import "./chunk-75T7ESEO.js";
-import "./chunk-2KXLYFAO.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-UJELJXJG.js";
-import "./chunk-FXQXCOII.js";
-import {
-  roundValueAuto
-} from "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/facet.js
-var Facet = class _Facet extends PlotBase {
-  static type = "facet";
-  constructor(opts) {
-    super(opts);
-    this.type = _Facet.type;
-    const holder = opts.holder;
-    const controlsHolder = holder.append("div").style("display", "inline-block");
-    const mainDiv = holder.append("div").style("display", "inline-block");
-    this.dom = {
-      holder: opts.holder.style("padding", "20px"),
-      header: opts.header,
-      controlsHolder,
-      mainDiv,
-      tip: opts.tip || new Menu()
-    };
-  }
-  async init(appState) {
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (this.dom.header)
-      this.dom.header.html(
-        `${config.columnTw.term.name} <span style="font-size:.8em">(COLUMN)</span> ${config.rowTw.term.name} <span style="font-size:.8em">(ROW) &nbsp; FACET TABLE</span>`
-      );
-    const parentConfig = this.parentId && appState.plots.find((p) => p.id === this.parentId);
-    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
-    return {
-      config,
-      vocab: appState.vocab,
-      termfilter,
-      groups: appState.groups
-    };
-  }
-  async main() {
-    this.config = JSON.parse(JSON.stringify(this.state.config));
-    this.hasTermCollection = this.config.columnTw.term.type == "termCollection" || this.config.rowTw.term.type == "termCollection";
-    await this.setControls();
-    await this.renderTable();
-  }
-  async renderTable() {
-    const config = this.config;
-    this.dom.mainDiv.selectAll("*").remove();
-    this.dom.tip.clear().hide();
-    const table = this.dom.mainDiv.append("table");
-    const tbody = table.append("tbody");
-    const headerRow = tbody.append("tr").style("text-align", "center");
-    headerRow.append("th");
-    const samplesAuth = this.app.vocabApi.hasVerifiedToken();
-    if (samplesAuth) {
-      table.style("border-spacing", "0px");
-      const { result, categories, categories2 } = await this.getSampleTableData(config);
-      if (!categories.length || !categories2.length) {
-        this.showNoSampleMessage(this.dom.mainDiv);
-        return;
-      }
-      for (const category of categories) {
-        const label = config.columnTw.term.type == "termCollection" ? getTermCollectionName(config.columnTw, category) : config.columnTw.term.values?.[category]?.label || category;
-        this.addHeader(headerRow, label);
-      }
-      this.renderSampleTable(tbody, config, result, categories, categories2);
-    } else {
-      table.style("border-spacing", "5px");
-      const { rows, filteredCols, total } = await this.getStaticTableData(config);
-      if (!rows.size || !filteredCols.length) {
-        this.showNoSampleMessage(this.dom.mainDiv);
-        return;
-      }
-      for (const col of filteredCols) {
-        const label = config.columnTw.term.values?.[col.seriesId]?.label || col.seriesId;
-        this.addHeader(headerRow, label);
-      }
-      this.renderStaticTable(tbody, config, rows, total);
-    }
-  }
-  renderSampleTable(tbody, config, result, categories, categories2) {
-    const cells = {};
-    const aggregateBy = config.settings.facet.aggregateBy;
-    if (this.hasTermCollection) {
-      const isColTermCollection = config.columnTw.term.type == "termCollection";
-      const isRowTermCollection = config.rowTw.term.type == "termCollection";
-      if (isColTermCollection && isRowTermCollection) throw "row and col terms cannot both be termCollection";
-      if (aggregateBy != "avg" && aggregateBy != "sum") throw "unexpected aggregateBy value";
-      for (const category2 of categories2) {
-        cells[category2] = {};
-        const tr = tbody.append("tr");
-        const label2 = isRowTermCollection ? getTermCollectionName(config.rowTw, category2) : config.rowTw.term.values?.[category2]?.label || category2;
-        this.addRowLabel(tr, label2);
-        for (const category of categories) {
-          const td = tr.append("td");
-          const samples = result.lst.filter((s) => {
-            const colPass = isColTermCollection ? getTermCollectionData(s, config.columnTw, category) : s[config.columnTw.$id]?.key == category;
-            const rowPass = isRowTermCollection ? getTermCollectionData(s, config.rowTw, category2) : s[config.rowTw.$id]?.key == category2;
-            return colPass && rowPass;
-          });
-          if (samples.length) {
-            const data = samples.map(
-              (s) => isColTermCollection ? getTermCollectionData(s, config.columnTw, category) : getTermCollectionData(s, config.rowTw, category2)
-            );
-            const total = data.reduce((sum, v) => sum + v, 0);
-            const value = aggregateBy == "avg" ? total / data.length : total;
-            td.classed("sja_menuoption", true).style("text-align", "center").style("border", "2.5px solid white").text(roundValueAuto(value));
-          } else {
-            td.classed("highlightable-cell", true);
-          }
-        }
-      }
-    } else {
-      for (const category2 of categories2) {
-        cells[category2] = {};
-        const tr = tbody.append("tr");
-        const label2 = config.rowTw.term.values?.[category2]?.label || category2;
-        this.addRowLabel(tr, label2);
-        for (const category of categories) {
-          const samples = result.lst.filter(
-            (s) => s[config.columnTw.$id]?.key == category && s[config.rowTw.$id]?.key == category2
-          );
-          const percent = this.config.settings.facet.showPercents ? ` <span style="color:gray;"> (${roundValueAuto(
-            samples.length / result.lst.length * 100,
-            true,
-            1
-          )}%)</span>` : "";
-          cells[category2][category] = { samples, selected: false };
-          const td = tr.append("td");
-          if (!samples.length) td.classed("highlightable-cell", true);
-          if (samples.length > 0) {
-            const colIdx = categories.indexOf(category) + 2;
-            td.classed("sja_menuoption", true).style("text-align", "center").style("border", "2.5px solid white").html(`${samples.length}${percent}`).on("mouseover", () => {
-              this.highlightColRow(tbody, tr, colIdx, "#fffec8");
-            }).on("mouseout", () => {
-              this.highlightColRow(tbody, tr, colIdx, "transparent");
-            }).on("click", () => {
-              const selected = cells[category2][category].selected = !cells[category2][category].selected;
-              if (selected) {
-                td.style("border", "1px solid blue");
-              } else {
-                td.style("border", "2.5px solid white");
-              }
-              for (const category22 of categories2) {
-                for (const category3 of categories) {
-                  if (cells[category22][category3].selected) {
-                    buttonDiv.style("display", "");
-                    prompt.text("Choose how to use samples:");
-                    return;
-                  }
-                }
-              }
-              buttonDiv.style("display", "none");
-              prompt.text("Click on cells to select samples");
-            });
-          }
-        }
-      }
-    }
-    const prompt = this.dom.mainDiv.append("div").attr("data-testid", "sjpp-facet-start-prompt").style("margin", "20px 0px 0px 15px").style("opacity", "0.7").text(
-      this.hasTermCollection ? `Values in cells are ${aggregateBy == "avg" ? "averages" : "sums"}` : "Click on cells to select samples"
-    );
-    const buttonDiv = this.dom.mainDiv.append("div").style("margin", "20px 0px 0px 25px").style("display", "none");
-    const btns = [
-      {
-        text: "Show samples view",
-        // disabled: () => {}, add this if needed later
-        callback: () => {
-          const samples = this.getSelectedSamples(categories, categories2, cells);
-          this.app.dispatch({
-            type: "plot_create",
-            config: {
-              chartType: "sampleView",
-              samples: samples.map((d) => ({
-                sampleId: d.sample,
-                sampleName: result.refs.bySampleId[d.sample].label
-              }))
-            }
-          });
-        }
-      },
-      {
-        text: "List samples",
-        callback: () => {
-          const samples = this.getSelectedSamples(categories, categories2, cells);
-          const sampleRows = samples.map((d) => [
-            result.refs.bySampleId[d.sample].label,
-            d[config.columnTw.$id].key,
-            d[config.rowTw.$id].key
-          ]);
-          this.dom.tip.clear().showunder(buttonDiv.node());
-          const tbody2 = this.dom.tip.d.append("table").append("tbody");
-          const headerRow = tbody2.append("tr").style("text-align", "center");
-          headerRow.append("th").text("Sample");
-          headerRow.append("th").text(config.columnTw.term.name);
-          headerRow.append("th").text(config.rowTw.term.name);
-          for (const row of sampleRows) {
-            const tr = tbody2.append("tr");
-            tr.append("td").text(row[0]);
-            tr.append("td").text(row[1]);
-            tr.append("td").text(row[2]);
-          }
-        }
-      },
-      {
-        text: "Create group",
-        callback: () => {
-          this.addGroup(categories, categories2, cells);
-        }
-      }
-      // {
-      // 	text: 'Add group and filter',
-      // 	callback: () => {
-      // 		const groupFilter = this.addGroup(categories, categories2, cells)
-      // 		const filterUiRoot = getFilterItemByTag(this.state.termfilter.filter, 'filterUiRoot')
-      // 		const filter = filterJoin([filterUiRoot, groupFilter])
-      // 		filter.tag = 'filterUiRoot'
-      // 		this.app.dispatch({
-      // 			type: 'filter_replace',
-      // 			filter
-      // 		})
-      // 	}
-      // }
-    ];
-    for (const btn of btns) {
-      this.addBtn(buttonDiv, btn);
-    }
-  }
-  highlightColRow = (tbody, tr, colIdx, color) => {
-    tbody.selectAll(`td.highlightable-cell:nth-child(${colIdx})`).style("background-color", `${color}`).style("border", `2.5px solid ${color}`);
-    tbody.select(`th:nth-child(${colIdx})`).style("background-color", `${color}`).style("border", `2.5px solid ${color}`);
-    tr.style("background-color", `${color}`);
-  };
-  addBtn(div, btn) {
-    return div.append("button").classed("sja_menuoption", true).style("padding", "0px 10px").style("margin", "0px 5px").text(btn.text).on("click", btn.callback);
-  }
-  addGroup(categories, categories2, cells) {
-    const group = {
-      name: "Group",
-      items: this.getSelectedSamples(categories, categories2, cells)
-    };
-    const filter = getFilter(getSamplelstTW([group]));
-    addNewGroup(this.app, filter, this.state.groups);
-    return filter;
-  }
-  getSelectedSamples(categories, categories2, cells) {
-    const samples = [];
-    for (const category2 of categories2) {
-      for (const category of categories) {
-        if (cells[category2][category].selected) {
-          samples.push(...cells[category2][category].samples);
-        }
-      }
-    }
-    return samples;
-  }
-  async getSampleTableData(config) {
-    const result = await this.app.vocabApi.getAnnotatedSampleData({
-      filter: this.state.termfilter.filter,
-      terms: [config.columnTw, config.rowTw]
-    });
-    const categories = this.getCategories(config.columnTw, result.lst);
-    const categories2 = this.getCategories(config.rowTw, result.lst);
-    return { result, categories, categories2 };
-  }
-  getCategories(tw, data) {
-    let categories = [];
-    if (tw.term.type == "termCollection") {
-      for (const sample of data) {
-        const value = sample[tw.$id]?.value;
-        if (value) {
-          const termids = Object.keys(value);
-          categories.push(...termids);
-        }
-      }
-    } else {
-      for (const sample of data) {
-        let key = sample[tw.$id]?.key;
-        if (key) {
-          if (!isNaN(key)) key = Number(key);
-          categories.push(key);
-        }
-      }
-    }
-    const set = new Set(categories);
-    categories = Array.from(set).sort();
-    if (isNumericTerm(tw.term)) {
-      if (tw.term.values) {
-        Object.values(tw.term.values).forEach((i) => {
-          if (i?.uncomputable) {
-            const index = categories.indexOf(i.label);
-            if (index > -1) categories.splice(index, 1);
-          }
-        });
-      }
-      categories = this.orderColNames(categories);
-    }
-    return categories;
-  }
-  orderColNames(cols) {
-    const tmpNums = [];
-    const tmpStrings = [];
-    for (const col of cols) {
-      const c = col.split(" to ");
-      const cx = c[0].replace(/[\>\≥\<\≤]/g, "");
-      const x = Number(cx);
-      if (!isNaN(x)) {
-        const key = !c[1] && (col.includes("<") || col.includes("\u2264")) ? x - 1 : !c[1] && (col.includes("\u2265") || col.includes(">")) ? x + 1 : x;
-        tmpNums.push({ key, label: col });
-      } else tmpStrings.push(cx);
-    }
-    return [...tmpNums.sort((a, b) => a.key - b.key).map((i) => i.label), ...tmpStrings.sort()];
-  }
-  renderStaticTable(tbody, config, rows, totalSamples) {
-    for (const row of rows) {
-      const tr = tbody.append("tr");
-      const label = config.rowTw.term.values?.[row[0]]?.label || row[0];
-      this.addRowLabel(tr, label);
-      for (const col of row[1]) {
-        const label2 = col[1].value > 0 ? col[1].value : "";
-        const percent = this.config.settings.facet.showPercents ? `<span style="color:gray;"> (${roundValueAuto(col[1].value / totalSamples * 100, true, 1)}%)</span>` : "";
-        const td = tr.append("td");
-        if (label2)
-          td.classed("sja_menuoption", true).style("border", "2.5px solid white").style("text-align", "center").html(`${label2}${percent}`);
-      }
-    }
-  }
-  async getStaticTableData(config) {
-    const opts = { term: config.columnTw, term2: config.rowTw, filter: this.state.termfilter.filter };
-    if (this.state.termfilter.filter0) opts.filter0 = this.state.termfilter.filter0;
-    await this.getDescrStats(opts.term);
-    await this.getDescrStats(opts.term2);
-    const result = await this.app.vocabApi.getNestedChartSeriesData(opts);
-    const rows = /* @__PURE__ */ new Map();
-    const filteredCols = result.data.refs.cols.map((col) => result.data.charts[0].serieses.find((s) => s.seriesId == col));
-    result.data.refs.rows.forEach((row) => {
-      rows.set(row, /* @__PURE__ */ new Map());
-      for (const col of filteredCols) {
-        rows.get(row).set(col.seriesId, { value: col.data.find((d) => d.dataId == row)?.total || 0, selected: false });
-      }
-    });
-    return { rows, filteredCols, total: result.data.charts[0].total };
-  }
-  async getDescrStats(tw) {
-    if (isNumericTerm(tw.term)) {
-      const data = await this.app.vocabApi.getDescrStats(tw, this.state.termfilter);
-      if (data.error) throw data.error;
-      tw.q.descrStats = data.values;
-    }
-  }
-  showNoSampleMessage(div) {
-    div.append("div").style("padding", "0px 50px").style("font-size", "1.15em").text("No overlapping samples");
-    return;
-  }
-  addHeader(headerRow, text) {
-    headerRow.append("th").attr("data-testid", "sjpp-facet-col-header").style("border", "2.5px solid white").style("padding", "0px 25px").text(text);
-  }
-  addRowLabel(tr, label) {
-    tr.append("td").attr("data-testid", "sjpp-facet-row-label").style("border", "2.5px solid white").style("font-weight", "bold").text(label);
-  }
-  async setControls() {
-    this.dom.controlsHolder.selectAll("*").remove();
-    const inputs = [
-      {
-        type: "term",
-        configKey: "columnTw",
-        chartType: this.type,
-        usecase: { target: this.type },
-        title: "Facet column categories",
-        label: "Columns",
-        vocabApi: this.app.vocabApi,
-        numericEditMenuVersion: ["discrete"],
-        defaultQ4fillTW: getT0T2defaultQ()
-      },
-      {
-        type: "term",
-        configKey: "rowTw",
-        chartType: this.type,
-        usecase: { target: this.type },
-        title: "Facet row categories",
-        label: "Rows",
-        vocabApi: this.app.vocabApi,
-        numericEditMenuVersion: ["discrete"],
-        defaultQ4fillTW: getT0T2defaultQ()
-      },
-      {
-        boxLabel: "",
-        label: "Show percent",
-        type: "checkbox",
-        chartType: "facet",
-        settingsKey: "showPercents",
-        title: `Option to show/hide percents per cell`
-      }
-    ];
-    if (this.hasTermCollection) {
-      inputs.push({
-        label: "Aggregate by",
-        type: "radio",
-        chartType: "facet",
-        settingsKey: "aggregateBy",
-        title: "Aggregate values by",
-        options: [
-          { label: "Average", value: "avg" },
-          { label: "Sum", value: "sum" }
-        ]
-      });
-    }
-    this.components = {
-      controls: await controlsInit({
-        app: this.app,
-        id: this.id,
-        holder: this.dom.controlsHolder,
-        inputs
-      })
-    };
-  }
-};
-function makeChartBtnMenu(holder, chartsInstance) {
-  const callback = (xterm, yterm) => {
-    const config = {
-      chartType: "facet",
-      columnTw: { term: xterm },
-      rowTw: { term: yterm }
-    };
-    if (isNumericTerm(xterm)) config.columnTw.term.q = { mode: "discrete" };
-    if (isNumericTerm(yterm)) config.rowTw.term.q = { mode: "discrete" };
-    chartsInstance.app.dispatch({
-      type: "plot_create",
-      config
-    });
-  };
-  select2Terms(chartsInstance.dom.tip, chartsInstance.app, "facet", "", callback);
-}
-var facetInit = getCompInit(Facet);
-var componentInit = facetInit;
-async function getPlotConfig(opts, app) {
-  const config = {
-    settings: {
-      facet: {
-        showPercents: false,
-        aggregateBy: "avg"
-      }
-    }
-  };
-  if (!opts.columnTw) throw ".columnTw{} missing";
-  await fillTermWrapper(
-    opts.columnTw,
-    app.vocabApi,
-    opts.columnTw.bins || opts.columnTw.q ? void 0 : getT0T2defaultQ()
-  );
-  if (!opts.rowTw) throw ".rowTw{} missing";
-  await fillTermWrapper(opts.rowTw, app.vocabApi, opts.rowTw.bins || opts.rowTw.q ? void 0 : getT0T2defaultQ());
-  const result = copyMerge(config, opts);
-  return result;
-}
-function getTermCollectionName(tw, termid) {
-  const term = tw.term.termlst.find((t) => t.id == termid);
-  if (!term) throw "term is missing";
-  return term.name;
-}
-function getTermCollectionData(s, tw, termid) {
-  if (tw.term.type != "termCollection") return;
-  const value = s[tw.$id]?.value;
-  if (value) {
-    const data = value[termid];
-    return data;
-  }
-}
-export {
-  componentInit,
-  facetInit,
-  getPlotConfig,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=facet-74LKIPTA.js.map

package/dist/facet-74LKIPTA.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/facet.js"],
-  "sourcesContent": ["import { getCompInit, copyMerge } from '#rx'\nimport { fillTermWrapper } from '#termsetting'\nimport { controlsInit } from './controls'\nimport { getT0T2defaultQ } from './summaryQ.ts'\nimport { select2Terms } from '#dom/select2Terms'\nimport { isNumericTerm } from '#shared/terms.js'\nimport { addNewGroup, getFilter, getSamplelstTW } from '../mass/groups'\n// import { filterJoin, getFilterItemByTag } from '#filter'\nimport { Menu } from '#dom/menu'\nimport { getCombinedTermFilter } from '#filter'\nimport { PlotBase } from '#plots/PlotBase.js'\nimport { roundValueAuto } from '#shared/roundValue.js'\n\n/*\nstate {\n\tcolumnTw {} // tw to determine columns -> historically .term{}\n\trowTw {} // tw to determine rows -> historically .term2{}\n}\n\nfacet table is always shown for secured or unsecured ds, as it does not reveal sample-level info\nclick on table cells allow to select corresponding samples, this is only allowed when hasVerifiedToken() is true\n*/\n\nclass Facet extends PlotBase {\n\tstatic type = 'facet'\n\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.type = Facet.type\n\t\tconst holder = opts.holder\n\n\t\tconst controlsHolder = holder.append('div').style('display', 'inline-block')\n\t\tconst mainDiv = holder.append('div').style('display', 'inline-block')\n\n\t\tthis.dom = {\n\t\t\tholder: opts.holder.style('padding', '20px'),\n\t\t\theader: opts.header,\n\t\t\tcontrolsHolder,\n\t\t\tmainDiv,\n\t\t\ttip: opts.tip || new Menu()\n\t\t}\n\t}\n\n\tasync init(appState) {}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (this.dom.header)\n\t\t\tthis.dom.header.html(\n\t\t\t\t`${config.columnTw.term.name} <span style=\"font-size:.8em\">(COLUMN)</span> ${config.rowTw.term.name} <span style=\"font-size:.8em\">(ROW) &nbsp; FACET TABLE</span>`\n\t\t\t)\n\t\tconst parentConfig = this.parentId && appState.plots.find(p => p.id === this.parentId)\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\n\t\treturn {\n\t\t\tconfig,\n\t\t\tvocab: appState.vocab,\n\t\t\ttermfilter,\n\t\t\tgroups: appState.groups\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.config = JSON.parse(JSON.stringify(this.state.config))\n\t\tthis.hasTermCollection =\n\t\t\tthis.config.columnTw.term.type == 'termCollection' || this.config.rowTw.term.type == 'termCollection'\n\t\tawait this.setControls()\n\t\tawait this.renderTable()\n\t}\n\n\tasync renderTable() {\n\t\tconst config = this.config\n\t\tthis.dom.mainDiv.selectAll('*').remove()\n\t\tthis.dom.tip.clear().hide()\n\t\tconst table = this.dom.mainDiv.append('table')\n\t\tconst tbody = table.append('tbody')\n\t\tconst headerRow = tbody.append('tr').style('text-align', 'center')\n\t\t//blank space left for row labels\n\t\theaderRow.append('th')\n\n\t\tconst samplesAuth = this.app.vocabApi.hasVerifiedToken()\n\t\tif (samplesAuth) {\n\t\t\t//overrides the default sja_root table style\n\t\t\ttable.style('border-spacing', '0px')\n\t\t\t/** If samples level data available, render interative\n\t\t\t * facet table. Clicking cells creates the list of samples\n\t\t\t * and on submit launches the sample view plot\n\t\t\t */\n\t\t\tconst { result, categories, categories2 } = await this.getSampleTableData(config)\n\t\t\tif (!categories.length || !categories2.length) {\n\t\t\t\t//Show message if no overlapping samples\n\t\t\t\tthis.showNoSampleMessage(this.dom.mainDiv)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tfor (const category of categories) {\n\t\t\t\tconst label =\n\t\t\t\t\tconfig.columnTw.term.type == 'termCollection'\n\t\t\t\t\t\t? getTermCollectionName(config.columnTw, category)\n\t\t\t\t\t\t: config.columnTw.term.values?.[category]?.label || category\n\t\t\t\tthis.addHeader(headerRow, label)\n\t\t\t}\n\t\t\tthis.renderSampleTable(tbody, config, result, categories, categories2)\n\t\t} else {\n\t\t\ttable.style('border-spacing', '5px')\n\t\t\t/** If sample data is not available or not authorized for this user,\n\t\t\t * render a static table with counts. No interactivity. */\n\t\t\tconst { rows, filteredCols, total } = await this.getStaticTableData(config)\n\t\t\tif (!rows.size || !filteredCols.length) {\n\t\t\t\tthis.showNoSampleMessage(this.dom.mainDiv)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tfor (const col of filteredCols) {\n\t\t\t\tconst label = config.columnTw.term.values?.[col.seriesId]?.label || col.seriesId\n\t\t\t\tthis.addHeader(headerRow, label)\n\t\t\t}\n\t\t\tthis.renderStaticTable(tbody, config, rows, total)\n\t\t}\n\t}\n\n\trenderSampleTable(tbody, config, result, categories, categories2) {\n\t\tconst cells = {}\n\t\tconst aggregateBy = config.settings.facet.aggregateBy\n\t\tif (this.hasTermCollection) {\n\t\t\t// termCollection term present\n\t\t\tconst isColTermCollection = config.columnTw.term.type == 'termCollection'\n\t\t\tconst isRowTermCollection = config.rowTw.term.type == 'termCollection'\n\t\t\tif (isColTermCollection && isRowTermCollection) throw 'row and col terms cannot both be termCollection'\n\t\t\tif (aggregateBy != 'avg' && aggregateBy != 'sum') throw 'unexpected aggregateBy value'\n\t\t\tfor (const category2 of categories2) {\n\t\t\t\tcells[category2] = {}\n\t\t\t\tconst tr = tbody.append('tr')\n\t\t\t\tconst label2 = isRowTermCollection\n\t\t\t\t\t? getTermCollectionName(config.rowTw, category2)\n\t\t\t\t\t: config.rowTw.term.values?.[category2]?.label || category2\n\t\t\t\tthis.addRowLabel(tr, label2)\n\t\t\t\tfor (const category of categories) {\n\t\t\t\t\tconst td = tr.append('td')\n\t\t\t\t\tconst samples = result.lst.filter(s => {\n\t\t\t\t\t\tconst colPass = isColTermCollection\n\t\t\t\t\t\t\t? getTermCollectionData(s, config.columnTw, category)\n\t\t\t\t\t\t\t: s[config.columnTw.$id]?.key == category\n\t\t\t\t\t\tconst rowPass = isRowTermCollection\n\t\t\t\t\t\t\t? getTermCollectionData(s, config.rowTw, category2)\n\t\t\t\t\t\t\t: s[config.rowTw.$id]?.key == category2\n\t\t\t\t\t\treturn colPass && rowPass\n\t\t\t\t\t})\n\t\t\t\t\tif (samples.length) {\n\t\t\t\t\t\t// samples have data for both categories\n\t\t\t\t\t\t// render aggregate termCollection data in cell\n\t\t\t\t\t\tconst data = samples.map(s =>\n\t\t\t\t\t\t\tisColTermCollection\n\t\t\t\t\t\t\t\t? getTermCollectionData(s, config.columnTw, category)\n\t\t\t\t\t\t\t\t: getTermCollectionData(s, config.rowTw, category2)\n\t\t\t\t\t\t)\n\t\t\t\t\t\tconst total = data.reduce((sum, v) => sum + v, 0)\n\t\t\t\t\t\tconst value = aggregateBy == 'avg' ? total / data.length : total\n\t\t\t\t\t\ttd.classed('sja_menuoption', true)\n\t\t\t\t\t\t\t.style('text-align', 'center')\n\t\t\t\t\t\t\t.style('border', '2.5px solid white')\n\t\t\t\t\t\t\t.text(roundValueAuto(value))\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// cell does not have samples\n\t\t\t\t\t\ttd.classed('highlightable-cell', true)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\t// no termCollection term present\n\t\t\tfor (const category2 of categories2) {\n\t\t\t\tcells[category2] = {}\n\t\t\t\tconst tr = tbody.append('tr')\n\t\t\t\tconst label2 = config.rowTw.term.values?.[category2]?.label || category2\n\t\t\t\tthis.addRowLabel(tr, label2)\n\t\t\t\tfor (const category of categories) {\n\t\t\t\t\tconst samples = result.lst.filter(\n\t\t\t\t\t\ts => s[config.columnTw.$id]?.key == category && s[config.rowTw.$id]?.key == category2\n\t\t\t\t\t)\n\t\t\t\t\tconst percent = this.config.settings.facet.showPercents\n\t\t\t\t\t\t? ` <span style=\"color:gray;\"> (${roundValueAuto(\n\t\t\t\t\t\t\t\t(samples.length / result.lst.length) * 100,\n\t\t\t\t\t\t\t\ttrue,\n\t\t\t\t\t\t\t\t1\n\t\t\t\t\t\t  )}%)</span>`\n\t\t\t\t\t\t: ''\n\t\t\t\t\tcells[category2][category] = { samples, selected: false }\n\t\t\t\t\tconst td = tr.append('td')\n\t\t\t\t\tif (!samples.length) td.classed('highlightable-cell', true)\n\t\t\t\t\tif (samples.length > 0) {\n\t\t\t\t\t\tconst colIdx = categories.indexOf(category) + 2\n\t\t\t\t\t\ttd.classed('sja_menuoption', true)\n\t\t\t\t\t\t\t.style('text-align', 'center')\n\t\t\t\t\t\t\t.style('border', '2.5px solid white')\n\t\t\t\t\t\t\t.html(`${samples.length}${percent}`)\n\t\t\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\t\t\tthis.highlightColRow(tbody, tr, colIdx, '#fffec8')\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\t\t\tthis.highlightColRow(tbody, tr, colIdx, 'transparent')\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\tconst selected = (cells[category2][category].selected = !cells[category2][category].selected)\n\t\t\t\t\t\t\t\tif (selected) {\n\t\t\t\t\t\t\t\t\ttd.style('border', '1px solid blue')\n\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\ttd.style('border', '2.5px solid white')\n\t\t\t\t\t\t\t\t}\n\n\t\t\t\t\t\t\t\tfor (const category2 of categories2) {\n\t\t\t\t\t\t\t\t\tfor (const category of categories) {\n\t\t\t\t\t\t\t\t\t\tif (cells[category2][category].selected) {\n\t\t\t\t\t\t\t\t\t\t\tbuttonDiv.style('display', '')\n\t\t\t\t\t\t\t\t\t\t\tprompt.text('Choose how to use samples:')\n\t\t\t\t\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tbuttonDiv.style('display', 'none')\n\t\t\t\t\t\t\t\tprompt.text('Click on cells to select samples')\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tconst prompt = this.dom.mainDiv\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-facet-start-prompt')\n\t\t\t.style('margin', '20px 0px 0px 15px')\n\t\t\t.style('opacity', '0.7')\n\t\t\t.text(\n\t\t\t\tthis.hasTermCollection\n\t\t\t\t\t? `Values in cells are ${aggregateBy == 'avg' ? 'averages' : 'sums'}`\n\t\t\t\t\t: 'Click on cells to select samples'\n\t\t\t)\n\t\tconst buttonDiv = this.dom.mainDiv.append('div').style('margin', '20px 0px 0px 25px').style('display', 'none')\n\t\tconst btns = [\n\t\t\t{\n\t\t\t\ttext: 'Show samples view',\n\t\t\t\t// disabled: () => {}, add this if needed later\n\t\t\t\tcallback: () => {\n\t\t\t\t\tconst samples = this.getSelectedSamples(categories, categories2, cells)\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tchartType: 'sampleView',\n\t\t\t\t\t\t\tsamples: samples.map(d => ({\n\t\t\t\t\t\t\t\tsampleId: d.sample,\n\t\t\t\t\t\t\t\tsampleName: result.refs.bySampleId[d.sample].label\n\t\t\t\t\t\t\t}))\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\ttext: 'List samples',\n\t\t\t\tcallback: () => {\n\t\t\t\t\tconst samples = this.getSelectedSamples(categories, categories2, cells)\n\t\t\t\t\tconst sampleRows = samples.map(d => [\n\t\t\t\t\t\tresult.refs.bySampleId[d.sample].label,\n\t\t\t\t\t\td[config.columnTw.$id].key,\n\t\t\t\t\t\td[config.rowTw.$id].key\n\t\t\t\t\t])\n\t\t\t\t\tthis.dom.tip.clear().showunder(buttonDiv.node())\n\t\t\t\t\t// this.dom.tip.d.append('div').style('padding', '0px 5px 5px 5px').text('Selected samples:')\n\t\t\t\t\tconst tbody = this.dom.tip.d.append('table').append('tbody')\n\t\t\t\t\tconst headerRow = tbody.append('tr').style('text-align', 'center')\n\t\t\t\t\theaderRow.append('th').text('Sample')\n\t\t\t\t\theaderRow.append('th').text(config.columnTw.term.name)\n\t\t\t\t\theaderRow.append('th').text(config.rowTw.term.name)\n\t\t\t\t\tfor (const row of sampleRows) {\n\t\t\t\t\t\tconst tr = tbody.append('tr')\n\t\t\t\t\t\ttr.append('td').text(row[0])\n\t\t\t\t\t\ttr.append('td').text(row[1])\n\t\t\t\t\t\ttr.append('td').text(row[2])\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\ttext: 'Create group',\n\t\t\t\tcallback: () => {\n\t\t\t\t\tthis.addGroup(categories, categories2, cells)\n\t\t\t\t}\n\t\t\t}\n\t\t\t// {\n\t\t\t// \ttext: 'Add group and filter',\n\t\t\t// \tcallback: () => {\n\t\t\t// \t\tconst groupFilter = this.addGroup(categories, categories2, cells)\n\t\t\t// \t\tconst filterUiRoot = getFilterItemByTag(this.state.termfilter.filter, 'filterUiRoot')\n\t\t\t// \t\tconst filter = filterJoin([filterUiRoot, groupFilter])\n\t\t\t// \t\tfilter.tag = 'filterUiRoot'\n\t\t\t// \t\tthis.app.dispatch({\n\t\t\t// \t\t\ttype: 'filter_replace',\n\t\t\t// \t\t\tfilter\n\t\t\t// \t\t})\n\t\t\t// \t}\n\t\t\t// }\n\t\t]\n\n\t\tfor (const btn of btns) {\n\t\t\tthis.addBtn(buttonDiv, btn)\n\t\t}\n\t}\n\n\thighlightColRow = (tbody, tr, colIdx, color) => {\n\t\ttbody\n\t\t\t.selectAll(`td.highlightable-cell:nth-child(${colIdx})`)\n\t\t\t.style('background-color', `${color}`)\n\t\t\t.style('border', `2.5px solid ${color}`)\n\t\ttbody\n\t\t\t.select(`th:nth-child(${colIdx})`)\n\t\t\t.style('background-color', `${color}`)\n\t\t\t.style('border', `2.5px solid ${color}`)\n\t\ttr.style('background-color', `${color}`)\n\t}\n\n\taddBtn(div, btn) {\n\t\treturn div\n\t\t\t.append('button')\n\t\t\t.classed('sja_menuoption', true)\n\t\t\t.style('padding', '0px 10px')\n\t\t\t.style('margin', '0px 5px')\n\t\t\t.text(btn.text)\n\t\t\t.on('click', btn.callback)\n\t}\n\n\taddGroup(categories, categories2, cells) {\n\t\tconst group = {\n\t\t\tname: 'Group',\n\t\t\titems: this.getSelectedSamples(categories, categories2, cells)\n\t\t}\n\t\tconst filter = getFilter(getSamplelstTW([group]))\n\t\taddNewGroup(this.app, filter, this.state.groups)\n\t\treturn filter\n\t}\n\n\tgetSelectedSamples(categories, categories2, cells) {\n\t\tconst samples = []\n\t\tfor (const category2 of categories2) {\n\t\t\tfor (const category of categories) {\n\t\t\t\tif (cells[category2][category].selected) {\n\t\t\t\t\tsamples.push(...cells[category2][category].samples)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn samples\n\t}\n\n\tasync getSampleTableData(config) {\n\t\tconst result = await this.app.vocabApi.getAnnotatedSampleData({\n\t\t\tfilter: this.state.termfilter.filter,\n\t\t\tterms: [config.columnTw, config.rowTw]\n\t\t})\n\t\tconst categories = this.getCategories(config.columnTw, result.lst)\n\t\tconst categories2 = this.getCategories(config.rowTw, result.lst)\n\t\treturn { result, categories, categories2 }\n\t}\n\n\tgetCategories(tw, data) {\n\t\tlet categories = []\n\t\tif (tw.term.type == 'termCollection') {\n\t\t\t// termCollection\n\t\t\tfor (const sample of data) {\n\t\t\t\tconst value = sample[tw.$id]?.value\n\t\t\t\tif (value) {\n\t\t\t\t\tconst termids = Object.keys(value)\n\t\t\t\t\tcategories.push(...termids)\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\t// not termCollection\n\t\t\tfor (const sample of data) {\n\t\t\t\tlet key = sample[tw.$id]?.key\n\t\t\t\tif (key) {\n\t\t\t\t\tif (!isNaN(key)) key = Number(key)\n\t\t\t\t\tcategories.push(key)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tconst set = new Set(categories)\n\t\tcategories = Array.from(set).sort()\n\n\t\tif (isNumericTerm(tw.term)) {\n\t\t\tif (tw.term.values) {\n\t\t\t\tObject.values(tw.term.values).forEach(i => {\n\t\t\t\t\tif (i?.uncomputable) {\n\t\t\t\t\t\tconst index = categories.indexOf(i.label)\n\t\t\t\t\t\tif (index > -1) categories.splice(index, 1)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t\tcategories = this.orderColNames(categories)\n\t\t}\n\n\t\treturn categories\n\t}\n\n\torderColNames(cols) {\n\t\t//Show ranges first, then strings\n\t\tconst tmpNums = []\n\t\tconst tmpStrings = []\n\t\tfor (const col of cols) {\n\t\t\tconst c = col.split(' to ')\n\t\t\tconst cx = c[0].replace(/[\\>\\\u2265\\<\\\u2264]/g, '')\n\t\t\tconst x = Number(cx)\n\t\t\tif (!isNaN(x)) {\n\t\t\t\tconst key =\n\t\t\t\t\t!c[1] && (col.includes('<') || col.includes('\u2264'))\n\t\t\t\t\t\t? x - 1\n\t\t\t\t\t\t: !c[1] && (col.includes('\u2265') || col.includes('>'))\n\t\t\t\t\t\t? x + 1\n\t\t\t\t\t\t: x\n\t\t\t\ttmpNums.push({ key, label: col })\n\t\t\t} else tmpStrings.push(cx)\n\t\t}\n\t\treturn [...tmpNums.sort((a, b) => a.key - b.key).map(i => i.label), ...tmpStrings.sort()]\n\t}\n\n\trenderStaticTable(tbody, config, rows, totalSamples) {\n\t\tfor (const row of rows) {\n\t\t\tconst tr = tbody.append('tr')\n\t\t\tconst label = config.rowTw.term.values?.[row[0]]?.label || row[0]\n\t\t\tthis.addRowLabel(tr, label)\n\t\t\tfor (const col of row[1]) {\n\t\t\t\tconst label = col[1].value > 0 ? col[1].value : ''\n\t\t\t\tconst percent = this.config.settings.facet.showPercents\n\t\t\t\t\t? `<span style=\"color:gray;\"> (${roundValueAuto((col[1].value / totalSamples) * 100, true, 1)}%)</span>`\n\t\t\t\t\t: ''\n\t\t\t\tconst td = tr.append('td')\n\t\t\t\tif (label)\n\t\t\t\t\ttd.classed('sja_menuoption', true)\n\t\t\t\t\t\t.style('border', '2.5px solid white')\n\t\t\t\t\t\t.style('text-align', 'center')\n\t\t\t\t\t\t.html(`${label}${percent}`)\n\t\t\t}\n\t\t}\n\t}\n\n\tasync getStaticTableData(config) {\n\t\t//*** Do show uncomputeable values when table is static\n\n\t\t// config.settings = {\n\t\t// \texclude: {\n\t\t// \t\tcols: Object.keys(config.term.q?.hiddenValues || {})\n\t\t// \t\t\t.filter(id => config.term.q.hiddenValues[id])\n\t\t// \t\t\t.map(id => {\n\t\t// \t\t\t\treturn config.term.term.type == 'categorical'\n\t\t// \t\t\t\t\t? id\n\t\t// \t\t\t\t\t: config.settings.cols?.includes(id)\n\t\t// \t\t\t\t\t? id\n\t\t// \t\t\t\t\t: config.term.term.values[id]?.label\n\t\t// \t\t\t\t\t? config.term.term.values[id].label\n\t\t// \t\t\t\t\t: id\n\t\t// \t\t\t}),\n\t\t// \t\trows: !config.term2?.q?.hiddenValues\n\t\t// \t\t\t? []\n\t\t// \t\t\t: Object.keys(config.term2.q.hiddenValues)\n\t\t// \t\t\t\t\t.filter(id => config.term2.q.hiddenValues[id])\n\t\t// \t\t\t\t\t.map(id =>\n\t\t// \t\t\t\t\t\tconfig.term2.term.type == 'categorical'\n\t\t// \t\t\t\t\t\t\t? id\n\t\t// \t\t\t\t\t\t\t: config.settings.rows?.includes(id)\n\t\t// \t\t\t\t\t\t\t? id\n\t\t// \t\t\t\t\t\t\t: config.term2.term.values[id]?.label\n\t\t// \t\t\t\t\t\t\t? config.term2.term.values[id].label\n\t\t// \t\t\t\t\t\t\t: id\n\t\t// \t\t\t\t\t)\n\t\t// \t}\n\t\t// }\n\n\t\tconst opts = { term: config.columnTw, term2: config.rowTw, filter: this.state.termfilter.filter }\n\t\tif (this.state.termfilter.filter0) opts.filter0 = this.state.termfilter.filter0\n\n\t\t//Need to get the totals\n\t\tawait this.getDescrStats(opts.term)\n\t\tawait this.getDescrStats(opts.term2)\n\n\t\tconst result = await this.app.vocabApi.getNestedChartSeriesData(opts)\n\t\tconst rows = new Map()\n\n\t\t//These columns and rows are in the correct ascending 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'term',\n\t\t\t\tconfigKey: 'rowTw',\n\t\t\t\tchartType: this.type,\n\t\t\t\tusecase: { target: this.type },\n\t\t\t\ttitle: 'Facet row categories',\n\t\t\t\tlabel: 'Rows',\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\t\tdefaultQ4fillTW: getT0T2defaultQ()\n\t\t\t},\n\t\t\t{\n\t\t\t\tboxLabel: '',\n\t\t\t\tlabel: 'Show percent',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'facet',\n\t\t\t\tsettingsKey: 'showPercents',\n\t\t\t\ttitle: `Option to show/hide percents per cell`\n\t\t\t}\n\t\t]\n\n\t\tif (this.hasTermCollection) {\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Aggregate by',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'facet',\n\t\t\t\tsettingsKey: 'aggregateBy',\n\t\t\t\ttitle: 'Aggregate values by',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Average', value: 'avg' },\n\t\t\t\t\t{ label: 'Sum', value: 'sum' }\n\t\t\t\t]\n\t\t\t})\n\t\t}\n\n\t\tthis.components = {\n\t\t\tcontrols: await controlsInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: this.dom.controlsHolder,\n\t\t\t\tinputs\n\t\t\t})\n\t\t}\n\t}\n}\n\nexport function makeChartBtnMenu(holder, chartsInstance) {\n\tconst callback = (xterm, yterm) => {\n\t\tconst config = {\n\t\t\tchartType: 'facet',\n\t\t\tcolumnTw: { term: xterm },\n\t\t\trowTw: { term: yterm }\n\t\t}\n\n\t\tif (isNumericTerm(xterm)) config.columnTw.term.q = { mode: 'discrete' }\n\t\tif (isNumericTerm(yterm)) config.rowTw.term.q = { mode: 'discrete' }\n\n\t\tchartsInstance.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig\n\t\t})\n\t}\n\tselect2Terms(chartsInstance.dom.tip, chartsInstance.app, 'facet', '', callback)\n}\n\nexport const facetInit = getCompInit(Facet)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = facetInit\n\nexport async function getPlotConfig(opts, app) {\n\tconst config = {\n\t\tsettings: {\n\t\t\tfacet: {\n\t\t\t\tshowPercents: false,\n\t\t\t\taggregateBy: 'avg'\n\t\t\t}\n\t\t}\n\t}\n\tif (!opts.columnTw) throw '.columnTw{} missing'\n\t// supply the default q if opts.term0/2.bins/q is undefined\n\t// so that the default q does not override bins or q from user\n\tawait fillTermWrapper(\n\t\topts.columnTw,\n\t\tapp.vocabApi,\n\t\topts.columnTw.bins || opts.columnTw.q ? undefined : getT0T2defaultQ()\n\t)\n\tif (!opts.rowTw) throw '.rowTw{} missing'\n\tawait fillTermWrapper(opts.rowTw, app.vocabApi, opts.rowTw.bins || opts.rowTw.q ? undefined : getT0T2defaultQ())\n\tconst result = copyMerge(config, opts)\n\treturn result\n}\n\nfunction getTermCollectionName(tw, termid) {\n\tconst term = tw.term.termlst.find(t => t.id == termid)\n\tif (!term) throw 'term is missing'\n\treturn term.name\n}\n\nfunction getTermCollectionData(s, tw, termid) {\n\tif (tw.term.type != 'termCollection') return\n\tconst value = s[tw.$id]?.value\n\tif (value) {\n\t\tconst data = value[termid]\n\t\treturn data\n\t}\n}\n"],
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