@sjcrh/proteinpaint-client 2.206.0 → 2.207.0

package/dist/facet-GVZQ3RPN.js

@@ -1,519 +0,0 @@
-import {
-  PlotBase,
-  addNewGroup,
-  controlsInit,
-  fillTermWrapper,
-  getCombinedTermFilter,
-  getFilter,
-  getSamplelstTW,
-  getT0T2defaultQ,
-  select2Terms
-} from "./chunk-Q5SK3U2T.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-54KC7DAB.js";
-import "./chunk-N7DVQTPC.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-RPDVFM7E.js";
-import "./chunk-M4XXKTH2.js";
-import {
-  isNumericTerm
-} from "./chunk-5ILEFNXJ.js";
-import "./chunk-IZUYLFOX.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.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-HS5PO5ZQ.js";
-
-// plots/facet.ts
-var Facet = class _Facet extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.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}`);
-    };
-    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()
-    };
-  }
-  static {
-    this.type = "facet";
-  }
-  async init() {
-  }
-  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);
-    }
-  }
-  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.vocabApi?.getAnnotatedSampleData({
-      filter: this.state.termfilter.filter,
-      terms: [config.columnTw, config.rowTw]
-    });
-    if (!result || !result.lst || !result.lst.length) return { result: { lst: [] }, categories: [], categories2: [] };
-    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.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.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-GVZQ3RPN.js.map

package/dist/gb-HEPGVYEK.js

@@ -1,81 +0,0 @@
-import {
-  appInit
-} from "./chunk-NSRGYBDM.js";
-import "./chunk-HJSGHFJ6.js";
-import "./chunk-ZWCVRVV4.js";
-import "./chunk-BMQDU7KN.js";
-import "./chunk-WPDM57B5.js";
-import "./chunk-5UO7MKCO.js";
-import "./chunk-X46YA4CB.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-ANGLZ4XR.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-Q5SK3U2T.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-54KC7DAB.js";
-import "./chunk-N7DVQTPC.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-RPDVFM7E.js";
-import "./chunk-M4XXKTH2.js";
-import "./chunk-5ILEFNXJ.js";
-import "./chunk-IZUYLFOX.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// gdc/gb.ts
-async function init(arg, holder, genomes) {
-  const useGenome = arg.genome || "hg38";
-  const useDslabel = arg.dslabel || "GDC";
-  const genome = genomes[useGenome];
-  const massApi = await appInit({
-    //debug: arg.debugmode, // is debug accepted?
-    genome,
-    holder,
-    state: {
-      genome: useGenome,
-      dslabel: useDslabel,
-      termfilter: { filter0: arg.filter0 },
-      nav: { activeTab: 1, header_mode: "hidden" },
-      plots: [{ chartType: "genomeBrowser" }]
-    },
-    genomeBrowser: arg.opts?.genomeBrowser || {},
-    app: arg.opts?.app || {}
-  });
-  const api = {
-    update: async (updateArg) => {
-      if (!massApi) return;
-      if ("filter0" in updateArg) {
-        massApi.dispatch({
-          type: "app_refresh",
-          subactions: [
-            {
-              type: "filter_replace",
-              filter0: updateArg.filter0
-            }
-          ]
-        });
-      }
-    },
-    triggerAbort: (reason = "") => massApi.triggerAbort(reason)
-  };
-  return api;
-}
-export {
-  init
-};
-//# sourceMappingURL=gb-HEPGVYEK.js.map