@sjcrh/proteinpaint-client 2.222.0 → 2.224.0

package/dist/chunk-VZ2JWFSX.js

@@ -1,296 +0,0 @@
-import {
-  getSortOptions
-} from "./chunk-5DI4UNH5.js";
-import {
-  defaultUiLabels,
-  fillTermWrapper
-} from "./chunk-4ASBDE27.js";
-import {
-  isDictionaryType
-} from "./chunk-JHLF2ZC2.js";
-import {
-  CNVClasses,
-  dtcnv,
-  mclass,
-  mutationClasses,
-  proteinChangingMutations,
-  synonymousMutations,
-  truncatingMutations
-} from "./chunk-WJLRU5OF.js";
-import {
-  copyMerge
-} from "./chunk-HBNB5TRH.js";
-
-// plots/matrix/matrix.config.js
-async function getPlotConfig(opts = {}, app) {
-  const controlLabels = structuredClone(defaultUiLabels);
-  const devicePixelRatio = opts.devicePixelRatio || window.devicePixelRatio;
-  const config = {
-    // data configuration
-    termgroups: [],
-    samplegroups: [],
-    divideBy: null,
-    legendValueFilter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    legendGrpFilter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    filter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    // cnvCutoffs: {},
-    // rendering options
-    settings: {
-      matrix: {
-        svgCanvasSwitch: 1e3,
-        // the number of samples to trigger switching between svg and canvas
-        useMinPixelWidth: true,
-        // canvas may be hazy if false, but more accurately reflects column density
-        cellEncoding: "",
-        // can be "oncoprint" | "stacked" | "single"
-        margin: {
-          top: 10,
-          right: 5,
-          bottom: 20,
-          left: 50
-        },
-        // set any dataset-defined sample limits and sort priority, otherwise undefined
-        // put in settings, so that later may be overridden by a user
-        maxGenes: opts.settings?.maxGenes || 50,
-        maxSample: opts.settings?.maxSample || 1e3,
-        sampleNameFilter: "",
-        sortSamplesBy: "a",
-        sortPriority: void 0,
-        // will be filled-in
-        sortBySampleAncestry: app.vocabApi.termdbConfig.hasSampleAncestry ? "last" : false,
-        // indicates sorting priority by sample ancestry
-        mapChildren2Root: false,
-        // for a dataset with sample ancestry, show one column per root sample (e.g. patient)
-        // sortByMutation: 'consequence', computed
-        // sortByCNV: true, computed
-        //sortOptions: getSortOptions(app.vocabApi.termdbConfig, controlLabels),
-        sortSampleGrpsBy: "name",
-        // 'hits' | 'name' | 'sampleCount'
-        sortSamplesTieBreakers: [{
-          $id: "sample",
-          sortSamples: {}
-          /*split: {char: '', index: 0}*/
-        }],
-        sortTermsBy: "sampleCount",
-        // or 'as listed'
-        // do not show number of samples at hiercluster gene row labels
-        samplecount4gene: opts.chartType == "hierCluster" ? "" : "abs",
-        //true, // 'abs' (default, previously true), 'pct', ''  (previously false)
-        geneVariantCountSamplesSkipMclass: [],
-        cellbg: "#ececec",
-        showGrid: "",
-        // false | 'pattern' | 'rect'
-        // whether to show these controls buttons
-        addMutationCNVButtons: false,
-        truncatingMutations,
-        proteinChangingMutations,
-        synonymousMutations,
-        mutationClasses,
-        CNVClasses,
-        gridStroke: "#fff",
-        outlineStroke: "#ccc",
-        beamStroke: "#f00",
-        colw: 0,
-        colwMin: 0.1 / devicePixelRatio,
-        colwMax: 16,
-        colspace: 1,
-        colgspace: 8,
-        colglabelpos: true,
-        collabelpos: "bottom",
-        collabelvisible: true,
-        collabelgap: 5,
-        collabelpad: 1,
-        collabelmaxchars: 32,
-        rowh: 18,
-        //use 0 to auto-compute row height, previous default=18,
-        rowhMin: 1,
-        rowhMax: 20,
-        rowspace: 1,
-        rowgspace: 8,
-        rowlabelpos: "left",
-        // | 'right'
-        rowlabelgap: 5,
-        rowlabelvisible: true,
-        rowlabelpad: 1,
-        rowlabelmaxchars: 32,
-        legendGrpLabelMaxChars: 26,
-        grpLabelFontSize: 12,
-        minLabelFontSize: 6,
-        maxLabelFontSize: 14,
-        transpose: false,
-        // 'auto' shows column labels only when columns are wide enough (colw >= minLabelFontSize);
-        sampleLabelsToggle: "auto",
-        // 'auto' | 'hide'
-        sampleLabelOffset: 120,
-        sampleGrpLabelOffset: 120,
-        sampleGrpLabelMaxChars: 32,
-        termLabelOffset: 80,
-        termGrpLabelOffset: 80,
-        termGrpLabelMaxChars: 32,
-        duration: 0,
-        zoomLevel: 1,
-        zoomCenterPct: 0,
-        zoomIndex: 0,
-        zoomGrpIndex: 0,
-        zoomMin: 0.5,
-        zoomIncrement: 0.1,
-        zoomStep: 1,
-        // renderedWMax should not be exposed as a user-input
-        // 60000 pixels is based on laptop and external monitor tests,
-        // when a canvas dataURL image in a zoomed-in matrix svg stops rendering
-        imgWMax: 6e4 / devicePixelRatio,
-        scrollHeight: 12,
-        controlLabels,
-        cnvUnit: "log2ratio",
-        ignoreCnvValues: false,
-        //will ignore numeric CNV values if true
-        barh: 32,
-        // default bar height for continuous terms,
-        // possible string entries:
-        // - "genesetEdit", for gene-centric embedders only like GDC OncoMatrix
-        // - may add other optional hints later
-        showHints: [],
-        genesetEditUiVersion: "",
-        // '' | 'withTabs'
-        // settings for a specific tw
-        twSpecificSettings: {},
-        oncoPrintSNVindelCellBorder: false,
-        // whether to show white cell border for SNVindel in oncoPrint mode
-        cnvValues: {
-          //Properties match the args for the ColorScales
-          //numericInput arg
-          cutoffMode: "percentile",
-          defaultPercentile: 99,
-          min: null,
-          max: null,
-          percentile: 99
-        }
-      }
-    }
-  };
-  const s = config.settings;
-  const fontsize = Math.max(s.matrix.rowh + s.matrix.rowspace - 3 * s.matrix.rowlabelpad, 12);
-  s.legend = {
-    ontop: false,
-    lineh: 25,
-    padx: 5,
-    padleft: 0,
-    //150,
-    padright: 20,
-    padbtm: 30,
-    fontsize,
-    iconh: fontsize - 2,
-    iconw: fontsize - 2,
-    hangleft: 1,
-    linesep: false
-  };
-  const overrides = app.vocabApi.termdbConfig.matrix || {};
-  copyMerge(config.settings.matrix, overrides.settings);
-  if (overrides.legendGrpFilter) config.legendGrpFilter = overrides.legendGrpFilter;
-  if (overrides.legendValueFilter) config.legendValueFilter = overrides.legendValueFilter;
-  if (overrides.filter) config.filter = overrides.filter;
-  if (opts.name) {
-    const data = await app.vocabApi.getMatrixByName(opts.name);
-    if (!data) throw "error from getMatrixByName()";
-    if (data.error) throw data.error;
-    copyMerge(config, data);
-  }
-  const os = opts?.settings?.matrix;
-  if (os) {
-    if ((os.sortSamplesBy == "custom" || os.sortSamplesBy == "asListed") && os.sortOptions?.custom.label == "against alteration type") {
-      os.sortSamplesBy = "a";
-    }
-    if (os.sortOptions) {
-      delete os.sortOptions.custom;
-      delete os.sortOptions.asListed;
-    }
-  }
-  copyMerge(config, opts);
-  const m = config.settings.matrix;
-  m.sortOptions = getSortOptions(app.vocabApi.termdbConfig, controlLabels, m);
-  m.duration = 0;
-  m.colw = 0;
-  if (m.sortSamplesBy != "asListed" && !m.sortOptions?.[m.sortSamplesBy]) m.sortSamplesBy = "a";
-  else if (["selectedTerms", "class", "dt", "hits"].includes(m.sortSamplesBy)) m.sortSamplesBy = "a";
-  if (m.samplecount4gene === true || m.samplecount4gene === 1) m.samplecount4gene = "abs";
-  if (window.location.hostname == "localhost") {
-    if (window.location.hash == "#canvas") m.svgCanvasSwitch = 0;
-  }
-  for (const grp of config.termgroups) {
-    const promises = [];
-    for (const tw of grp.lst) {
-      if (!tw.term?.type || isDictionaryType(tw.term.type)) {
-        if (!tw.id && tw.term.type != "samplelst" && tw.term.type != "termCollection") {
-          if (!tw.term.id) throw `missing tw.id and tw.term.id`;
-          tw.id = tw.term.id;
-        }
-        if (tw.term?.type != "samplelst" && tw.term?.type != "termCollection") delete tw.term;
-      }
-      promises.push(fillTermWrapper(tw, app.vocabApi));
-    }
-    grp.lst = await Promise.all(promises);
-  }
-  if (config.divideBy) config.divideBy = await fillTermWrapper(config.divideBy, app.vocabApi);
-  return config;
-}
-function setComputedConfig(config) {
-  const s = config.settings.matrix;
-  const allClasses = [...s.mutationClasses, ...s.CNVClasses];
-  s.filterByClass = { isAtomic: true };
-  for (const f of config.legendGrpFilter.lst) {
-    if (!f.dt) continue;
-    allClasses.filter((m) => f.dt.includes(mclass[m].dt)).forEach((key2) => {
-      s.filterByClass[key2] = "value";
-    });
-  }
-  for (const f of config.legendValueFilter.lst) {
-    if (!f.legendGrpName || f.tvs?.term?.type !== "geneVariant") continue;
-    if (f.tvs.values?.[0].mclasslst)
-      f.tvs.values[0].mclasslst.forEach((key2) => {
-        s.filterByClass[key2] = f.legendFilterType?.endsWith("_hard") ? "case" : "value";
-      });
-    else if (f.tvs.values)
-      f.tvs.values.forEach((v) => {
-        s.filterByClass[key] = "value";
-      });
-    else throw `unhandled tvs from legendValueFilter`;
-  }
-  s.hiddenVariants = Object.keys(s.filterByClass).filter((c) => c !== "isAtomic");
-  const hiddenCNVs = new Set(s.hiddenVariants.filter((key2) => mclass[key2]?.dt === dtcnv));
-  s.hiddenCNVs = [...hiddenCNVs];
-  s.showMatrixCNV = !hiddenCNVs.size ? "all" : hiddenCNVs.size == s.CNVClasses.length ? "none" : "bySelection";
-  s.allMatrixCNVHidden = hiddenCNVs.size == s.CNVClasses.length;
-  const hiddenMutations = new Set(s.hiddenVariants.filter((key2) => s.mutationClasses.find((k) => k === key2)));
-  s.hiddenMutations = [...hiddenMutations];
-  const PCset = new Set(s.proteinChangingMutations);
-  const TMset = new Set(s.truncatingMutations);
-  s.showMatrixMutation = !hiddenMutations.size ? "all" : hiddenMutations.size == s.mutationClasses.length ? "none" : hiddenMutations.size === s.mutationClasses.length - PCset.size && [...hiddenMutations].every((m) => !PCset.has(m)) ? "onlyPC" : hiddenMutations.size === s.mutationClasses.length - TMset.size && [...hiddenMutations].every((m) => !TMset.has(m)) ? "onlyTruncating" : "bySelection";
-  s.allMatrixMutationHidden = hiddenMutations.size == s.mutationClasses.length;
-  const tiebreakers = s.sortOptions.a?.sortPriority.find((sp) => sp.types.length == 1 && sp.types[0] == "geneVariant")?.tiebreakers || [];
-  s.sortByMutation = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 1)?.isOrdered ? "consequence" : "presence";
-  s.sortByCNV = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 4)?.disabled !== true;
-}
-
-export {
-  getPlotConfig,
-  setComputedConfig
-};
-//# sourceMappingURL=chunk-VZ2JWFSX.js.map

package/dist/chunk-W5GR42L2.js

@@ -1,159 +0,0 @@
-import {
-  NumericDensity
-} from "./chunk-V2D7DA2M.js";
-import {
-  HandlerBase,
-  Tabs
-} from "./chunk-4ASBDE27.js";
-
-// termsetting/handlers/NumericHandler.ts
-var NumericHandler = class extends HandlerBase {
-  constructor(opts) {
-    super(opts);
-    this.tabs = [];
-    this.handlerByMode = {};
-    this.dom = {};
-    this.opts = opts;
-    this.termsetting = opts.termsetting;
-    this.tw = opts.termsetting.tw;
-    this.tabs = this.setTabData();
-    this.density = new NumericDensity(opts);
-  }
-  getPillStatus() {
-    this.tw = this.termsetting.tw;
-    const status = this.tw.getStatus(this.termsetting.usecase, this.termsetting.data);
-    if (this.tw.term.type == "geneExpression" && this.tw.term.sampleTypeLabel)
-      status.text += ` (${this.tw.term.sampleTypeLabel})`;
-    return status;
-  }
-  setTabData() {
-    const self = this.termsetting;
-    const tabs = [];
-    const callback = async (event, tabData) => {
-      if (event) event.stopPropagation();
-      try {
-        await this.setEditHandler(tabData);
-        await this.editHandler.showEditMenu(tabData.contentHolder);
-      } catch (e) {
-        this.dom.errdiv.style("display", "").text(e);
-      }
-    };
-    const numTabs = self.opts.numericEditMenuVersion.length;
-    if (self.opts.numericEditMenuVersion.includes("continuous")) {
-      tabs.push({
-        mode: "continuous",
-        label: self.term.type == "survival" ? "Time to Event" : "Continuous",
-        callback,
-        active: this.tw.q.mode === "continuous" || numTabs === 1
-      });
-    }
-    if (self.opts.numericEditMenuVersion.includes("discrete")) {
-      tabs.push({
-        mode: "discrete",
-        label: self.term.type == "survival" ? "Exit code" : "Discrete",
-        callback,
-        active: this.tw.q.mode === "discrete" || numTabs === 1
-      });
-    }
-    if (self.opts.numericEditMenuVersion.includes("spline")) {
-      tabs.push({
-        mode: "spline",
-        label: "Cubic spline",
-        callback,
-        active: this.tw.q.mode === "spline" || numTabs === 1
-      });
-    }
-    if (self.opts.numericEditMenuVersion.includes("binary")) {
-      tabs.push({
-        mode: "binary",
-        label: "Binary",
-        callback,
-        active: this.tw.q.mode === "binary" || numTabs === 1
-      });
-    }
-    return tabs;
-  }
-  async setEditHandler(tabData) {
-    if (!this.handlerByMode[tabData.mode]) {
-      switch (tabData.mode) {
-        case "continuous": {
-          const { NumContEditor } = await import("./NumContEditor-VMCE5LUM.js");
-          this.handlerByMode.continuous = new NumContEditor(this.opts, this);
-          break;
-        }
-        case "discrete": {
-          const { NumDiscreteEditor } = await import("./NumDiscreteEditor-YZ3Q4J4M.js");
-          this.handlerByMode.discrete = new NumDiscreteEditor(this.opts, this);
-          break;
-        }
-        case "binary": {
-          const { NumBinaryEditor } = await import("./NumBinaryEditor-45I5YNHI.js");
-          this.handlerByMode.binary = new NumBinaryEditor(this.opts, this);
-          break;
-        }
-        case "spline": {
-          const { NumSplineEditor } = await import("./NumSplineEditor-OMJUFDSC.js");
-          this.handlerByMode.spline = new NumSplineEditor(this.opts, this);
-          break;
-        }
-        default:
-          throw `unexpected numeric tabData.mode='${tabData.mode}'`;
-          break;
-      }
-    }
-    this.editHandler = this.handlerByMode[tabData.mode];
-  }
-  async showEditMenu(div) {
-    try {
-      this.showLoading(div);
-      this.dom.errdiv = div.append("div").attr("class", "sja_errorbar").style("display", "none");
-      this.tw = this.termsetting.tw;
-      const self = this.tw;
-      for (const t of this.tabs) {
-        t.active = this.tabs.length === 1 || self.q.mode == t.mode || t.mode == "continuous" && !self.q.mode;
-      }
-      this.density_data = await this.density.setData();
-      await this.setEditHandler(this.tabs.find((t) => t.active));
-      this.dom.editDiv = div.append("div").attr("data-testid", "sjpp-num-ts-edit-div");
-      this.dom.btnDiv = div.append("div").style("margin", "0px 0px 5px 5px");
-      this.renderButtons(this.dom.btnDiv);
-      if (this.tabs.length > 1) {
-        this.dom.topBar = this.dom.editDiv.append("div").attr("data-testid", "sja-ts-numeric-edit-top-bar").style("padding", "10px");
-        this.dom.topBar.append("span").html("Use as ");
-        new Tabs({
-          holder: this.dom.topBar.append("div").style("display", "inline-block"),
-          contentHolder: this.dom.editDiv.append("div"),
-          noTopContentStyle: true,
-          tabs: this.tabs
-        }).main();
-      } else {
-        await this.editHandler.showEditMenu(this.dom.editDiv);
-      }
-      this.dom.loadingDiv.style("display", "none");
-    } catch (e) {
-      this.hideLoading();
-      this.dom.errdiv.style("display", "").text(typeof e == "object" ? e.message || e.error || e : e);
-    }
-  }
-  renderButtons(btnDiv) {
-    btnDiv.append("button").style("margin", "5px").attr("data-testId", "sjpp_numeric_edit_apply").html("Apply").on("click", () => {
-      this.termsetting.q = this.editHandler.getEditedQ();
-      this.termsetting.dom.tip.hide();
-      this.termsetting.api.runCallback();
-    });
-    btnDiv.append("button").style("margin", "5px").attr("data-testId", "sjpp_numeric_edit_reset").html("Reset").on("click", () => {
-      this.editHandler.undoEdits();
-    });
-  }
-  destroy() {
-    for (const s of Object.values(this.dom)) {
-      if (typeof s.remove == "function") s.remove();
-    }
-    this.density.destroy();
-  }
-};
-
-export {
-  NumericHandler
-};
-//# sourceMappingURL=chunk-W5GR42L2.js.map