@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/chunk-ROMW4AK2.js

@@ -1,102 +0,0 @@
-import {
-  getPlotConfig
-} from "./chunk-EGPNRSPF.js";
-import {
-  fillTermWrapper
-} from "./chunk-TKW5TW4Z.js";
-import {
-  dictionaryNumericTypes,
-  numericTypes
-} from "./chunk-7JRDJNLR.js";
-import {
-  copyMerge
-} from "./chunk-M3J4MINX.js";
-
-// plots/matrix/hierCluster.config.js
-async function getPlotConfig2(opts = {}, app) {
-  opts.chartType = "hierCluster";
-  if (dictionaryNumericTypes.has(opts.dataType) || opts.dataType == "numericDictTerm") {
-    const grp = opts.termgroups?.find((g) => g.type == "hierCluster");
-    for (const tw of grp?.lst || []) tw.q = { ...tw.q, mode: "continuous" };
-  }
-  const config = await getPlotConfig(opts, app);
-  delete config.genes;
-  if (config.dataType == "numericDictTerm") {
-    const lst = config.termgroups?.find((g) => g.type == "hierCluster")?.lst;
-    config.dataType = lst?.[0]?.term?.type || "float";
-  }
-  config.settings.hierCluster = {
-    /* type of data used for clustering
-    exciting todo: (to introduce new dt values)
-    - gene dependency
-    - numeric dic term
-    - non-gene genomic stuff that resolves into numeric quantities (cpg meth)
-    - metabolite
-    */
-    dataType: config.dataType,
-    // adjust the default group name based on automatically detected term types
-    // Done in matrix.cells.js: setHierClusterCellProps
-    // termGroupName: 'Expression',
-    clusterSamples: true,
-    clusterRows: true,
-    clusterMethod: "average",
-    // complete
-    distanceMethod: "euclidean",
-    zScoreCap: 5,
-    zScoreTransformation: true,
-    xDendrogramHeight: 100,
-    yDendrogramHeight: 200,
-    colorScale: "blueWhiteRed"
-  };
-  const overrides = app.vocabApi.termdbConfig.hierCluster || {};
-  const numericDictTermClusterOverrides = dictionaryNumericTypes.has(config.dataType) && app.vocabApi.termdbConfig.numericDictTermCluster ? app.vocabApi.termdbConfig.numericDictTermCluster : {};
-  copyMerge(
-    config.settings.hierCluster,
-    overrides.settings,
-    opts.settings?.hierCluster || {},
-    numericDictTermClusterOverrides.settings
-  );
-  {
-    const c = config.settings.hierCluster.colorScale;
-    if (!c) throw "colorScale missing";
-  }
-  config.settings.matrix.collabelpos = "top";
-  const termGroupName = config.settings.hierCluster.termGroupName;
-  const hcTermGroup = config.termgroups.find((g) => g.type == "hierCluster" || g.name == termGroupName) || {
-    name: termGroupName
-  };
-  hcTermGroup.type = "hierCluster";
-  if (!hcTermGroup.lst?.length) {
-    if (!Array.isArray(opts.terms)) throw "opts.terms[] not array (may show geneset edit ui)";
-    const promises = [];
-    for (const i of opts.terms) {
-      const tw = i.term ? i : { term: i };
-      if (!tw.term.type) {
-        if (config.dataType && numericTypes.has(config.dataType)) {
-          tw.term.type = config.dataType;
-        } else {
-          throw `term type missing and cannot be assigned by dataType '${config.dataType}'`;
-        }
-      } else if (!numericTypes.has(tw.term.type)) {
-        throw "term type is not numeric";
-      } else if (config.dataType && !canTermBeInHierGrp(config.dataType, tw.term.type)) {
-        throw `cannot have term type ${tw.term.type} in ${config.dataType} term group`;
-      }
-      if (dictionaryNumericTypes.has(tw.term.type)) tw.q = { ...tw.q, mode: "continuous" };
-      promises.push(fillTermWrapper(tw, app.vocabApi));
-    }
-    hcTermGroup.lst = await Promise.all(promises);
-    if (config.termgroups.indexOf(hcTermGroup) == -1) config.termgroups.unshift(hcTermGroup);
-  }
-  config.settings.matrix.maxSample = 1e5;
-  return config;
-}
-function canTermBeInHierGrp(grpType, twType) {
-  if (dictionaryNumericTypes.has(grpType) && dictionaryNumericTypes.has(twType)) return true;
-  return twType == grpType;
-}
-
-export {
-  getPlotConfig2 as getPlotConfig
-};
-//# sourceMappingURL=chunk-ROMW4AK2.js.map

package/dist/chunk-RR5U35N7.js

@@ -1,230 +0,0 @@
-import {
-  keyupEnter
-} from "./chunk-TKW5TW4Z.js";
-import {
-  get_bin_label,
-  get_bin_range_equation
-} from "./chunk-MPSLUEI4.js";
-
-// termsetting/handlers/NumCustomBinEditor.ts
-var NumCustomBinEditor = class {
-  constructor(editHandler) {
-    this.dom = {};
-    this.editHandler = editHandler;
-    this.opts = editHandler.opts;
-    this.tw = editHandler.tw;
-    this.termsetting = editHandler.termsetting;
-  }
-  async render(div) {
-    this.tw = this.editHandler.tw;
-    this.q = this.getDefaultQ();
-    await this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-    if (this.dom.inputsDiv) {
-      if (this.editHandler.dom.binsDiv?.node().contains(this.dom.inputsDiv.node())) return;
-      else {
-        this.dom.inputsDiv.remove();
-        delete this.dom.inputsDiv;
-      }
-    }
-    this.dom.inputsDiv = div.append("div").style("display", "flex").style("width", "100%");
-    this.renderCustomBinInputs();
-  }
-  getBoundaryOpts() {
-    return {
-      values: this.q.lst.slice(1).map((bin) => ({ x: bin.startunbounded ? bin.stop : bin.start, isDraggable: true })),
-      callback: (d, value) => {
-        const boundaryValues = this.q.lst.slice(1).map((d2) => "start" in d2 ? d2.start : "");
-        boundaryValues[d.index] = value;
-        this.dom.customBinBoundaryInput.text(boundaryValues.join(",\n"));
-        this.handleInputChange("drag");
-        return 0;
-      }
-    };
-  }
-  getDefaultQ() {
-    if (this.tw.q.mode == "discrete" && this.tw.q.type == "custom-bin") {
-      const copy = JSON.parse(JSON.stringify(this.tw.q));
-      copy.lst.forEach((bin) => {
-        if (!bin.label) bin.label = get_bin_label(bin, this.tw.q, this.tw.term.valueConversion);
-        bin.range = get_bin_range_equation(bin, this.tw.q);
-      });
-      return copy;
-    }
-    const { min, max } = this.editHandler.handler.density_data;
-    const defaultCustomBoundary = (
-      /* when no sample is annotated by this term,
-      minvalue and maxvalue are both null
-      setting defaultCustomBoundary to arbitrary "0" will allow existing UI to work
-      but remains to be evaluated if is really okay to use 0
-      */
-      !Number.isFinite(min) || !Number.isFinite(max) ? 0 : (
-        // minvalue and maxvalue is valid number
-        max != min ? min + (max - min) / 2 : max
-      )
-    );
-    const firstBin = {
-      startunbounded: true,
-      startinclusive: false,
-      stopinclusive: false,
-      stop: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
-    };
-    const lastBin = {
-      stopunbounded: true,
-      startinclusive: true,
-      stopinclusive: false,
-      start: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
-    };
-    return {
-      mode: "discrete",
-      type: "custom-bin",
-      lst: [
-        // Type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' is not assignable to type 'StartUnboundedBin | FullyBoundedBin'.
-        // Property 'start' is missing in type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' but required in type 'FullyBoundedBin'.
-        {
-          ...firstBin,
-          label: get_bin_label(firstBin, this.tw.q, this.tw.term.valueConversion),
-          range: get_bin_range_equation(firstBin, this.tw.q)
-        },
-        {
-          ...lastBin,
-          label: get_bin_label(lastBin, this.tw.q, this.tw.term.valueConversion),
-          range: get_bin_range_equation(lastBin, this.tw.q)
-        }
-        //satisfies StopUnboundedBin
-      ]
-    };
-  }
-  /******************* Functions for Numerical Custom size bins *******************/
-  renderCustomBinInputs() {
-    const q = this.q;
-    const boundaryDiv = this.dom.inputsDiv.append("div").style("margin-right", "20px");
-    this.dom.rangeAndLabelDiv = this.dom.inputsDiv.append("div");
-    boundaryDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Bin boundaries");
-    this.dom.customBinBoundaryInput = boundaryDiv.append("textarea").style("width", "100px").style("height", "70px").text(
-      q.lst.slice(1).map((d) => "start" in d ? d.start : "").join("\n")
-    ).on("change", () => this.handleInputChange()).on("keyup", async (event) => {
-      if (!keyupEnter(event) && event.key != 8 && event.key != "Enter") return;
-      if (!this.dom.inputsDiv.selectAll("input").node().value) return;
-      this.handleInputChange();
-    });
-    boundaryDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
-    this.renderBoundaryInputDivs();
-  }
-  renderBoundaryInputDivs() {
-    const data = this.q.lst;
-    const holder = this.dom.rangeAndLabelDiv;
-    holder.selectAll("*").remove();
-    const grid = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center");
-    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
-    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Bin label");
-    for (const d of data) {
-      grid.append("div").attr("name", "range").html(d.range);
-      grid.append("div").append("input").attr("type", "text").style("margin", "2px 0px").property("value", d.label).on("change", function() {
-        d.label = this.value;
-      });
-    }
-    this.dom.customBinRanges = this.dom.inputsDiv.selectAll('div[name="range"]').data(data);
-    this.dom.customBinLabelInput = this.dom.inputsDiv.selectAll("input").data(data);
-  }
-  handleInputChange(eventType = "") {
-    const self = this.tw;
-    const inputs = this.dom.inputsDiv.selectAll("input");
-    inputs.property("value", "");
-    const data = this.processCustomBinInputs();
-    if (data == void 0) {
-      return;
-    }
-    if (self.q.hiddenValues) this.tw.q.hiddenValues = self.q.hiddenValues;
-    if (this.binsChanged(data, this.q.lst)) {
-      this.q.lst = data;
-    }
-    this.renderBoundaryInputDivs();
-    if (eventType != "drag") this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-  binsChanged(data, qlst) {
-    if (data.length != qlst.length) return true;
-    if (Object.keys(data[0]).length !== Object.keys(qlst[0]).length) return true;
-    for (const [i, bin] of qlst.entries()) {
-      for (const k of Object.keys(bin)) {
-        if (bin[k] && bin[k] !== data[i][k]) {
-          return true;
-        }
-      }
-    }
-    return false;
-  }
-  processCustomBinInputs() {
-    const self = this.termsetting;
-    const startinclusive = this.editHandler.boundaryInclusion == "startinclusive";
-    const stopinclusive = this.editHandler.boundaryInclusion == "stopinclusive";
-    const inputs = this.dom.inputsDiv.node().querySelectorAll("input");
-    const inputData = this.dom.customBinBoundaryInput.property("value").split("\n").filter((d) => d != "" && !isNaN(d));
-    const trackBins = new Set(inputData);
-    if (!trackBins.size) return this.tw.q.lst;
-    const sortedBins = Array.from(trackBins).map(Number).sort((a, b) => a - b);
-    const data = [
-      // first bin: StartUnbounded type
-      {
-        startunbounded: true,
-        stop: sortedBins[0],
-        startinclusive: false,
-        stopinclusive,
-        label: inputs[0].value
-      }
-    ];
-    if (!data[0].label) data[0].label = get_bin_label(data[0], self.q, self.term.valueConversion);
-    if (!data[0].range) data[0].range = get_bin_range_equation(data[0], self.q);
-    for (const [i, d] of sortedBins.entries()) {
-      let bin;
-      const label = inputs[i + 1]?.value || "";
-      if (i !== trackBins.size - 1) {
-        bin = {
-          start: +d,
-          startinclusive,
-          stopinclusive,
-          stop: sortedBins[i + 1],
-          label
-          //range: ''
-        };
-      } else {
-        bin = {
-          start: +d,
-          startinclusive,
-          stopinclusive: false,
-          stopunbounded: true,
-          label
-          //range: ''
-        };
-      }
-      if (bin.label === "" || bin.label === void 0) bin.label = get_bin_label(bin, self.q, self.term.valueConversion);
-      if (bin.range === "" || bin.range === void 0) bin.range = get_bin_range_equation(bin, self.q);
-      data.push(bin);
-    }
-    return data;
-  }
-  getEditedQ(destroyDom = true) {
-    const lst = this.processCustomBinInputs();
-    if (destroyDom) {
-      for (const name of Object.keys(this.dom)) {
-        this.dom[name].remove();
-        delete this.dom[name];
-      }
-    }
-    return {
-      mode: "discrete",
-      type: "custom-bin",
-      lst
-    };
-  }
-  undoEdits() {
-    this.q = this.getDefaultQ();
-    this.dom.inputsDiv.selectAll("*").remove();
-    this.renderCustomBinInputs();
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-};
-
-export {
-  NumCustomBinEditor
-};
-//# sourceMappingURL=chunk-RR5U35N7.js.map

package/dist/chunk-RR5U35N7.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termsetting/handlers/NumCustomBinEditor.ts"],
-  "sourcesContent": ["import { keyupEnter } from '#src/client'\nimport type { NumCustomBins } from '#tw'\nimport type { NumDiscreteEditor } from './NumDiscreteEditor.ts'\nimport type { BoundaryOpts, LineData } from './NumericDensity.ts'\nimport type { TermSetting } from '../TermSetting.ts'\nimport type { CustomNumericBinConfig, CustomNumericBinConfigLst, StartUnboundedBin, StopUnboundedBin } from '#types'\nimport { get_bin_label, get_bin_range_equation } from '#shared/termdb.bins.js'\n\n// This is a bin editor for NumDiscreteEditor\n// NumericHandler (handler) -> NumDiscreteEditor (editor) -> NumCustomBinEditor (bin editor)\nexport class NumCustomBinEditor {\n\ttw: NumCustomBins\n\tq!: CustomNumericBinConfig\n\teditHandler: NumDiscreteEditor\n\ttermsetting: TermSetting\n\topts: any\n\tdom: {\n\t\t[elemName: string]: any\n\t} = {}\n\n\tconstructor(editHandler) {\n\t\tthis.editHandler = editHandler\n\t\tthis.opts = editHandler.opts\n\t\tthis.tw = editHandler.tw\n\t\tthis.termsetting = editHandler.termsetting\n\t}\n\n\tasync render(div) {\n\t\tthis.tw = this.editHandler.tw as NumCustomBins\n\t\tthis.q = this.getDefaultQ()\n\t\tawait this.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t\tif (this.dom.inputsDiv) {\n\t\t\tif (this.editHandler.dom.binsDiv?.node().contains(this.dom.inputsDiv.node())) return\n\t\t\telse {\n\t\t\t\tthis.dom.inputsDiv.remove()\n\t\t\t\tdelete this.dom.inputsDiv\n\t\t\t}\n\t\t}\n\t\tthis.dom.inputsDiv = div.append('div').style('display', 'flex').style('width', '100%')\n\t\tthis.renderCustomBinInputs()\n\t}\n\n\tgetBoundaryOpts(): BoundaryOpts {\n\t\treturn {\n\t\t\tvalues: this.q.lst.slice(1).map(bin => ({ x: bin.startunbounded ? bin.stop : bin.start, isDraggable: true })),\n\t\t\tcallback: (d: LineData, value) => {\n\t\t\t\tconst boundaryValues = this.q.lst.slice(1).map(d => ('start' in d ? d.start : ''))\n\t\t\t\tboundaryValues[d.index] = value\n\t\t\t\tthis.dom.customBinBoundaryInput.text(boundaryValues.join(',\\n'))\n\t\t\t\tthis.handleInputChange('drag')\n\t\t\t\treturn 0\n\t\t\t}\n\t\t}\n\t}\n\n\tgetDefaultQ(): CustomNumericBinConfig {\n\t\tif (this.tw.q.mode == 'discrete' && this.tw.q.type == 'custom-bin') {\n\t\t\tconst copy = JSON.parse(JSON.stringify(this.tw.q))\n\t\t\tcopy.lst.forEach(bin => {\n\t\t\t\tif (!bin.label) bin.label = get_bin_label(bin, this.tw.q, this.tw.term.valueConversion)\n\t\t\t\tbin.range = get_bin_range_equation(bin, this.tw.q)\n\t\t\t})\n\t\t\treturn copy\n\t\t}\n\t\tconst { min, max } = this.editHandler.handler.density_data\n\t\tconst defaultCustomBoundary =\n\t\t\t/* when no sample is annotated by this term,\n\t\t\tminvalue and maxvalue are both null\n\t\t\tsetting defaultCustomBoundary to arbitrary \"0\" will allow existing UI to work\n\t\t\tbut remains to be evaluated if is really okay to use 0\n\t\t\t*/\n\t\t\t!Number.isFinite(min) || !Number.isFinite(max)\n\t\t\t\t? 0\n\t\t\t\t: // minvalue and maxvalue is valid number\n\t\t\t\tmax != min\n\t\t\t\t? min + (max - min) / 2\n\t\t\t\t: max\n\n\t\tconst firstBin = {\n\t\t\tstartunbounded: true,\n\t\t\tstartinclusive: false,\n\t\t\tstopinclusive: false,\n\t\t\tstop: +defaultCustomBoundary.toFixed(this.tw.term.type == 'integer' ? 0 : 2)\n\t\t} satisfies StartUnboundedBin\n\n\t\tconst lastBin = {\n\t\t\tstopunbounded: true,\n\t\t\tstartinclusive: true,\n\t\t\tstopinclusive: false,\n\t\t\tstart: +defaultCustomBoundary.toFixed(this.tw.term.type == 'integer' ? 0 : 2)\n\t\t} satisfies StopUnboundedBin\n\n\t\treturn {\n\t\t\tmode: 'discrete',\n\t\t\ttype: 'custom-bin',\n\t\t\tlst: [\n\t\t\t\t// Type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' is not assignable to type 'StartUnboundedBin | FullyBoundedBin'.\n\t\t\t\t// Property 'start' is missing in type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' but required in type 'FullyBoundedBin'.\n\t\t\t\t{\n\t\t\t\t\t...firstBin,\n\t\t\t\t\tlabel: get_bin_label(firstBin, this.tw.q, this.tw.term.valueConversion),\n\t\t\t\t\trange: get_bin_range_equation(firstBin, this.tw.q)\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\t...lastBin,\n\t\t\t\t\tlabel: get_bin_label(lastBin, this.tw.q, this.tw.term.valueConversion),\n\t\t\t\t\trange: get_bin_range_equation(lastBin, this.tw.q)\n\t\t\t\t} //satisfies StopUnboundedBin\n\t\t\t]\n\t\t}\n\t}\n\n\t/******************* Functions for Numerical Custom size bins *******************/\n\trenderCustomBinInputs() {\n\t\tconst q = this.q\n\t\t// boundaryDiv for entering bin boundaries\n\t\t// rangeAndLabelDiv for rendering ranges and labels\n\t\tconst boundaryDiv = this.dom.inputsDiv.append('div').style('margin-right', '20px')\n\t\tthis.dom.rangeAndLabelDiv = this.dom.inputsDiv.append('div')\n\n\t\tboundaryDiv.append('div').style('margin-bottom', '5px').style('color', 'rgb(136, 136, 136)').text('Bin boundaries')\n\n\t\tthis.dom.customBinBoundaryInput = boundaryDiv\n\t\t\t.append('textarea')\n\t\t\t.style('width', '100px')\n\t\t\t.style('height', '70px')\n\t\t\t.text(\n\t\t\t\tq.lst\n\t\t\t\t\t.slice(1)\n\t\t\t\t\t.map(d => ('start' in d ? d.start : ''))\n\t\t\t\t\t.join('\\n')\n\t\t\t)\n\t\t\t.on('change', () => this.handleInputChange())\n\t\t\t.on('keyup', async (event: any) => {\n\t\t\t\t// enter or backspace/delete\n\t\t\t\t// i don't think backspace works\n\t\t\t\tif (!keyupEnter(event) && event.key != 8 && event.key != 'Enter') return\n\t\t\t\tif (!this.dom.inputsDiv.selectAll('input').node().value) return\n\t\t\t\t// Fix for if user hits enter with no values. 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-  "names": ["d"]
-}

package/dist/chunk-RVKADD4L.js

@@ -1,148 +0,0 @@
-import {
-  storeInit
-} from "./chunk-4KRGCOTL.js";
-import {
-  recoverInit
-} from "./chunk-4KY4XKJV.js";
-import {
-  AppBase,
-  sayerror,
-  vocabInit
-} from "./chunk-TKW5TW4Z.js";
-import {
-  importPlot
-} from "./chunk-3SHZTAGF.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  AppApi
-} from "./chunk-M3J4MINX.js";
-
-// plots/plot.app.ts
-var PlotApp = class _PlotApp extends AppBase {
-  constructor(opts, api) {
-    super(opts);
-    this.components = {};
-    this.wasDestroyed = false;
-    this.api = api;
-    this.type = _PlotApp.type;
-    this.dom = this.getDom(opts);
-  }
-  static {
-    this.type = "app";
-  }
-  getDom(opts) {
-    const dom = {
-      holder: opts.holder,
-      errdiv: opts.holder.append("div"),
-      plotDiv: opts.holder.append("div")
-    };
-    const controls = opts.violin?.mode == "minimal" ? null : opts.holder.append("div").style("white-space", "nowrap");
-    if (controls) {
-      dom.plotControls = controls.append("div").style("display", "inline-block");
-      dom.recoverControls = controls.append("div").style("display", "inline-block");
-    }
-    return dom;
-  }
-  async preApiFreeze(api) {
-    try {
-      api.tip = new Menu({ padding: "5px" });
-      api.printError = (e) => this.printError(e);
-      const vocab = this.opts.state.vocab;
-      api.vocabApi = this.opts.vocabApi ? this.opts.vocabApi : await vocabInit({
-        app: api,
-        state: {
-          vocab: {
-            // either (genome + dslabel) XOR (terms) can be undefined
-            genome: vocab?.genome || this.opts.state.genome,
-            dslabel: vocab?.dslabel || this.opts.state.dslabel,
-            terms: vocab?.terms
-          }
-        },
-        fetchOpts: this.opts.fetchOpts
-      });
-      this.opts.state.vocab = api.vocabApi.vocab;
-    } catch (e) {
-      console.log(`preApiFreeze error`, e);
-      throw e;
-    }
-  }
-  async init() {
-    try {
-      this.opts.state.nav = { header_mode: "hidden" };
-      this.store = await storeInit({ app: this.api, state: this.opts.state });
-      this.state = await this.store.copyState();
-      this.components = {
-        plots: {}
-      };
-      if (this.opts.app?.features?.includes("recover"))
-        this.components.recover = await recoverInit({
-          app: this.api,
-          holder: this.dom.recoverControls,
-          // TODO: ???? may limit the tracked state to only the filter, activeCohort ???
-          getState: (appState) => appState,
-          //reactsTo: action => true, //action.type != 'plot_edit' || action.type == 'app_refresh',
-          maxHistoryLen: 10
-        });
-      if (this.opts.app?.doNotAwaitInitRender) {
-        this.api.dispatch();
-      } else {
-        await this.api.dispatch();
-      }
-    } catch (e) {
-      this.printError(e);
-      throw e;
-    }
-  }
-  async main() {
-    this.api.vocabApi.main();
-    for (const id in this.components.plots) {
-      const plot = this.components.plots[id];
-      if (!this.state.plots.find((p) => p.id === plot.id)) {
-        plot.destroy();
-        delete this.components.plots[id];
-      }
-    }
-    for (const plot of this.state.plots.values()) {
-      if (plot.parentId) continue;
-      if (!this.components.plots[plot.id]) {
-        const holder = this.opts?.app?.getPlotHolder ? this.opts.app.getPlotHolder(plot, this.dom.holder) : this.dom.holder.append("div");
-        if (!this.dom.plotDiv) this.dom.plotDiv = holder;
-        const { componentInit } = await importPlot(plot.chartType);
-        const plotApi = await componentInit({
-          id: plot.id,
-          app: this.api,
-          holder,
-          controls: this.dom.plotControls
-        });
-        this.components.plots[plot.id] = plotApi;
-      }
-    }
-  }
-  printError(e) {
-    sayerror(this.dom.errdiv, "Error: " + (e.message || e));
-    if (e.stack) console.log(e.stack);
-    this.bus.emit("error");
-  }
-  skipPrevActionAbort(action) {
-    if (!action) return false;
-    if (action.type.startsWith("filter")) return false;
-    if (action.type.startsWith("cohort")) return false;
-    if (action.type == "app_refresh") {
-      if (action.subactions) {
-        return action.subactions.find((a) => a.type.startsWith("filter") || a.type.startsWith("cohort")) ? false : true;
-      }
-    }
-    return true;
-  }
-  destroy() {
-    if (this.dom?.holder) this.dom.holder.selectAll("*").remove();
-  }
-};
-var appInit = AppApi.getInitFxn(PlotApp);
-
-export {
-  appInit
-};
-//# sourceMappingURL=chunk-RVKADD4L.js.map

package/dist/chunk-RVKADD4L.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/plot.app.ts"],
-  "sourcesContent": ["import { AppApi, type RxApp, type ComponentApi } from '../rx'\nimport { AppBase } from '#plots/AppBase.ts'\nimport { storeInit } from '#mass/store'\nimport { vocabInit } from '#termdb/vocabulary'\nimport { recoverInit } from '../rx/src/recover'\nimport { sayerror, Menu } from '#dom'\nimport { importPlot } from '#plots/importPlot.js'\n\n/*\nthe purpose of this wrapper is to allow a mass plot to be used with control options outside of mass app\n\nTODO allow to hide controls. e.g. in the cuminc plot integrated into cox-snplocus, allowing to get rid of duplicating code of Cuminc class in cuminc.js\n\nFIXME convert to ts and fully type opts\n\nconstructor options (opts)\n\n\t.holder\n\t\td3-wrapped DOM container\n\n\t.vocabApi\n\t\trequired if state.vocab is not provided\n\n\t.violin{}\n\t\t.mode='minimal'??\n\n\t.app{}\n\t\t.features{}\n\t\t.getPlotHolder() ??\n\n\t.fetchOpts{}\n\t.state: {\n\t\t\n\t\t// required if opts.vocabApi is not provided\n\t\t.vocab: { \n\t\t\tgenome\n\t\t\tdslabel\n\t\t}\n\t\t\n\t\t// required\n\t\tplots[{}] options for rendering 1 or more plot(s), for example:\n\n\t\t[{\n\t\t\tchartType: 'summary',\n\t\t\tchildType: 'barchart',\n\t\t\tterm: {},\n\t\t\tterm2: {},\n\t\t\tsettings: {\n\t\t\t\tbarchart: {\n\t\t\t\t\tunit: 'pct'\n\t\t\t\t}\n\t\t\t}\n\t\t}]\n\t}\n*/\n\nclass PlotApp extends AppBase implements RxApp {\n\tstatic type = 'app'\n\n\t// expected RxApp, some are already declared/set in AppBase\n\tapi: AppApi\n\ttype: string\n\tparentId?: string\n\tdom!: {\n\t\t[index: string]: any\n\t}\n\tcomponents: {\n\t\t[name: string]: ComponentApi | { [name: string]: ComponentApi }\n\t} = {}\n\n\twasDestroyed = false\n\tstore: any\n\tbus!: any\n\n\tconstructor(opts, api) {\n\t\tsuper(opts)\n\t\tthis.api = api\n\t\tthis.type = PlotApp.type\n\t\tthis.dom = this.getDom(opts)\n\t}\n\n\tgetDom(opts) {\n\t\t// this will create divs in the correct stacking order\n\t\tconst dom: { [index: string]: any } = {\n\t\t\tholder: opts.holder,\n\t\t\terrdiv: opts.holder.append('div'),\n\t\t\tplotDiv: opts.holder.append('div')\n\t\t}\n\t\tconst controls = opts.violin?.mode == 'minimal' ? null : opts.holder.append('div').style('white-space', 'nowrap')\n\t\tif (controls) {\n\t\t\tdom.plotControls = controls.append('div').style('display', 'inline-block')\n\t\t\tdom.recoverControls = controls.append('div').style('display', 'inline-block')\n\t\t}\n\t\treturn dom\n\t}\n\n\tasync preApiFreeze(api) {\n\t\ttry {\n\t\t\tapi.tip = new Menu({ padding: '5px' })\n\t\t\tapi.printError = e => this.printError(e)\n\n\t\t\tconst vocab = this.opts.state.vocab\n\n\t\t\tapi.vocabApi = this.opts.vocabApi\n\t\t\t\t? this.opts.vocabApi\n\t\t\t\t: await vocabInit({\n\t\t\t\t\t\tapp: api,\n\t\t\t\t\t\tstate: {\n\t\t\t\t\t\t\tvocab: {\n\t\t\t\t\t\t\t\t// either (genome + dslabel) XOR (terms) can be undefined\n\t\t\t\t\t\t\t\tgenome: vocab?.genome || this.opts.state.genome,\n\t\t\t\t\t\t\t\tdslabel: vocab?.dslabel || this.opts.state.dslabel,\n\t\t\t\t\t\t\t\tterms: vocab?.terms\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t},\n\t\t\t\t\t\tfetchOpts: this.opts.fetchOpts\n\t\t\t\t  })\n\n\t\t\t// the vocabApi's vocab may be reprocessed from the original input\n\t\t\tthis.opts.state.vocab = api.vocabApi.vocab\n\t\t} catch (e) {\n\t\t\tconsole.log(`preApiFreeze error`, e)\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tasync init() {\n\t\t// catch initialization error\n\t\ttry {\n\t\t\t// this plot.app does not create a this.components.nav, unlike mass/app.js\n\t\t\t// so the nav is always hidden, can be hardcoded here\n\t\t\tthis.opts.state.nav = { header_mode: 'hidden' }\n\t\t\tthis.store = await storeInit({ app: this.api, state: this.opts.state })\n\t\t\tthis.state = await this.store.copyState()\n\t\t\tthis.components = {\n\t\t\t\tplots: {}\n\t\t\t}\n\t\t\tif (this.opts.app?.features?.includes('recover'))\n\t\t\t\tthis.components.recover = await recoverInit({\n\t\t\t\t\tapp: this.api,\n\t\t\t\t\tholder: this.dom.recoverControls,\n\t\t\t\t\t// TODO: ???? may limit the tracked state to only the filter, activeCohort ???\n\t\t\t\t\tgetState: appState => appState,\n\t\t\t\t\t//reactsTo: action => true, //action.type != 'plot_edit' || action.type == 'app_refresh',\n\t\t\t\t\tmaxHistoryLen: 10\n\t\t\t\t})\n\n\t\t\tif (this.opts.app?.doNotAwaitInitRender) {\n\t\t\t\t// do not await to return the instance sooner and allow calling appApi.triggerAbort() before initial render,\n\t\t\t\t// instead of waiting for initial data loading and rendering\n\t\t\t\tthis.api.dispatch()\n\t\t\t} else {\n\t\t\t\tawait this.api.dispatch()\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tthis.printError(e)\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.api.vocabApi.main()\n\n\t\tfor (const id in this.components.plots) {\n\t\t\tconst plot = this.components.plots[id]\n\t\t\tif (!this.state.plots.find(p => p.id === plot.id)) {\n\t\t\t\tplot.destroy()\n\t\t\t\tdelete this.components.plots[id]\n\t\t\t}\n\t\t}\n\n\t\tfor (const plot of this.state.plots.values()) {\n\t\t\t/** plots with parentId means the parent plot will trigger the plot instead of being triggered here\n\t\t\t * (e.g. subplots with SC app). Mimics the same behavior in client/mass/app.ts main() */\n\t\t\tif (plot.parentId) continue\n\t\t\tif (!this.components.plots[plot.id]) {\n\t\t\t\tconst holder = this.opts?.app?.getPlotHolder\n\t\t\t\t\t? this.opts.app.getPlotHolder(plot, this.dom.holder)\n\t\t\t\t\t: this.dom.holder.append('div')\n\n\t\t\t\t// quick fix to only track the plotDiv for the first plot\n\t\t\t\t// TODO: reliably handle the case where a plotApp instance may have multiple plots/holders\n\t\t\t\tif (!this.dom.plotDiv) this.dom.plotDiv = holder\n\t\t\t\tconst { componentInit } = await importPlot(plot.chartType)\n\t\t\t\tconst plotApi = await componentInit({\n\t\t\t\t\tid: plot.id,\n\t\t\t\t\tapp: this.api,\n\t\t\t\t\tholder,\n\t\t\t\t\tcontrols: this.dom.plotControls\n\t\t\t\t})\n\t\t\t\tthis.components.plots[plot.id] = plotApi\n\t\t\t}\n\t\t}\n\t}\n\n\tprintError(e) {\n\t\tsayerror(this.dom.errdiv, 'Error: ' + (e.message || e))\n\t\tif (e.stack) console.log(e.stack)\n\t\tthis.bus.emit('error')\n\t}\n\n\tskipPrevActionAbort(action) {\n\t\t// may skip aborting previously dispatched actions in AppApi.dispatch()\n\t\t// if the new dispatched action doesn't affect all components; this will\n\t\t// allow plots and control menus to continue rendering while creating,\n\t\t// editing, or deleting another plot\n\t\tif (!action) return false\n\t\tif (action.type.startsWith('filter')) return false\n\t\tif (action.type.startsWith('cohort')) return false\n\t\tif (action.type == 'app_refresh') {\n\t\t\tif (action.subactions) {\n\t\t\t\treturn action.subactions.find(a => a.type.startsWith('filter') || a.type.startsWith('cohort')) ? false : true\n\t\t\t}\n\t\t}\n\t\treturn true\n\t}\n\n\tdestroy() {\n\t\tif (this.dom?.holder) this.dom.holder.selectAll('*').remove()\n\t}\n}\n\nexport const appInit = AppApi.getInitFxn(PlotApp)\n"],
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package/dist/chunk-RZGEKL77.js

@@ -1,117 +0,0 @@
-import {
-  copyMerge,
-  getInitFxn
-} from "./chunk-M3J4MINX.js";
-
-// termdb/termInfo.js
-var defaultState = { isVisible: false, term: null };
-var TdbTermInfo = class {
-  /*
-  		Will display background information about a term, 
-  		such as rubric, publication source, description, etc
-  
-  		opts{}
-  			.content_holder: required d3-wrapped DOM element
-  				****TODO: Create menu on the fly if content_holder is not supplied****
-  			
-  			.icon_holder: optional, creates information icon for terms
-  			
-  			.vocabApi: 
-  				- for termInfoInit(), required as opts.vocabApi
-  				- for termInfoComp(), required as part of opts.app
-  				- a vocabulary API that has a getTermInfo() method
-  			
-  			.state{} optional, see defaultState value above
-  				.isVisible: boolean, optional
-  				.term: {id, ...} optional (may be supplied with either getState() or main({state}))
-  	*/
-  constructor(opts) {
-    this.vocabApi = opts.vocabApi || opts.app && opts.app.vocabApi;
-    this.state = Object.assign({}, defaultState, opts.state ? opts.state : {});
-    this.api = this;
-    setInteractivity(this);
-    setRenderers(this);
-    this.initUI(opts);
-  }
-  /*
-  	state: replace 1 or more state values by attribute key
-  */
-  async main(state = {}) {
-    copyMerge(this.state, state);
-    this.dom.content_holder.style("display", this.state.isVisible ? "block" : "none");
-    this.dom.icon_holder.style("background-color", this.state.isVisible ? "darkgray" : "transparent").style("color", this.state.isVisible ? "white" : "#797a7a");
-    if (!this.state.isVisible) return;
-    const data = await this.vocabApi.getTermInfo(this.state.term.id);
-    this.render(data);
-  }
-};
-var termInfoInit = getInitFxn(TdbTermInfo);
-function setRenderers(self) {
-  self.initUI = function(opts) {
-    self.dom = {
-      content_holder: opts.content_holder.style("margin-left", "25px").attr("class", "term_info_div").style("display", self.state.isVisible ? "block" : "none").style("white-space", "normal").style("padding-bottom", "20px"),
-      //Term information/description
-      details: opts.content_holder.append("div"),
-      tbody: opts.content_holder.append("table").append("tbody"),
-      //Information icon button div. Term description appears in content_holder
-      icon_holder: opts.icon_holder.style("margin", "1px 0px 1px 5px").style("padding", "2px 5px").style("font-family", "Times New Roman").style("font-size", "14px").style("font-weight", "bold").style("cursor", "pointer").style("background-color", "transparent").style("color", "#797a7a").style("align-items", "center").style("justify-content", "center").style("border", "none").style("border-radius", "3px").attr("aria-label", "Term Information").html("ⓘ").on("mouseenter", () => {
-        if (self.state.isVisible == true) return;
-        self.dom.icon_holder.style("color", "blue");
-      }).on("mouseleave", () => {
-        if (self.state.isVisible == true) return;
-        self.dom.icon_holder.style("color", "#797a7a");
-      }).on("click", self.toggleDescription)
-    };
-  };
-  self.render = function(data) {
-    if (!data?.terminfo) {
-      self.dom.details.append("div").style("margin-top", "10px").text("No definition found.");
-      return;
-    }
-    self.dom.tbody.selectAll("*").remove();
-    if (data.terminfo.src) {
-      for (let s of data.terminfo.src) {
-        const source_td = self.dom.tbody.append("tr").append("td").style("padding", "5px 0");
-        source_td.append("div").style("font-weight", "bold").text("Source");
-        source_td.append("div").style("margin-left", "20px").text(s.pub);
-        source_td.append("div").style("margin-left", "20px").html(s.title + ":&nbsp;<i>" + s.section + "</i>");
-      }
-    }
-    if (data.terminfo.rubric) {
-      const grade_td = self.dom.tbody.append("tr").append("td").style("padding", "5px 0").append("div").style("font-weight", "bold").text("Grading Rubric").append("ol").style("margin", "0px");
-      for (let grade of data.terminfo.rubric) {
-        grade_td.append("li").style("font-weight", "normal").text(grade);
-      }
-    }
-    self.dom.details.selectAll("*").remove();
-    if (data.terminfo.description) {
-      const header = self.dom.details.append("div").style("padding-top", "20px").style("padding-bottom", "10px").style("font-weight", "bold").text("Description");
-      for (const d of data.terminfo.description) {
-        self.renderDetail(d, self.dom.details.append("div").style("padding-bottom", "3px"));
-      }
-    }
-  };
-  self.renderDetail = function(d, div) {
-    if (Array.isArray(d.value)) {
-      div.append("span").html("<i>" + d.label + "</i>");
-      const section = div.append("div").style("padding-left", "20px");
-      for (const v of d.value) {
-        v.label = "- " + v.label;
-        self.renderDetail(v, section.append("div"));
-      }
-    } else {
-      div.html("<i>" + d.label + ":</i>&nbsp;" + d.value);
-    }
-  };
-}
-function setInteractivity(self) {
-  self.toggleDescription = function() {
-    self.state.isVisible = !self.state.isVisible;
-    self.main({ isVisible: self.state.isVisible });
-  };
-}
-
-export {
-  termInfoInit
-};
-//# sourceMappingURL=chunk-RZGEKL77.js.map