@sjcrh/proteinpaint-client 2.183.0 → 2.183.1

package/dist/chunk-S7T7OZC7.js

@@ -1,158 +0,0 @@
-import {
-  NumericDensity
-} from "./chunk-5HCB4HNL.js";
-import {
-  Tabs
-} from "./chunk-OXJ2TWDO.js";
-import {
-  HandlerBase
-} from "./chunk-LSEFWW72.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;
-    return this.tw.getStatus(this.termsetting.usecase, this.termsetting.data);
-  }
-  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-G75O4YZE.js");
-          this.handlerByMode.continuous = new NumContEditor(this.opts, this);
-          break;
-        }
-        case "discrete": {
-          const { NumDiscreteEditor } = await import("./NumDiscreteEditor-5K3OKUOE.js");
-          this.handlerByMode.discrete = new NumDiscreteEditor(this.opts, this);
-          break;
-        }
-        case "binary": {
-          const { NumBinaryEditor } = await import("./NumBinaryEditor-SDQFJ3FW.js");
-          this.handlerByMode.binary = new NumBinaryEditor(this.opts, this);
-          break;
-        }
-        case "spline": {
-          const { NumSplineEditor } = await import("./NumSplineEditor-KE4UPODZ.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");
-      this.renderButtons(this.dom.btnDiv);
-      if (this.tabs.length > 1) {
-        this.dom.topBar = this.dom.editDiv.append("div").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").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").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-S7T7OZC7.js.map

package/dist/chunk-SEQLC4AD.js

@@ -1,177 +0,0 @@
-import {
-  decimalPlacesUntilFirstNonZero
-} from "./chunk-L4QG7XZE.js";
-import {
-  basis_default,
-  line_default
-} from "./chunk-IH7ILDJS.js";
-import {
-  axisTop
-} from "./chunk-LOZEKOES.js";
-import {
-  linear
-} from "./chunk-OAWQ6LOO.js";
-import {
-  brushX
-} from "./chunk-SEEYV6P2.js";
-import {
-  rgb
-} from "./chunk-OMR2DT66.js";
-
-// dom/numericRangeInput.ts
-var NumericRangeInput = class {
-  constructor(holder, range, callback, opts) {
-    this.input = holder.append("input").attr("name", "rangeInput").attr("aria-label", "Leave blank for the allowed minimum value").style("width", opts?.width || "250px").style("margin", "3px 5px").on("change", () => {
-      try {
-        this.parseRange();
-      } catch (ex) {
-        alert(ex);
-        this.setRange();
-      }
-    });
-    this.setRange(range);
-    this.callback = callback;
-  }
-  getInput() {
-    return this.input;
-  }
-  parseRange() {
-    const str = this.input.node().value;
-    const new_range = parseRange(str);
-    if (this.range?.min != void 0) {
-      if (!new_range.startunbounded && this.range?.min > new_range.start) throw "Invalid start value < minimum allowed";
-      if (!new_range.stopunbounded && this.range?.min >= new_range.stop) throw "Invalid stop value >= minimum allowed";
-    }
-    if (this.range?.max != void 0) {
-      if (!new_range.stopunbounded && this.range?.max < new_range.stop) throw "Invalid stop value > maximum allowed";
-      if (!new_range.startunbounded && new_range.start >= this.range?.max)
-        throw "Invalid start value >= maximum allowed";
-    }
-    this.range = new_range;
-    this.callback(new_range);
-    return new_range;
-  }
-  getRange() {
-    return this.range;
-  }
-  setRange(range) {
-    if (!range) range = this.range;
-    else this.range = range;
-    if (!range) return;
-    const start = range.start != void 0 ? `${range.start} <=` : "";
-    const stop = range.stop != void 0 ? `<= ${range.stop}` : "";
-    this.input.node().value = range.value != void 0 ? ` x=${range.value} ` : `${start} x ${stop}`;
-  }
-};
-function parseRange(str) {
-  if (!str) throw "Empty range";
-  const tokens = str.replace(/\s/g, "").split("x");
-  let start, stop, startinclusive, stopinclusive, value;
-  if (tokens[0]) parseRangeToken(tokens[0]);
-  if (tokens[1]) parseRangeToken(tokens[1]);
-  if (value != void 0) return { value, label: `x = ${value}` };
-  const startunbounded = start === void 0;
-  const stopunbounded = stop === void 0;
-  if (!startunbounded && !stopunbounded && start > stop) throw "start must be lower than stop";
-  return { start, stop, value, startinclusive, stopinclusive, startunbounded, stopunbounded };
-  function parseRangeToken(rangeToken) {
-    const floatExpr = "[+-]?\\d+(\\.\\d+)?";
-    if (new RegExp(`^${floatExpr}<$`).test(rangeToken) || new RegExp(`^>${floatExpr}$`).test(rangeToken)) {
-      start = parseFloat(rangeToken.match(floatExpr));
-      startinclusive = false;
-    } else if (new RegExp(`^${floatExpr}<=$`).test(rangeToken) || new RegExp(`^>=${floatExpr}$`).test(rangeToken)) {
-      start = parseFloat(rangeToken.match(floatExpr));
-      startinclusive = true;
-    } else if (new RegExp(`^${floatExpr}>$`).test(rangeToken) || new RegExp(`^<${floatExpr}$`).test(rangeToken)) {
-      stop = parseFloat(rangeToken.match(floatExpr));
-      stopinclusive = false;
-    } else if (new RegExp(`^${floatExpr}>=$`).test(rangeToken) || new RegExp(`^<=${floatExpr}$`).test(rangeToken)) {
-      stop = parseFloat(rangeToken.match(floatExpr));
-      stopinclusive = true;
-    } else if (new RegExp(`^${floatExpr}=$`).test(rangeToken) || new RegExp(`^=${floatExpr}$`).test(rangeToken)) {
-      value = parseFloat(rangeToken.match(floatExpr));
-      stopinclusive = true;
-      startinclusive = true;
-    } else throw `Could not parse expression '${rangeToken}'`;
-  }
-}
-
-// dom/violinRenderer.js
-var violinRenderer = class {
-  constructor({
-    holder,
-    rd,
-    radius = 10,
-    width = 500,
-    height = 100,
-    shiftx = 20,
-    shifty = 20,
-    callback = null,
-    scaleFactor = 1
-  }) {
-    this.holder = holder;
-    this.rd = rd;
-    this.vd = rd.charts?.[""]?.plots?.[0];
-    if (!this.vd) throw "No density plot data to render.";
-    this.width = width;
-    this.height = height;
-    this.radius = radius;
-    this.callback = callback;
-    this.shiftx = shiftx;
-    this.shifty = shifty;
-    this.svg = holder.append("svg").attr("width", `${width + 50}px`).attr("height", `${height + 50}px`);
-    this.axisScale = linear().domain([rd.min, rd.max]).range([0, width]);
-    this.axisScaleUI = linear().domain([rd.min * scaleFactor, rd.max * scaleFactor]).range([0, width]);
-    this.wScale = linear().domain([this.vd.density.densityMax, this.vd.density.densityMin]).range([height * 0.45, 0]);
-  }
-  render() {
-    this.svg.selectAll("*").remove();
-    this.violinG = this.svg.append("g").attr("transform", `translate(${this.shiftx}, ${this.height / 2 + this.shifty})`);
-    this.brushG = this.svg.append("g").attr("transform", `translate(${this.shiftx}, ${this.shifty})`);
-    this.scaleG = this.svg.append("g").attr("transform", `translate(${this.shiftx}, ${this.shifty})`);
-    this.scaleG.call(axisTop(this.axisScaleUI).tickValues(this.axisScaleUI.ticks()));
-    this.renderArea(false);
-    this.renderArea(true);
-    if (this.vd.src) {
-      this.violinG.append("image").classed("sjpp-beans-img", true).attr("xlink:href", this.vd.src).attr("transform", `translate(0, -${this.radius / 2})`).attr("width", this.width);
-    }
-    if (this.callback)
-      this.svg.append("g").call(
-        brushX().extent([
-          [this.shiftx, this.shifty],
-          [this.width + this.shiftx, this.height + this.shifty]
-        ]).on("end", async (event) => {
-          const selection = event.selection;
-          if (!selection) return;
-          const range_start = this.axisScale.invert(selection[0] - this.shiftx);
-          const range_end = this.axisScale.invert(selection[1] - this.shiftx);
-          this.callback({ range_start, range_end });
-        })
-      );
-  }
-  renderArea(invert) {
-    if (this.vd.densityMax == 0) return;
-    const areaBuilder = line_default().curve(basis_default).x((d) => this.axisScale(d.x0)).y((d) => invert ? -this.wScale(d.density) : this.wScale(d.density));
-    const color = this.vd.color || "#dddddd";
-    this.violinG.append("path").style("fill", color).style("opacity", 0).attr("stroke", rgb(color).darker()).attr("stroke-width", 1).attr("stroke-linejoin", "round").style("opacity", "0.8").attr("d", areaBuilder(this.vd.density.bins));
-  }
-};
-
-// dom/niceNumLabels.ts
-function niceNumLabels(nums) {
-  const sorted = nums.sort((a, b) => a - b);
-  const abs = Math.abs(sorted[0] - sorted[sorted.length - 1]);
-  const zeroDecimalNum = decimalPlacesUntilFirstNonZero(abs);
-  const decimals2Show = abs >= 10 ? 0 : abs >= 1 ? 1 : zeroDecimalNum + 2;
-  return nums.map((num) => {
-    if (Math.abs(num) < 1 && decimals2Show == 0) return Number(num.toPrecision(1));
-    return Number(num.toFixed(decimals2Show));
-  });
-}
-
-export {
-  NumericRangeInput,
-  violinRenderer,
-  niceNumLabels
-};
-//# sourceMappingURL=chunk-SEQLC4AD.js.map

package/dist/chunk-TEZLFSOV.js

@@ -1,54 +0,0 @@
-import {
-  addGeneSearchbox
-} from "./chunk-OXJ2TWDO.js";
-import {
-  Menu
-} from "./chunk-A6TQGNDQ.js";
-
-// termdb/handlers/snp.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: opts.holder,
-      searchOnly: "snp",
-      allowVariant: true,
-      callback: () => this.selectSnp(geneSearch)
-    });
-  }
-  async selectSnp(geneSearch) {
-    const { chr, ref, alt, fromWhat } = geneSearch;
-    if (!chr || !ref || !alt || !fromWhat) throw "missing chr, ref, alt, or fromWhat of snp";
-    let start, stop;
-    if (!geneSearch.start && !geneSearch.stop) {
-      if (geneSearch.pos) {
-        start = geneSearch.pos - 1;
-        stop = geneSearch.pos;
-      } else {
-        throw "missing coordinate of snp";
-      }
-    } else {
-      start = geneSearch.start;
-      stop = geneSearch.stop;
-    }
-    const term = {
-      id: fromWhat,
-      chr,
-      start,
-      stop,
-      name: fromWhat,
-      ref,
-      alt: typeof alt == "string" ? [alt] : alt,
-      // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays
-      type: "snp"
-    };
-    this.callback(term);
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-TEZLFSOV.js.map

package/dist/chunk-TFI7ZZJG.js

@@ -1,50 +0,0 @@
-import {
-  addGeneSearchbox,
-  getSCGEunit
-} from "./chunk-OXJ2TWDO.js";
-import {
-  Menu
-} from "./chunk-A6TQGNDQ.js";
-import {
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-6ITDJ5UR.js";
-
-// termdb/handlers/singleCellGeneExpression.ts
-var SearchHandler = class {
-  init(opts) {
-    this.validateOpts(opts);
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => this.selectGene(geneSearch.geneSymbol, opts.usecase?.specialCase?.config?.sample)
-    });
-  }
-  /**TODO: scge tw handler will validate that a sample is included. Need to resolve issue
-   * with sample info not included.*/
-  async selectGene(gene, sample) {
-    if (!gene) throw new Error("No gene selected");
-    const unit = getSCGEunit(this.app.vocabApi);
-    const name = `${gene} ${unit}`;
-    this.callback({ gene, name, type: SINGLECELL_GENE_EXPRESSION, sample });
-  }
-  validateOpts(opts) {
-    if (opts.callback == null) throw new Error("callback is required");
-    if (opts.app == null) throw new Error("app is required");
-    if (opts.holder == null) throw new Error("holder is required");
-    if (opts.genomeObj == null) throw new Error("genomeObj is required");
-    if (opts.usecase == null) throw new Error("usecase is required");
-    if (!opts.usecase?.specialCase?.config?.sample) {
-      throw new Error("usecase.specialCase.config.sample is required for singleCellGeneExpression handler");
-    }
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-TFI7ZZJG.js.map

package/dist/chunk-TV74I3Y5.js

@@ -1,43 +0,0 @@
-// ../shared/utils/src/helpers.js
-function isNumeric(n) {
-  const v = typeof n != "string" || n === "" ? n : Number(n);
-  const f = parseFloat(n);
-  return !isNaN(f) && Number.isFinite(v) && v === f;
-}
-function isStrictNumeric(n) {
-  return typeof n === "number" && Number.isFinite(n);
-}
-function convertUnits(v, fromUnit, toUnit, scaleFactor, compact) {
-  if (scaleFactor >= 1) {
-    const toUnitV2 = Math.floor(v * scaleFactor);
-    if (compact) return `${toUnitV2}${toUnit.charAt(0)}`;
-    return `${toUnitV2} ${toUnitV2 > 1 ? toUnit + "s" : ""}`;
-  }
-  const toUnitV = Math.floor(v * scaleFactor);
-  const fromUnitV = Math.ceil(v % (1 / scaleFactor));
-  if (fromUnitV == 0) {
-    if (compact) return `${toUnitV}${toUnit.charAt(0)}`;
-    return `${toUnitV} ${toUnitV > 1 ? toUnit + "s" : ""}`;
-  }
-  if (compact)
-    return `${toUnitV}${toUnit.charAt(0)}${fromUnitV}${fromUnit.charAt(0)}`;
-  return `${toUnitV} ${toUnitV > 1 ? toUnit + "s" : toUnit} ${fromUnitV} ${fromUnitV > 1 ? fromUnit + "s" : fromUnit}`;
-}
-var CustomError = class extends Error {
-  level = "";
-  // '' | 'warn'
-  constructor(message, opts = {}) {
-    super(message);
-    if (opts.name) this.name = opts.name;
-    if (opts.code) this.code = opts.code;
-    if (opts.level) this.level = opts.level;
-  }
-};
-
-export {
-  isNumeric,
-  isStrictNumeric,
-  convertUnits,
-  CustomError
-};
-//# sourceMappingURL=chunk-TV74I3Y5.js.map

package/dist/chunk-TV74I3Y5.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/helpers.js"],
-  "sourcesContent": ["/*\nthis is a helper file with a collection of functions to be used in backend and client side code. Here is a list.\n\n1. isNumeric(n)\n2. strictNumeric(n) \n2. convertUnits\n3. TODO - move computepercentile, roundValue, etc here?\n*/\n\n// checks whether given argument n is Numeric, with option to cast from string\nexport function isNumeric(n) {\n\tconst v = typeof n != \"string\" || n === \"\" ? n : Number(n)\n\tconst f = parseFloat(n)\n\treturn !isNaN(f) && Number.isFinite(v) && v === f\n}\n\n// like isNumeric but does not cast from string\nexport function isStrictNumeric(n) {\n\treturn typeof n === \"number\" && Number.isFinite(n)\n}\n\n// converts a value from a unit to another unit\nexport function convertUnits(v, fromUnit, toUnit, scaleFactor, compact) {\n\t// do floor() on toUnit\n\t// do ceil() on fromUnit, in case v is decimal (from violin range selection) and to keep showing integer fromUnit\n\tif (scaleFactor >= 1) {\n\t\tconst toUnitV = Math.floor(v * scaleFactor)\n\t\tif (compact) return `${toUnitV}${toUnit.charAt(0)}`\n\t\treturn `${toUnitV} ${toUnitV > 1 ? toUnit + \"s\" : \"\"}`\n\t}\n\tconst toUnitV = Math.floor(v * scaleFactor)\n\tconst fromUnitV = Math.ceil(v % (1 / scaleFactor))\n\n\tif (fromUnitV == 0) {\n\t\tif (compact) return `${toUnitV}${toUnit.charAt(0)}`\n\t\treturn `${toUnitV} ${toUnitV > 1 ? toUnit + \"s\" : \"\"}`\n\t}\n\n\tif (compact)\n\t\treturn `${toUnitV}${toUnit.charAt(0)}${fromUnitV}${fromUnit.charAt(0)}`\n\treturn `${toUnitV} ${toUnitV > 1 ? toUnit + \"s\" : toUnit} ${fromUnitV} ${\n\t\tfromUnitV > 1 ? fromUnit + \"s\" : fromUnit\n\t}`\n}\n\nexport function deepEqual(x, y) {\n\tif (x === y) {\n\t\treturn true\n\t} else if (\n\t\ttypeof x == \"object\" &&\n\t\tx != null &&\n\t\ttypeof y == \"object\" &&\n\t\ty != null\n\t) {\n\t\tif (Object.keys(x).length != Object.keys(y).length) {\n\t\t\treturn false\n\t\t}\n\n\t\tfor (var prop in x) {\n\t\t\tif (y.hasOwnProperty(prop)) {\n\t\t\t\tif (!deepEqual(x[prop], y[prop])) return false\n\t\t\t} else {\n\t\t\t\treturn false\n\t\t\t}\n\t\t}\n\t\treturn true\n\t} else return false\n}\n\nexport function deepFreeze(obj) {\n\tObject.freeze(obj)\n\t// not using for..in loop, in order to not descend into inherited props/methods\n\tfor (const value of Object.values(obj)) {\n\t\tif (value !== null && typeof value == \"object\") deepFreeze(value)\n\t}\n\treturn obj\n}\n\nexport class CustomError extends Error {\n\tlevel = \"\" // '' | 'warn'\n\n\tconstructor(message, opts = {}) {\n\t\tsuper(message)\n\t\tif (opts.name) this.name = opts.name\n\t\tif (opts.code) this.code = opts.code\n\t\tif (opts.level) this.level = opts.level\n\t}\n}\n"],
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