@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/chunk-ECIBJXFT.js

@@ -1,352 +0,0 @@
-import {
-  StoreBase,
-  getAppInit,
-  getStoreInit
-} from "./chunk-M3J4MINX.js";
-
-// test/Locator.ts
-var Locator = class _Locator {
-  // arg could be one of the following, must always
-  // - DOM element
-  // - string selector
-  // - d3-selection
-  constructor(arg, opts = {}) {
-    //HTMLElement | SVGElement | SVGGElement | SVGLineElement | SVGRectElement | SVGSVGElement | SVGTextElement
-    this.opts = {
-      intervalWait: 25,
-      maxWait: 3e3
-    };
-    this.pending = [];
-    this.result = [];
-    Object.assign(this.opts, opts);
-    this.setRoot(arg);
-  }
-  // convenience method to allow await Locator.init(elem).whenVisible('')
-  static init(elem) {
-    return new _Locator(elem);
-  }
-  setRoot(arg) {
-    if (typeof arg == "string") {
-      const node = document.body.querySelector(arg);
-      if (!node) throw `missing elem by selector='${arg}'`;
-      this.rootElem = node;
-    } else if (typeof arg.node == "function") {
-      const numMatch = arg.size();
-      if (!numMatch) throw `missing elem from d3-selection`;
-      this.rootElem = arg.node();
-    } else {
-      this.rootElem = arg;
-    }
-    this.pending = [];
-  }
-  root(arg) {
-    if (arg) this.setRoot(arg);
-    return this.rootElem;
-  }
-  // selector: string selector such as '#my-id', '.my-class', `[data-testid='my-id-here']`, `[role='button']`, etc
-  shows(selector, opts = {}) {
-    this.pending.push([
-      shows,
-      {
-        selector,
-        targetCount: opts.count || 1,
-        //'>=1',
-        visibility: opts.visibility ?? true,
-        intervalWait: opts.intervalWait || this.opts.intervalWait,
-        maxWait: opts.maxWait || this.opts.maxWait,
-        attr: opts.attr || {}
-      }
-    ]);
-    return this;
-  }
-  // same argument as this.shows(), but visibility is not checked
-  // and assumes that the elements targeted by the selector are
-  // ready to be queried
-  find(selector) {
-    this.pending.push([find, { selector }]);
-    return this;
-  }
-  // cannot chain another method after get(), since
-  // the retured promise would require wrapping in parentheses
-  //
-  // get()
-  // - run the pending functions in sequence and return the resolved
-  //   queried elems or its properties based on the argument
-  //
-  // Arguments:
-  //  arg: undefined | string | number | callback
-  //
-  // returns
-  //  - no argument: get the matched elements as an array
-  //  - callback function: passes the matched elements to the callback and returns its returned value
-  //  - number: use as index key to return elems[index]
-  //  - string: see the processing in the
-  async get(arg) {
-    const pending = this.pending;
-    this.pending = [];
-    let elems = [this.rootElem];
-    for (const [fxn, opts] of pending) {
-      elems = await fxn(elems, opts);
-    }
-    if (!arguments.length || arg === void 0) return elems;
-    if (typeof arg === "function") return arg(elems);
-    if (typeof arg === "number") return elems[arg];
-    if (typeof arg === "string") {
-      if (arg == "length") return elems.length;
-      const key = arg.slice(1);
-      if (!key) return elems;
-      const char = arg[0];
-      if (char === ".") return elems.map((elem) => elem[key]);
-      if (char === "@") return elems.map((elem) => elem.getAttribute(key));
-      if (char === ":") return elems.map((elem) => elem.style[key]);
-    }
-    throw `invalid Locator.get() argument='${arg}'`;
-  }
-  // propName: string property name, can be dot-separated like 'style.padding'
-  // value: string, number, boolean, any valid value for the given property name
-  async set(propName, value2) {
-    if (!propName) throw `invalid Locator.set() propName='${propName}'`;
-    const keyChain = propName.split(".");
-    const lastKey = keyChain.pop();
-    if (!lastKey) throw `invalid Locator.set() propName='${propName}'`;
-    const elems = await this.get();
-    for (const elem of elems) {
-      let obj = elem;
-      for (const key of keyChain) obj = obj[key];
-      obj[lastKey] = value2;
-    }
-    return elems;
-  }
-  /*** convenient aliased methods for .get(arg) ***/
-  async length() {
-    return await this.get("length");
-  }
-  async value(val) {
-    if (arguments.length) return await this.set("value", val);
-    return await this.get(".value");
-  }
-  async text(str) {
-    if (arguments.length) return await this.set("innerText", str);
-    return await this.get(".innerText");
-  }
-  hides(selector) {
-    return this.shows(selector, { visibility: false });
-  }
-  async click(arg) {
-    const elems = await this.get(arg);
-    const arr = Array.isArray(elems) ? elems : [elems];
-    for (const elem of arr) {
-      const box = elem.getBoundingClientRect();
-      const clientX = box.x + 0.5 * box.width;
-      const clientY = box.y + box.height;
-      elem.dispatchEvent(new MouseEvent("click", { bubbles: true, clientX, clientY }));
-    }
-    return elems;
-  }
-};
-async function shows(elems, opts) {
-  return new Promise((resolve) => {
-    const { selector, targetCount, intervalWait, maxWait, visibility, attr } = opts;
-    const matchedElems = /* @__PURE__ */ new Set();
-    let elapsed = 0, pending = false;
-    const i = setInterval(() => {
-      if (pending) return;
-      pending = true;
-      for (const elem of elems) {
-        for (const descendant of elem.querySelectorAll(selector)) {
-          if (matchedElems.has(descendant)) continue;
-          if (descendant.checkVisibility() === visibility) {
-            if (!attr) matchedElems.add(descendant);
-            else {
-              const kvEntries = Object.entries(attr);
-              const matchedKeys = [];
-              for (const [key, value2] of kvEntries) {
-                if (elem.getAttribute(key) !== value2) matchedKeys.push(key);
-              }
-              if (matchedKeys.length === kvEntries.length) matchedElems.add(descendant);
-            }
-          }
-        }
-      }
-      elapsed += intervalWait;
-      if (matchedElems.size >= targetCount || elapsed > maxWait) {
-        clearInterval(i);
-        resolve([...matchedElems]);
-      }
-      pending = false;
-    }, intervalWait);
-  });
-}
-async function find(elems, opts) {
-  for (const elem of elems) {
-    const match = elem.querySelector(opts.selector);
-    if (match) {
-      return [match];
-    }
-  }
-  return [];
-}
-
-// test/test.helpers.js
-function sleep(ms) {
-  return new Promise((resolve) => setTimeout(resolve, ms));
-}
-async function detectLst(_opts = {}) {
-  const defaults = {
-    target: _opts.target || _opts.elem,
-    selector: _opts.selector,
-    maxTime: 12e3,
-    // default is increased from 5 to 12 specifically for gdc live tests with high latency
-    observe: {
-      childList: true,
-      subtree: true,
-      attributes: true,
-      characterData: true
-    }
-  };
-  if (!_opts.matcher) {
-    defaults.count = 1;
-    defaults.matchAs = "=";
-  }
-  const opts = Object.assign(defaults, _opts);
-  if (!opts.target) throw `missing opts.target (alias for opts.elem)`;
-  if (!opts.trigger && opts.count > 0) await sleep(0);
-  const start = Date.now();
-  return new Promise((resolve, reject) => {
-    if (!opts.matcher && opts.selector) {
-      const elems = opts.target.querySelectorAll(opts.selector);
-      const matched = matchedCount(elems.length, opts);
-      if (matched) {
-        resolve([...elems]);
-        return;
-      }
-    }
-    const callback = (mutations) => {
-      const elems = opts.selector ? [...opts.target.querySelectorAll(opts.selector)] : [opts.target];
-      const mutated = mutations.filter((m) => elems.includes(m.target));
-      if (!mutated.length && opts.count !== 0) return;
-      const matched = opts.matcher ? opts.matcher(mutated, observer) : matchedCount(elems.length, opts);
-      const expired = Date.now() - start > opts.maxTime;
-      if (matched || expired) {
-        observer.disconnect();
-        if (t) clearTimeout(t);
-        if (matched) resolve(Array.isArray(matched) ? matched : elems);
-        else reject(`test exceeded maxTime=${opts.maxTime}`);
-      }
-    };
-    const observer = new MutationObserver(callback);
-    observer.observe(opts.target, opts.observe);
-    let t;
-    if (opts.maxTime) {
-      t = setTimeout(() => {
-        if (opts.count === 0) {
-        } else reject(`the elem '${opts.target}' did not render within ${opts.maxTime} milliseconds`);
-      }, opts.maxTime);
-    }
-    if (opts.trigger) opts.trigger();
-  });
-}
-function matchedCount(actual, opts) {
-  const expected = opts.count;
-  switch (opts.matchAs) {
-    case "=":
-      return actual === expected;
-    case "<":
-      return actual < expected;
-    case "<=":
-      return actual <= expected;
-    case ">":
-      return actual > expected;
-    case ">=":
-      return actual >= expected;
-    default:
-      throw `unknown matchAs='${opts.matchAs}'`;
-  }
-}
-async function detectStyle(opts) {
-  if (!opts.observe) opts.observe = {};
-  opts.observe.attributes = true;
-  opts.observe.attributeFilter = ["style"];
-  const lst = await detectLst(opts);
-  return lst;
-}
-async function detectGt(opts) {
-  opts.matchAs = ">";
-  const lst = await detectLst(opts);
-  return lst;
-}
-async function detectGte(opts) {
-  opts.matchAs = ">=";
-  const lst = await detectLst(opts);
-  return lst;
-}
-async function detectOne(opts) {
-  opts.count = 1;
-  const lst = await detectLst(opts);
-  return lst[0];
-}
-async function whenVisible(elem, opts = {}) {
-  const intervalWait = 25;
-  const totalWait = opts.wait || 5e3;
-  const numRepeats = totalWait / intervalWait;
-  return new Promise((resolve, reject) => {
-    let j = 0;
-    const i = setInterval(() => {
-      if (elem.style.display != "none") {
-        clearInterval(i);
-        resolve(elem);
-      } else {
-        j++;
-        if (j > numRepeats) {
-          reject(`elem did not become visible within 5 seconds`);
-          clearInterval(i);
-        }
-      }
-    }, intervalWait);
-  });
-}
-var TestAppStore = class _TestAppStore extends StoreBase {
-  static type = "store";
-  constructor(opts) {
-    super(opts);
-    this.type = _TestAppStore.type;
-    this.defaultState = {
-      debug: true
-    };
-  }
-  async init() {
-  }
-};
-var storeInit = getStoreInit(TestAppStore);
-var TestApp = class {
-  static type = "app";
-  constructor(opts) {
-    this.type = "app";
-    this.opts = opts;
-    this.fetchOpts = opts.fetchOpts;
-  }
-  async init() {
-    try {
-      this.store = await storeInit({ app: this.api, state: this.opts.state });
-      this.state = await this.store.copyState();
-      if (this.opts.dom) this.dom = this.opts.dom;
-      await this.api.dispatch();
-    } catch (e) {
-      if (e.stack) console.log(e.stack);
-      else throw `TestApp Error: ${e}`;
-    }
-  }
-};
-var testAppInit = getAppInit(TestApp);
-
-export {
-  Locator,
-  sleep,
-  detectLst,
-  detectStyle,
-  detectGt,
-  detectGte,
-  detectOne,
-  whenVisible
-};
-//# sourceMappingURL=chunk-ECIBJXFT.js.map

package/dist/chunk-EGPNRSPF.js

@@ -1,292 +0,0 @@
-import {
-  getSortOptions
-} from "./chunk-R6NM2HSH.js";
-import {
-  defaultUiLabels,
-  fillTermWrapper
-} from "./chunk-TKW5TW4Z.js";
-import {
-  isDictionaryType
-} from "./chunk-7JRDJNLR.js";
-import {
-  copyMerge
-} from "./chunk-M3J4MINX.js";
-import {
-  CNVClasses,
-  dtcnv,
-  mclass,
-  mutationClasses,
-  proteinChangingMutations,
-  synonymousMutations,
-  truncatingMutations
-} from "./chunk-6PNPHACF.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
-        // 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-EGPNRSPF.js.map