@sjcrh/proteinpaint-client 2.200.0 → 2.201.0

package/dist/chunk-BQHPJY2M.js

@@ -1,347 +0,0 @@
-import {
-  storeInit
-} from "./chunk-4KRGCOTL.js";
-import {
-  summaryInit
-} from "./chunk-NUWJ4RN7.js";
-import {
-  navInit
-} from "./chunk-CY4RQ5L6.js";
-import {
-  AppBase,
-  downloadSVGsAsPdf,
-  filterRxCompInit,
-  newSandboxDiv,
-  sayerror,
-  vocabInit
-} from "./chunk-TKW5TW4Z.js";
-import {
-  importPlot
-} from "./chunk-3SHZTAGF.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  AppApi,
-  getCompInit,
-  multiInit
-} from "./chunk-M3J4MINX.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// mass/plot.js
-var MassPlot = class _MassPlot {
-  static type = "plot";
-  constructor(opts) {
-    this.type = _MassPlot.type;
-    setRenderers(this);
-    this.initUi(opts);
-  }
-  reactsTo(action) {
-    if (action.type.includes("cache_termq")) return true;
-    if (action.type.endsWith("_group")) return true;
-    if (action.type.startsWith("plot_")) {
-      return action.id === this.id || action.id == this.parentId || action.config?.parentId === this.id || action.parentId === this.id;
-    }
-    if (action.type.startsWith("filter")) return true;
-    if (action.type.startsWith("cohort")) return true;
-    if (action.type == "app_refresh") return true;
-    if (action.type.endsWith("customTerm")) return true;
-  }
-  // !!! NOTE: This getState() method is reused by the plot-specific recover component.
-  // When logging something within getState, it may have been called by either the plot or recover instance
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      termfilter: appState.termfilter,
-      config,
-      groups: appState.groups,
-      // quick fix to skip history tracking as needed
-      _scope_: appState._scope_
-    };
-  }
-  async main() {
-    this.dom.errdiv.style("display", "none").style("background-color", "rgba(255,100,100,0.2)").html("");
-    if (!this.components) await this.setComponents(this.opts);
-  }
-  async setComponents(opts) {
-    const _ = await importPlot(opts.chartType);
-    const promises = {
-      // recover: recoverInit({
-      // 	app: this.app,
-      // 	holder: this.dom.localRecoverDiv,
-      // 	getState: appState => this.getState(appState),
-      // 	reactsTo: action =>
-      // 		action.id == this.id &&
-      // 		(action.type == 'plot_edit' || action.type == 'plot_nestedEdits') &&
-      // 		action._track_ != 'none',
-      // 	plot_id: this.id,
-      // 	maxHistoryLen: 10,
-      // 	hideLabel: true
-      // }),
-      chart: _.componentInit({
-        app: this.app,
-        holder: this.dom.viz,
-        header: this.dom.paneTitleDiv,
-        id: this.id,
-        plotDiv: select_default(this.dom.holder.app_div.node().parentNode),
-        /******* reason for passing plotDiv to chart ********
-        				- this plot instance may allow to launch a new plot as a persistent sandbox
-        				  inside mass plotDiv, maintaining the uniform plot appearance despite it's ad-hoc
-        				  the new plot is not a formal mass plot type, and cannot be done via app.dispatch()
-        				  thus the need to directly access plotDiv
-        				- example: mds3 tk from genome browser can launch disco etc
-        				- having access to plotDiv may offer flexibility for the plot to do stuff
-        
-        				since plot.js has no access to mass app .dom.plotDiv in which all apps are shown,
-        				this workarounds gets the parent node of sandbox.app_div which is app.dom.plotDiv
-        				*/
-        getFilterImage: async () => this.components.filter.getFilterImage()
-      })
-    };
-    if (!this.state.config.hidePlotFilter) {
-      const filterDisabledMsg = this.app.vocabApi.termdbConfig?.plotFilter?.disabledMessage;
-      const filterHolder = filterDisabledMsg ? this.dom.filterDiv.append("div").style("pointer-events", "none").style("opacity", 0.5) : this.dom.filterDiv;
-      if (filterDisabledMsg) this.dom.filterDiv.attr("title", filterDisabledMsg).style("cursor", "not-allowed");
-      promises.filter = filterRxCompInit({
-        app: this.app,
-        vocabApi: this.app.vocabApi,
-        parentId: this.id,
-        holder: filterHolder,
-        hideLabel: true,
-        emptyLabel: "+Add new filter",
-        callback: (filter) => {
-          this.app.dispatch({
-            id: this.id,
-            type: "plot_edit",
-            config: { filter }
-          });
-        }
-      });
-    }
-    this.components = await multiInit(promises);
-  }
-  destroy() {
-    this.dom.holder.app_div.selectAll("*").remove();
-    this.dom.holder.app_div.remove();
-    for (const key in this.dom) {
-      delete this.dom[key];
-    }
-  }
-};
-var plotInit = getCompInit(MassPlot);
-function setRenderers(self) {
-  self.initUi = function(opts) {
-    const holder = opts.holder;
-    opts.holder.app_div.attr("data-testid", "sjpp-massplot-sandbox-" + opts.chartType);
-    holder.header.style("padding", 0);
-    try {
-      self.dom = {
-        tip: new Menu({ padding: "0px" }),
-        holder,
-        paneTitleDiv: holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px").style("vertical-align", "sub"),
-        localRecoverDiv: holder.header.append("div").style("display", "inline-block"),
-        filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9),
-        body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
-        // will hold no data notice or the page title in multichart views
-        errdiv: holder.body.append("div").style("display", "none").style("padding", "5px").style("background-color", "rgba(255,100,100,0.2)"),
-        // dom.viz will hold the rendered view
-        viz: holder.body.append("div")
-      };
-    } catch (e) {
-      self.dom.errdiv.style("display", "none").text(e);
-    }
-  };
-}
-
-// mass/app.ts
-var MassApp = class extends AppBase {
-  // expected class-specific props
-  constructor(opts, api) {
-    super(opts);
-    this.components = {};
-    this.wasDestroyed = false;
-    this.api = api;
-    if (opts.addLoginCallback) {
-      opts.addLoginCallback(() => this.api.dispatch({ type: "app_refresh" }));
-    }
-    this.type = "app";
-    this.dom = {
-      holder: opts.holder,
-      // do not modify holder style
-      topbar: opts.holder.append("div"),
-      errdiv: opts.holder.append("div"),
-      plotDiv: opts.holder.append("div")
-    };
-    if (opts.getPlotConfig_mutateSummary) {
-      if (typeof opts.getPlotConfig_mutateSummary != "function")
-        throw new Error("opts.getPlotConfig_mutateSummary is not function");
-    }
-    this.plotIdToSandboxId = {};
-  }
-  static {
-    this.type = "app";
-  }
-  async preApiFreeze(api) {
-    try {
-      api.tip = new Menu({ padding: "5px" });
-      api.tip.d.on("keyup", (event) => {
-        if (event.key == "Escape") api.tip.hide();
-      });
-      api.printError = (e) => this.printError(e);
-      api.vocabApi = await vocabInit({
-        app: api,
-        state: { vocab: this.opts.state.vocab },
-        fetchOpts: this.opts.fetchOpts,
-        getDatasetAccessToken: this.opts.getDatasetAccessToken
-      });
-      api.hasWebGL = function() {
-        try {
-          const canvas = document.createElement("canvas");
-          return !!(window.WebGLRenderingContext && (canvas.getContext("webgl") || canvas.getContext("experimental-webgl")));
-        } catch (_) {
-          return false;
-        }
-      };
-      this.opts.state.vocab = api.vocabApi.vocab;
-    } catch (e) {
-      console.log(`preApiFreeze error`, e);
-      throw e;
-    }
-  }
-  async init() {
-    try {
-      const debounceInterval = "debounceInterval" in this.opts ? this.opts.debounceInterval : 0;
-      const embeddedSessionState = this.opts.embeddedSessionState;
-      if (embeddedSessionState) {
-        Object.assign(this.opts.state, embeddedSessionState);
-      }
-      this.store = await storeInit({ app: this.api, state: this.opts.state, debounceInterval });
-      this.state = await this.store.copyState();
-      this.components = {};
-      if (this.state.nav.header_mode != "hidden") {
-        this.components.nav = await navInit({
-          app: this.api,
-          holder: this.dom.topbar,
-          header_mode: this.state && this.state.nav && this.state.nav.header_mode,
-          vocab: this.state.vocab,
-          massSessionDuration: this.state.termdbConfig.massSessionDuration,
-          // this.opts.massSessionDuration
-          pkgver: this.opts.pkgver,
-          downloadPlots: () => {
-            this.downloadPlots();
-          }
-        });
-      }
-      this.components.plots = {};
-      if (this.opts.app?.doNotAwaitInitRender) {
-        this.api.dispatch();
-      } else {
-        await this.api.dispatch();
-      }
-    } catch (e) {
-      this.printError(e);
-      throw e;
-    }
-  }
-  async main() {
-    await this.api.vocabApi.main();
-    this.dom.plotDiv?.style(
-      "display",
-      this.state.nav?.header_mode != "hidden" && this.state.nav?.activeTab == 0 ? "none" : "block"
-    );
-    const newPlots = {};
-    let sandbox;
-    for (const plot of this.state.plots) {
-      if (plot.parentId) continue;
-      if (this.components.plots && !(plot.id in this.components.plots)) {
-        sandbox = newSandboxDiv(this.dom.plotDiv, {
-          close: () => {
-            this.api.dispatch({
-              type: "plot_delete",
-              id: plot.id
-            });
-          },
-          plotId: plot.id,
-          beforePlotId: plot.insertBefore || null,
-          style: {
-            width: "98.5%"
-          }
-        });
-        if (plot.chartType == "summary")
-          newPlots[plot.id] = summaryInit(Object.assign({ app: this.api, holder: sandbox }, plot));
-        else newPlots[plot.id] = plotInit(Object.assign({ app: this.api, holder: sandbox }, plot));
-      }
-    }
-    const numNewPlots = Object.keys(newPlots).length;
-    if (numNewPlots) {
-      await Promise.all(Object.values(newPlots));
-      for (const plotId in newPlots) {
-        this.components.plots[plotId] = await newPlots[plotId];
-      }
-    }
-    for (const plotId in this.components.plots) {
-      if (!this.state.plots.find((p) => p.id === plotId)) {
-        this.components.plots[plotId].destroy();
-        delete this.components.plots[plotId];
-      }
-    }
-  }
-  printError(e) {
-    const errdiv = e.errdiv || this.dom.errdiv;
-    if (errdiv) errdiv.style("display", "").html("").style("background-color", "");
-    sayerror(errdiv || this.opts.holder, "Error: " + (e.message || e.error || e));
-    if (e.stack) console.log(e.stack);
-    this.bus.emit("error");
-    if (this.opts?.debug) {
-      console.groupCollapsed("Stack trace from MassApp.printError() call.");
-      console.trace();
-      console.groupEnd();
-    }
-  }
-  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;
-  }
-  async downloadPlots() {
-    const chartImagesAll = [];
-    let i = 1;
-    const values = Object.values(this.components.plots);
-    for (const plot of values) {
-      const chart = plot.type == "plot" ? plot.getComponents("chart") : plot;
-      const chartImages = chart.getChartImages ? chart.getChartImages() : null;
-      if (!chartImages) {
-        console.log(`The ${chart.type} does not support downloading images yet`);
-        continue;
-      }
-      for (const chartImage of chartImages) {
-        if (values.length > 1) chartImage.name = `${i}. ${chartImage.name}`;
-        chartImagesAll.push(chartImage);
-      }
-      i++;
-    }
-    if (chartImagesAll.length > 0) {
-      const filters = [];
-      const globalFilterImg = await this.components.nav.getComponents("filter").getFilterImage();
-      if (globalFilterImg) filters.push(globalFilterImg);
-      downloadSVGsAsPdf(chartImagesAll, "plots", "landscape", filters);
-    } else alert("No chart images available for download");
-  }
-};
-var appInit = AppApi.getInitFxn(MassApp);
-
-export {
-  appInit
-};
-//# sourceMappingURL=chunk-BQHPJY2M.js.map

package/dist/chunk-BZTWTH4Y.js

@@ -1,87 +0,0 @@
-// 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 || "180px").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, stop] = formatRangeBounds(range);
-    this.input.node().value = range.value != void 0 ? ` x=${range.value} ` : `${start} x ${stop}`;
-  }
-};
-function formatRangeBounds(range) {
-  const start = range.startunbounded || range.start == void 0 ? "" : `${range.start} ${range.startinclusive ? "<=" : "<"}`;
-  const stop = range.stopunbounded || range.stop == void 0 ? "" : `${range.stopinclusive ? "<=" : "<"} ${range.stop}`;
-  return [start, 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}'`;
-  }
-}
-
-export {
-  NumericRangeInput,
-  formatRangeBounds
-};
-//# sourceMappingURL=chunk-BZTWTH4Y.js.map

package/dist/chunk-BZTWTH4Y.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../dom/numericRangeInput.ts"],
-  "sourcesContent": ["import type { Elem, Input } from '../types/d3'\nimport type { FullyBoundedBin } from '#types'\n\ntype TvsRange = FullyBoundedBin & { value?: number }\ntype Opts = {\n\twidth?: string // width of input\n}\n\nexport class NumericRangeInput {\n\tcallback: (f: any) => void\n\tinput: Input\n\trange: any\n\n\tconstructor(holder: Elem, range: any, callback: () => void, opts?: Opts) {\n\t\tthis.input = holder\n\t\t\t.append('input')\n\t\t\t.attr('name', 'rangeInput')\n\t\t\t.attr('aria-label', 'Leave blank for the allowed minimum value')\n\t\t\t.style('width', opts?.width || '180px')\n\t\t\t.style('margin', '3px 5px')\n\t\t\t//.style('font-size', '20px')\n\t\t\t.on('change', () => {\n\t\t\t\ttry {\n\t\t\t\t\tthis.parseRange()\n\t\t\t\t} catch (ex) {\n\t\t\t\t\talert(ex)\n\t\t\t\t\tthis.setRange()\n\t\t\t\t}\n\t\t\t})\n\t\tthis.setRange(range)\n\t\tthis.callback = callback\n\t}\n\n\tgetInput() {\n\t\treturn this.input\n\t}\n\n\tparseRange() {\n\t\tconst str = this.input.node()!.value\n\t\tconst new_range = parseRange(str)\n\t\tif (this.range?.min != undefined) {\n\t\t\tif (!new_range.startunbounded && this.range?.min > new_range.start) throw 'Invalid start value < minimum allowed'\n\t\t\tif (!new_range.stopunbounded && this.range?.min >= new_range.stop) throw 'Invalid stop value >= minimum allowed'\n\t\t}\n\t\tif (this.range?.max != undefined) {\n\t\t\tif (!new_range.stopunbounded && this.range?.max < new_range.stop) throw 'Invalid stop value > maximum allowed'\n\n\t\t\tif (!new_range.startunbounded && new_range.start >= this.range?.max)\n\t\t\t\tthrow 'Invalid start value >= maximum allowed'\n\t\t}\n\n\t\tthis.range = new_range\n\t\tthis.callback(new_range)\n\t\treturn new_range\n\t}\n\n\tgetRange() {\n\t\treturn this.range\n\t}\n\n\tsetRange(range?: TvsRange) {\n\t\tif (!range) range = this.range\n\t\t//When an error is thrown the previous range is restored\n\t\telse this.range = range\n\n\t\t//So ts doesn't complain\n\t\tif (!range) return\n\t\tconst [start, stop] = formatRangeBounds(range)\n\t\tthis.input.node()!.value = range.value != undefined ? ` x=${range.value} ` : `${start} x ${stop}`\n\t}\n}\n\n/** Format the start and stop of a range as displayed to the user, e.g. ['10 <', '<= 20'].\n *\n * A bound is exclusive unless the range marks it inclusive, matching how a range is\n * evaluated elsewhere, e.g. isInRange() on the server and the tvs pill label. The displayed\n * expression must round-trip through parseRange(), since the input text is the only source\n * of the applied range: rendering an exclusive bound as inclusive would silently widen a\n * saved range on apply.\n */\nexport function formatRangeBounds(range: any): [string, string] {\n\tconst start =\n\t\trange.startunbounded || range.start == undefined ? '' : `${range.start} ${range.startinclusive ? '<=' : '<'}`\n\tconst stop = range.stopunbounded || range.stop == undefined ? '' : `${range.stopinclusive ? '<=' : '<'} ${range.stop}`\n\treturn [start, stop]\n}\n\nexport function parseRange(str: string) {\n\tif (!str) throw 'Empty range'\n\tconst tokens = str.replace(/\\s/g, '').split('x')\n\tlet start, stop, startinclusive, stopinclusive, value\n\n\tif (tokens[0]) parseRangeToken(tokens[0])\n\tif (tokens[1]) parseRangeToken(tokens[1])\n\tif (value != undefined) return { value, label: `x = ${value}` }\n\tconst startunbounded = start === undefined\n\tconst stopunbounded = stop === undefined\n\n\tif (!startunbounded && !stopunbounded && start > stop) throw 'start must be lower than stop'\n\treturn { start, stop, value, startinclusive, stopinclusive, startunbounded, stopunbounded }\n\n\tfunction parseRangeToken(rangeToken) {\n\t\tconst floatExpr = '[+-]?\\\\d+(\\\\.\\\\d+)?'\n\n\t\tif (new RegExp(`^${floatExpr}<$`).test(rangeToken) || new RegExp(`^>${floatExpr}$`).test(rangeToken)) {\n\t\t\tstart = parseFloat(rangeToken.match(floatExpr))\n\t\t\tstartinclusive = false\n\t\t} else if (new RegExp(`^${floatExpr}<=$`).test(rangeToken) || new RegExp(`^>=${floatExpr}$`).test(rangeToken)) {\n\t\t\tstart = parseFloat(rangeToken.match(floatExpr))\n\t\t\tstartinclusive = true\n\t\t} else if (new RegExp(`^${floatExpr}>$`).test(rangeToken) || new RegExp(`^<${floatExpr}$`).test(rangeToken)) {\n\t\t\tstop = parseFloat(rangeToken.match(floatExpr))\n\t\t\tstopinclusive = false\n\t\t} else if (new RegExp(`^${floatExpr}>=$`).test(rangeToken) || new RegExp(`^<=${floatExpr}$`).test(rangeToken)) {\n\t\t\tstop = parseFloat(rangeToken.match(floatExpr))\n\t\t\tstopinclusive = true\n\t\t} else if (new RegExp(`^${floatExpr}=$`).test(rangeToken) || new RegExp(`^=${floatExpr}$`).test(rangeToken)) {\n\t\t\tvalue = parseFloat(rangeToken.match(floatExpr))\n\t\t\tstopinclusive = true\n\t\t\tstartinclusive = true\n\t\t} else throw `Could not parse expression '${rangeToken}'`\n\t}\n}\n"],
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