@sjcrh/proteinpaint-client 2.220.0 → 2.221.0

package/dist/chunk-TVSNHVWX.js

@@ -1,194 +0,0 @@
-import {
-  violinRenderer
-} from "./chunk-PEKCVKJK.js";
-import {
-  getValueConversionFactor
-} from "./chunk-W5J3LTYS.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import {
-  drag_default
-} from "./chunk-5R63Q5KH.js";
-import {
-  pointer_default,
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// termsetting/handlers/NumericDensity.ts
-var NumericDensity = class {
-  constructor(opts) {
-    this.dom = {};
-    // WeakMap allows deletion of value when the object/DOM key is deleted,
-    // so better for avoiding memory leak
-    this.vrByDiv = /* @__PURE__ */ new WeakMap();
-    this.ranges = [];
-    this.no_density_data = false;
-    this.brushes = [];
-    this.plot_size = {
-      width: 500,
-      height: 100,
-      xpad: 10,
-      ypad: 20,
-      radius: 8
-    };
-    this.opts = opts;
-    this.termsetting = opts.termsetting;
-    this.tw = opts.termsetting.tw;
-  }
-  /* the boundary values exchanged with the bin/knot editors, and the domain of this.xscale, are in
-  	the term's user-facing unit; density_data is in the unit the values are stored in. only the two
-  	getters below cross that line, to put the plot's endpoints in the same unit as those values.
-  
-  	they multiply instead of calling toUserUnit(), which rounds: rounding is right for a number shown
-  	in an input, but a rounded domain endpoint distorts every scaled x by up to half of the last shown
-  	digit, and collapses the domain outright when the converted range is smaller than that (a stored
-  	range of under 2 days at scaleFactor=1/365.25). it would also disagree with violinRenderer, whose
-  	axis this plot's lines overlay and which scales its own domain unrounded */
-  get scaleFactor() {
-    return getValueConversionFactor(this.tw.term);
-  }
-  get displayMin() {
-    return this.density_data.min * this.scaleFactor;
-  }
-  get displayMax() {
-    return this.density_data.max * this.scaleFactor;
-  }
-  async setData() {
-    const self = this.termsetting;
-    const d = await self.vocabApi.getViolinBox(
-      {
-        plotType: "violin",
-        tw: { type: self.tw.type, term: self.term, q: self.q },
-        svgw: this.plot_size.width,
-        radius: this.plot_size.radius,
-        filter: self.filter
-      },
-      self.opts.getBodyParams?.()
-    );
-    if (d.error) throw d;
-    this.density_data = d;
-    return this.density_data;
-  }
-  async showViolin(div, boundaryOpts) {
-    await this.setData();
-    if (!this.vrByDiv.has(div)) {
-      div.style("padding", "5px").selectAll("*").remove();
-      const loadingDiv = div.append("div").style("padding", "10px").style("text-align", "center").html("Getting distribution data ...<br/>");
-      const densityDiv = div.append("div");
-      loadingDiv.remove();
-      const vr = new violinRenderer({
-        holder: densityDiv,
-        rd: this.density_data,
-        width: this.plot_size.width,
-        height: this.plot_size.height,
-        radius: this.plot_size.radius,
-        // axis ticks are labeled in the term's user-facing unit, e.g. years and not days
-        scaleFactor: this.scaleFactor
-      });
-      this.vrByDiv.set(div, vr);
-    }
-    this.vr = this.vrByDiv.get(div);
-    this.dom.svg = this.vr.svg;
-    this.vr.render();
-    if (boundaryOpts) await this.setBinLines(boundaryOpts);
-    return this.density_data;
-  }
-  async setBinLines(boundaryOpts) {
-    if (this.density_data.max == this.density_data.min) {
-      this.handleNoDensity();
-    } else {
-      if (this.dom.binsize_g) this.dom.binsize_g.selectAll("*").remove();
-      this.dom.binsize_g = this.dom.svg.append("g").attr("transform", `translate(${this.plot_size.xpad}, ${this.plot_size.ypad})`).attr("class", "binsize_g");
-      const maxvalue = this.displayMax;
-      const minvalue = this.displayMin;
-      this.xscale = linear().domain([minvalue, maxvalue]).range([this.plot_size.xpad, this.plot_size.width + this.plot_size.xpad]);
-      this.ranges = [];
-      this.brushes = [];
-      this.renderBinLines(boundaryOpts);
-    }
-  }
-  handleNoDensity() {
-    this.no_density_data = true;
-    this.ranges = [];
-    this.brushes = [];
-  }
-  renderBinLines(boundaryOpts) {
-    const { plot_size, tw, xscale, scaleFactor } = this;
-    if (!this.density_data) throw `Missing .density_data [density.ts, renderBinLines()]`;
-    const scaledMinX = Math.round(this.xscale(this.displayMin));
-    const scaledMaxX = Math.round(this.xscale(this.displayMax));
-    const lines = [];
-    for (const [index, v] of boundaryOpts.values.entries()) {
-      lines.push({ ...v, index, scaledX: Math.round(this.xscale(v.x)) });
-    }
-    const lastVisibleLine = lines.find((l) => l.isLastVisibleLine);
-    const lastVisibleScaledX = lastVisibleLine ? lastVisibleLine.scaledX : scaledMaxX;
-    const dragger = drag_default().on("drag", onDrag).on("end", onDrag);
-    this.dom.binsize_g.selectAll("line").remove();
-    this.dom.binsize_g.selectAll("line").data(lines).enter().append("line").style("stroke", (d) => d.isDraggable ? "#cc0000" : "#555").style("stroke-width", 1).attr("x1", (d) => d.scaledX).attr("y1", 0).attr("x2", (d) => d.scaledX).attr("y2", plot_size.height).style("cursor", (d) => d.isDraggable ? "ew-resize" : "").attr("display", (d) => !d.isDraggable && d.scaledX > lastVisibleScaledX ? "none" : "").on("mouseover", function(_, d) {
-      if (d.isDraggable) select_default(this).style("stroke-width", 3);
-    }).on("mouseout", function() {
-      select_default(this).style("stroke-width", 1);
-    }).each(function(d) {
-      if (d.isDraggable) select_default(this).call(dragger);
-    });
-    const lineElems = this.dom.binsize_g.node().querySelectorAll("line");
-    function toBoundaryValue(x) {
-      const inverted = xscale.invert(x);
-      return Number(
-        scaleFactor != 1 ? inverted.toFixed(2) : tw.term.type == "integer" ? Math.round(inverted) : inverted.toFixed(3)
-      );
-    }
-    function toLineValue(line) {
-      return line.draggedX === void 0 ? line.x : toBoundaryValue(line.draggedX);
-    }
-    function getNeighbors(d) {
-      const x = d.draggedX ?? d.scaledX;
-      let lower, upper;
-      for (const line of lines) {
-        if (line.index === d.index || !line.isDraggable) continue;
-        const lineX = line.draggedX ?? line.scaledX;
-        if (lineX <= x) {
-          if (!lower || lineX > (lower.draggedX ?? lower.scaledX)) lower = line;
-        } else if (!upper || lineX < (upper.draggedX ?? upper.scaledX)) upper = line;
-      }
-      return [lower, upper];
-    }
-    function onDrag(event, _d) {
-      const d = _d;
-      const [lower, upper] = getNeighbors(d);
-      const lowerX = Math.max(scaledMinX, lower ? lower.draggedX ?? lower.scaledX : scaledMinX);
-      const upperX = Math.min(scaledMaxX, upper ? upper.draggedX ?? upper.scaledX : scaledMaxX);
-      if (upperX - lowerX < 2) return;
-      const draggedX = Math.min(Math.max(pointer_default(event, this)[0], lowerX + 1), upperX - 1);
-      const value = toBoundaryValue(draggedX);
-      if (lower && value === toLineValue(lower)) return;
-      if (upper && value === toLineValue(upper)) return;
-      d.draggedX = draggedX;
-      select_default(this).attr("x1", d.draggedX).attr("y1", 0).attr("x2", d.draggedX).attr("y2", plot_size.height);
-      const lastVisibleScaledX2 = lastVisibleLine?.draggedX ?? lastVisibleLine?.scaledX ?? scaledMaxX;
-      const xOffset = d.draggedX - d.scaledX;
-      if (xOffset) {
-        for (const elem of lineElems) {
-          const c = elem.__data__;
-          if (c.movesWithLineIndex !== d.index) continue;
-          c.draggedX = c.scaledX + xOffset;
-          select_default(elem).attr("x1", c.draggedX).attr("x2", c.draggedX).style("display", c.draggedX >= lastVisibleScaledX2 ? "none" : "");
-        }
-        boundaryOpts.callback(d, value);
-      }
-    }
-  }
-  destroy() {
-    for (const [k, v] of Object.entries(this.dom)) {
-      delete this.dom[k];
-      if (typeof v.remove == "function") v.remove();
-    }
-  }
-};
-
-export {
-  NumericDensity
-};
-//# sourceMappingURL=chunk-TVSNHVWX.js.map

package/dist/chunk-U3CWWOHL.js

@@ -1,340 +0,0 @@
-import {
-  summaryInit
-} from "./chunk-6DESNDD5.js";
-import {
-  navInit
-} from "./chunk-B5IJAQG4.js";
-import {
-  skipPrevActionAbort,
-  storeInit
-} from "./chunk-DZBPF5QI.js";
-import {
-  AppBase,
-  downloadSVGsAsPdf,
-  filterRxCompInit,
-  newSandboxDiv,
-  sayerror,
-  vocabInit
-} from "./chunk-PEKCVKJK.js";
-import {
-  importPlot
-} from "./chunk-YR6EXI2K.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import {
-  AppApi,
-  getCompInit,
-  multiInit
-} from "./chunk-HBNB5TRH.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.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()
-      })
-    };
-    const plotFilterCfg = this.app.vocabApi.termdbConfig?.plotFilter;
-    if (!this.state.config.hidePlotFilter && !plotFilterCfg?.hide) {
-      const filterDisabledMsg = plotFilterCfg?.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) {
-    return skipPrevActionAbort(action);
-  }
-  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-U3CWWOHL.js.map

package/dist/chunk-VGC4STKW.js

@@ -1,56 +0,0 @@
-import {
-  sayerror
-} from "./chunk-PEKCVKJK.js";
-import {
-  TermTypeGroups
-} from "./chunk-WJLRU5OF.js";
-
-// termdb/handlers/singleCellNumericValue.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.validateOpts(opts);
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const scnvTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_NUMERIC_VALUE];
-    if (!scnvTerms?.length) {
-      sayerror(
-        holder,
-        `termType2terms[${TermTypeGroups.SINGLECELL_NUMERIC_VALUE}]:[] is required in termdbConfig for singleCellNumericValue handler`
-      );
-      return;
-    }
-    const usecaseConfig = opts.usecase?.specialCase?.config;
-    const plots = usecaseConfig?.sample?.plots;
-    const isMeta = usecaseConfig?.sample?.isMetaResult;
-    const filtered = plots ? scnvTerms.filter((t) => plots.includes(t.plot)) : usecaseConfig?.name ? scnvTerms.filter((t) => t.plot === usecaseConfig.name) : scnvTerms;
-    const getLabel = (t) => isMeta || plots?.length == 1 ? t.name : `${t.name} (${t.plot})`;
-    const filteredTerms = new Set(
-      plots || !usecaseConfig?.name ? filtered.map((t) => ({ ...t, label: getLabel(t) })) : filtered
-    );
-    for (const t of Array.from(filteredTerms)) {
-      holder.append("div").classed("termdiv", true).style("padding", "0px 5px").append("div").classed("termlabel sja_filter_tag_btn sja_tree_click_term ts_pill", true).style("display", "inline-block").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text(t.label || t.name).on("click", () => {
-        const term = this.makeTerm(t, usecaseConfig);
-        this.callback(term);
-      });
-    }
-  }
-  makeTerm(_term, usecaseConfig) {
-    const term = { ..._term };
-    if (!term.sample && usecaseConfig?.sample) term.sample = usecaseConfig.sample;
-    return term;
-  }
-  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.usecase == null) throw new Error("usecase is required");
-    if (!opts.app.vocabApi.termdbConfig?.termType2terms)
-      throw new Error("termType2terms is required in termdbConfig for singleCellNumericValue handler");
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-VGC4STKW.js.map