@sjcrh/proteinpaint-client 2.201.0 → 2.202.0

package/dist/chunk-HR7XPTAV.js

@@ -0,0 +1,340 @@
+import {
+  skipPrevActionAbort,
+  storeInit
+} from "./chunk-2TWVFQD2.js";
+import {
+  summaryInit
+} from "./chunk-BIDQ4OZH.js";
+import {
+  navInit
+} from "./chunk-WJTRQ3ZC.js";
+import {
+  AppBase,
+  downloadSVGsAsPdf,
+  filterRxCompInit,
+  newSandboxDiv,
+  sayerror,
+  vocabInit
+} from "./chunk-73PFJ2VF.js";
+import {
+  importPlot
+} from "./chunk-ZZMIDYRE.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  AppApi,
+  getCompInit,
+  multiInit
+} from "./chunk-H6INPPUC.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) {
+    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-HR7XPTAV.js.map

package/dist/chunk-HR7XPTAV.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../mass/plot.js", "../mass/app.ts"],
+  "sourcesContent": ["import { getCompInit, copyMerge, multiInit } from '#rx'\nimport { Menu } from '#dom/menu'\n// import { recoverInit } from '../rx/src/recover'\nimport { select as d3select } from 'd3-selection'\nimport { importPlot } from '#plots/importPlot.js'\nimport { filterRxCompInit } from '#filter'\n\n/*\n\tMassPlot is a \"wrapper\" for chart component(s).\n\tIt creates expected plot-specific elements like an error div, undo-redo buttons, and local filter.\n*/\nclass MassPlot {\n\tstatic type = 'plot'\n\n\tconstructor(opts) {\n\t\tthis.type = MassPlot.type\n\t\tsetRenderers(this)\n\t\tthis.initUi(opts)\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.includes('cache_termq')) return true\n\t\tif (action.type.endsWith('_group')) return true\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\t// action.parentId == this.id is a special case to react when deleting a child plot of this plot,\n\t\t\t// for example in the profile comparison, when closing one of the comparison plots\n\t\t\treturn (\n\t\t\t\taction.id === this.id ||\n\t\t\t\taction.id == this.parentId ||\n\t\t\t\taction.config?.parentId === this.id ||\n\t\t\t\taction.parentId === this.id\n\t\t\t)\n\t\t}\n\t\tif (action.type.startsWith('filter')) return true\n\t\tif (action.type.startsWith('cohort')) return true\n\t\tif (action.type == 'app_refresh') return true\n\t\tif (action.type.endsWith('customTerm')) return true\n\t}\n\n\t// !!! NOTE: This getState() method is reused by the plot-specific recover component.\n\t// When logging something within getState, it may have been called by either the plot or recover instance\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\treturn {\n\t\t\ttermfilter: appState.termfilter,\n\t\t\tconfig,\n\t\t\tgroups: appState.groups,\n\t\t\t// quick fix to skip history tracking as needed\n\t\t\t_scope_: appState._scope_\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.dom.errdiv.style('display', 'none').style('background-color', 'rgba(255,100,100,0.2)').html('')\n\t\tif (!this.components) await this.setComponents(this.opts)\n\t}\n\n\tasync setComponents(opts) {\n\t\tconst _ = await importPlot(opts.chartType)\n\t\tconst promises = {\n\t\t\t// recover: recoverInit({\n\t\t\t// \tapp: this.app,\n\t\t\t// \tholder: this.dom.localRecoverDiv,\n\t\t\t// \tgetState: appState => this.getState(appState),\n\t\t\t// \treactsTo: action =>\n\t\t\t// \t\taction.id == this.id &&\n\t\t\t// \t\t(action.type == 'plot_edit' || action.type == 'plot_nestedEdits') &&\n\t\t\t// \t\taction._track_ != 'none',\n\t\t\t// \tplot_id: this.id,\n\t\t\t// \tmaxHistoryLen: 10,\n\t\t\t// \thideLabel: true\n\t\t\t// }),\n\t\t\tchart: _.componentInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tholder: this.dom.viz,\n\t\t\t\theader: this.dom.paneTitleDiv,\n\t\t\t\tid: this.id,\n\t\t\t\tplotDiv: d3select(this.dom.holder.app_div.node().parentNode),\n\t\t\t\t/******* reason for passing plotDiv to chart ********\n\t\t\t\t- this plot instance may allow to launch a new plot as a persistent sandbox\n\t\t\t\t  inside mass plotDiv, maintaining the uniform plot appearance despite it's ad-hoc\n\t\t\t\t  the new plot is not a formal mass plot type, and cannot be done via app.dispatch()\n\t\t\t\t  thus the need to directly access plotDiv\n\t\t\t\t- example: mds3 tk from genome browser can launch disco etc\n\t\t\t\t- having access to plotDiv may offer flexibility for the plot to do stuff\n\n\t\t\t\tsince plot.js has no access to mass app .dom.plotDiv in which all apps are shown,\n\t\t\t\tthis workarounds gets the parent node of sandbox.app_div which is app.dom.plotDiv\n\t\t\t\t*/\n\t\t\t\tgetFilterImage: async () => this.components.filter.getFilterImage()\n\t\t\t})\n\t\t}\n\n\t\tif (!this.state.config.hidePlotFilter) {\n\t\t\tconst filterDisabledMsg = this.app.vocabApi.termdbConfig?.plotFilter?.disabledMessage\n\t\t\t/*\n\t\t\tWhen the local filter is disabled (e.g. for the public/unauthenticated view), render it\n\t\t\tinto an inner greyed, non-interactive div while the outer filterDiv keeps pointer events\n\t\t\tso its tooltip explaining why still appears on hover.\n\t\t\t*/\n\t\t\tconst filterHolder = filterDisabledMsg\n\t\t\t\t? this.dom.filterDiv.append('div').style('pointer-events', 'none').style('opacity', 0.5)\n\t\t\t\t: this.dom.filterDiv\n\t\t\tif (filterDisabledMsg) this.dom.filterDiv.attr('title', filterDisabledMsg).style('cursor', 'not-allowed')\n\t\t\tpromises.filter = filterRxCompInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tparentId: this.id,\n\t\t\t\tholder: filterHolder,\n\t\t\t\thideLabel: true,\n\t\t\t\temptyLabel: '+Add new filter',\n\t\t\t\tcallback: filter => {\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tconfig: { filter }\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\tthis.components = await multiInit(promises)\n\t}\n\n\tdestroy() {\n\t\t// the dom.holder itself is not a d3-selection,\n\t\t// so need to specify a destroy function here\n\t\t// since the default rx.componentApi.destroy()\n\t\t// does not work when dom.holder is not a d3-selection\n\t\tthis.dom.holder.app_div.selectAll('*').remove()\n\t\tthis.dom.holder.app_div.remove()\n\t\tfor (const key in this.dom) {\n\t\t\tdelete this.dom[key]\n\t\t}\n\t}\n}\n\nexport const plotInit = getCompInit(MassPlot)\n\nfunction setRenderers(self) {\n\tself.initUi = function (opts) {\n\t\t// opts={app, chartType:str, holder, id, debug}\n\n\t\tconst holder = opts.holder // \"sandbox\" obj: {app_div, body, header, header_row, id}\n\n\t\t// since chartType is already given in constructor opts, create test id with chart type as a simple way to identify the box\n\t\topts.holder.app_div.attr('data-testid', 'sjpp-massplot-sandbox-' + opts.chartType)\n\n\t\tholder.header.style('padding', 0)\n\n\t\ttry {\n\t\t\tself.dom = {\n\t\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\t\tholder,\n\t\t\t\tpaneTitleDiv: holder.header\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('color', '#555')\n\t\t\t\t\t.style('padding-left', '7px')\n\t\t\t\t\t.style('vertical-align', 'sub'),\n\t\t\t\tlocalRecoverDiv: holder.header.append('div').style('display', 'inline-block'),\n\t\t\t\tfilterDiv: holder.header.append('div').style('display', 'inline-block').style('zoom', 0.9),\n\t\t\t\tbody: holder.body.style('white-space', 'nowrap').style('overflow-x', 'auto'),\n\n\t\t\t\t// will hold no data notice or the page title in multichart views\n\t\t\t\terrdiv: holder.body\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'none')\n\t\t\t\t\t.style('padding', '5px')\n\t\t\t\t\t.style('background-color', 'rgba(255,100,100,0.2)'),\n\n\t\t\t\t// dom.viz will hold the rendered view\n\t\t\t\tviz: holder.body.append('div')\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tself.dom.errdiv.style('display', 'none').text(e)\n\t\t}\n\t}\n}\n", "import { AppApi, type StoreApi, type ComponentApi, type RxApp } from '#rx'\nimport { AppBase } from '#plots/AppBase.ts'\nimport { storeInit } from './store'\nimport { skipPrevActionAbort as skipAbortPolicy } from './skipPrevActionAbort.ts'\nimport { vocabInit } from '#termdb/vocabulary'\nimport { navInit } from './nav'\nimport { plotInit } from './plot'\nimport { summaryInit } from '#plots/summary.js'\nimport { sayerror, Menu, newSandboxDiv, downloadSVGsAsPdf } from '#dom'\n\n/*\nopts{}\n.genome{}\n\tclient-side genome object\n\tshould be required\n.state{}\n\trequired, will fill-in or override store.defaultState\n \t.genome\n \t.dslabel\n \t.tree{} etc\n\n.app\n\t.onFilterChange\n\tIf it is provided when the global filter is edited\n\tthis function is called (from mass/store). Used by the profile dataset so far,\n\tto clear the profile local filters\n*/\n\nclass MassApp 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!: StoreApi\n\tplotIdToSandboxId: { [plotId: string]: string }\n\tbus!: any\n\n\t// expected class-specific props\n\n\tconstructor(opts, api) {\n\t\tsuper(opts)\n\t\tthis.api = api\n\n\t\tif (opts.addLoginCallback) {\n\t\t\topts.addLoginCallback(() => this.api.dispatch({ type: 'app_refresh' }))\n\t\t}\n\n\t\tthis.type = 'app'\n\t\t// this will create divs in the correct order\n\t\tthis.dom = {\n\t\t\tholder: opts.holder, // do not modify holder style\n\t\t\ttopbar: opts.holder.append('div'),\n\t\t\terrdiv: opts.holder.append('div'),\n\t\t\tplotDiv: opts.holder.append('div')\n\t\t}\n\n\t\tif (opts.getPlotConfig_mutateSummary) {\n\t\t\t/* \n\t\t\ta simple fix to perform a targeted mutation for summary config in summary.ts getPlotConfig()\n\t\t\tthis is from runpp({mass:{getPlotConfig_mutateSummary}})\n\t\t\tnot doing this via termdbConfig flag is because it's hard to support \"if\" logic (if no term2, supply this term2)\n\t\t\t*/\n\t\t\tif (typeof opts.getPlotConfig_mutateSummary != 'function')\n\t\t\t\tthrow new Error('opts.getPlotConfig_mutateSummary is not function')\n\t\t}\n\n\t\t// track plots by ID, and assign\n\t\tthis.plotIdToSandboxId = {}\n\t}\n\n\tasync preApiFreeze(api) {\n\t\ttry {\n\t\t\tapi.tip = new Menu({ padding: '5px' })\n\t\t\tapi.tip.d.on('keyup', event => {\n\t\t\t\tif (event.key == 'Escape') api.tip.hide()\n\t\t\t})\n\t\t\tapi.printError = e => this.printError(e)\n\n\t\t\t// TODO: only pass state.genome, dslabel to vocabInit\n\t\t\tapi.vocabApi = await vocabInit({\n\t\t\t\tapp: api,\n\t\t\t\tstate: { vocab: this.opts.state.vocab },\n\t\t\t\tfetchOpts: this.opts.fetchOpts,\n\t\t\t\tgetDatasetAccessToken: this.opts.getDatasetAccessToken\n\t\t\t})\n\n\t\t\tapi.hasWebGL = function () {\n\t\t\t\t//Copied from static/js/WEBGL.js\n\t\t\t\ttry {\n\t\t\t\t\tconst canvas = document.createElement('canvas')\n\t\t\t\t\treturn !!(\n\t\t\t\t\t\twindow.WebGLRenderingContext &&\n\t\t\t\t\t\t(canvas.getContext('webgl') || canvas.getContext('experimental-webgl'))\n\t\t\t\t\t)\n\t\t\t\t} catch (_) {\n\t\t\t\t\treturn false\n\t\t\t\t}\n\t\t\t}\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// TODO: may default later to having a debouncer ???\n\t\t\tconst debounceInterval = 'debounceInterval' in this.opts ? this.opts.debounceInterval : 0\n\t\t\t// NOTE: Within the same browser tab, a refresh should load the embedder's intended page\n\t\t\t// and not the recovered session, to avoid confusing default page load behavior. If a user\n\t\t\t// wants to see the initial recovered state view in the embedder portal, they would have\n\t\t\t// to click on a link again. May revisit this approach and reactivate the commented out code below.\n\t\t\tconst embeddedSessionState = this.opts.embeddedSessionState // || JSON.parse(sessionStorage.getItem('embeddedSessionState') || `null`)\n\t\t\tif (embeddedSessionState) {\n\t\t\t\t// may assume session state recovery for an embedder portal\n\t\t\t\t// see the comment about potential race-condition in childCorsMessage embedder-helpers.js\n\t\t\t\tObject.assign(this.opts.state, embeddedSessionState)\n\t\t\t}\n\t\t\tthis.store = await storeInit({ app: this.api, state: this.opts.state, debounceInterval })\n\t\t\tthis.state = await this.store.copyState()\n\t\t\tthis.components = {}\n\t\t\tif (this.state.nav.header_mode != 'hidden') {\n\t\t\t\tthis.components.nav = await navInit({\n\t\t\t\t\tapp: this.api,\n\t\t\t\t\tholder: this.dom.topbar,\n\t\t\t\t\theader_mode: this.state && this.state.nav && this.state.nav.header_mode,\n\t\t\t\t\tvocab: this.state.vocab,\n\t\t\t\t\tmassSessionDuration: this.state.termdbConfig.massSessionDuration, // this.opts.massSessionDuration\n\t\t\t\t\tpkgver: this.opts.pkgver,\n\t\t\t\t\tdownloadPlots: () => {\n\t\t\t\t\t\tthis.downloadPlots()\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t\tthis.components.plots = {}\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\tawait this.api.vocabApi.main()\n\t\t//Do not show the plots below the about tab\n\t\tthis.dom.plotDiv?.style(\n\t\t\t'display',\n\t\t\tthis.state.nav?.header_mode != 'hidden' && this.state.nav?.activeTab == 0 ? 'none' : 'block'\n\t\t)\n\n\t\tconst newPlots = {}\n\t\tlet sandbox\n\t\tfor (const plot of this.state.plots) {\n\t\t\t// plots with parentId means the parent plot will trigger the plot instead of being triggered here\n\t\t\tif (plot.parentId) continue\n\t\t\tif (this.components.plots && !(plot.id in this.components.plots)) {\n\t\t\t\tsandbox = newSandboxDiv(this.dom.plotDiv, {\n\t\t\t\t\tclose: () => {\n\t\t\t\t\t\tthis.api.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_delete',\n\t\t\t\t\t\t\tid: plot.id\n\t\t\t\t\t\t})\n\t\t\t\t\t},\n\t\t\t\t\tplotId: plot.id,\n\t\t\t\t\tbeforePlotId: plot.insertBefore || null,\n\t\t\t\t\tstyle: {\n\t\t\t\t\t\twidth: '98.5%'\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\tif (plot.chartType == 'summary')\n\t\t\t\t\tnewPlots[plot.id] = summaryInit(Object.assign({ app: this.api, holder: sandbox }, plot))\n\t\t\t\telse newPlots[plot.id] = plotInit(Object.assign({ app: this.api, holder: sandbox }, plot))\n\t\t\t}\n\t\t}\n\n\t\t// simultaneous initialization of multiple new plots;\n\t\t// if done inside the for-of loop above, the await kewyword\n\t\t// will delay subsequent plot initializations\n\t\tconst numNewPlots = Object.keys(newPlots).length\n\t\tif (numNewPlots) {\n\t\t\tawait Promise.all(Object.values(newPlots))\n\t\t\tfor (const plotId in newPlots) {\n\t\t\t\tthis.components.plots[plotId] = await newPlots[plotId]\n\t\t\t}\n\t\t}\n\n\t\tfor (const plotId in this.components.plots) {\n\t\t\tif (!this.state.plots.find(p => p.id === plotId)) {\n\t\t\t\tthis.components.plots[plotId].destroy()\n\t\t\t\tdelete this.components.plots[plotId]\n\t\t\t}\n\t\t}\n\t}\n\n\tprintError(e) {\n\t\tconst errdiv = e.errdiv || this.dom.errdiv\n\t\tif (errdiv) errdiv.style('display', '').html('').style('background-color', '')\n\t\tsayerror(errdiv || this.opts.holder, 'Error: ' + (e.message || e.error || e))\n\t\tif (e.stack) console.log(e.stack)\n\t\tthis.bus.emit('error')\n\t\t/** .printError() maybe called from any component without a helpful\n\t\t * message or error object. Include the trace when in debug mode to\n\t\t * help identify the source of the error.\n\t\t * Collapsed for convenience. */\n\t\tif (this.opts?.debug) {\n\t\t\tconsole.groupCollapsed('Stack trace from MassApp.printError() call.')\n\t\t\tconsole.trace()\n\t\t\tconsole.groupEnd()\n\t\t}\n\t}\n\n\tskipPrevActionAbort(action) {\n\t\treturn skipAbortPolicy(action)\n\t}\n\n\tasync downloadPlots() {\n\t\tconst chartImagesAll: any[] = []\n\t\tlet i = 1\n\t\tconst values: any[] = Object.values(this.components.plots)\n\t\tfor (const plot of values) {\n\t\t\tconst chart = plot.type == 'plot' ? plot.getComponents('chart') : plot // implies summary plot\n\t\t\tconst chartImages = chart.getChartImages ? chart.getChartImages() : null\n\t\t\tif (!chartImages) {\n\t\t\t\tconsole.log(`The ${chart.type} does not support downloading images yet`)\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tfor (const chartImage of chartImages) {\n\t\t\t\tif (values.length > 1) chartImage.name = `${i}. ${chartImage.name}`\n\t\t\t\tchartImagesAll.push(chartImage)\n\t\t\t}\n\t\t\ti++\n\t\t}\n\t\tif (chartImagesAll.length > 0) {\n\t\t\tconst filters: any[] = []\n\t\t\tconst globalFilterImg = await (this.components.nav as ComponentApi).getComponents('filter').getFilterImage()\n\t\t\tif (globalFilterImg) filters.push(globalFilterImg)\n\t\t\tdownloadSVGsAsPdf(chartImagesAll, 'plots', 'landscape', filters)\n\t\t} else alert('No chart images available for download')\n\t}\n}\n\nexport const appInit = AppApi.getInitFxn(MassApp)\n"],
+  "mappings": 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+  "names": []
+}

package/dist/chunk-HV3GD2F3.js

@@ -0,0 +1,54 @@
+import {
+  addGeneSearchbox
+} from "./chunk-73PFJ2VF.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.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-HV3GD2F3.js.map

package/dist/chunk-IGVKT4CE.js

@@ -0,0 +1,56 @@
+import {
+  sayerror
+} from "./chunk-73PFJ2VF.js";
+import {
+  TermTypeGroups
+} from "./chunk-GEQUQ3GG.js";
+
+// termdb/handlers/singleCellCellType.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 scctTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE];
+    if (!scctTerms) {
+      sayerror(
+        holder,
+        `termType2terms[${TermTypeGroups.SINGLECELL_CELLTYPE}]:[] is required in termdbConfig for singleCellCellType handler`
+      );
+      return;
+    }
+    const usecaseConfig = opts.usecase?.specialCase?.config;
+    const plots = usecaseConfig?.sample?.plots;
+    const isMeta = usecaseConfig?.sample?.isMetaResult;
+    const filtered = plots ? scctTerms.filter((t) => plots.includes(t.plot)) : usecaseConfig?.name ? scctTerms.filter((t) => t.plot === usecaseConfig.name) : scctTerms;
+    const getLabel = (t) => isMeta || plots?.length == 1 ? t.name : `${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 singleCellCellType handler");
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-IGVKT4CE.js.map

package/dist/chunk-IMKIDF2H.js

@@ -0,0 +1,123 @@
+import {
+  pickCollectionFraction,
+  renderTable
+} from "./chunk-73PFJ2VF.js";
+
+// termdb/handlers/termCollection.ts
+var SearchHandler = class {
+  async init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    opts.holder.style("display", "");
+    const termlst = opts.details.termlst ?? [];
+    const memberType = opts.details.memberType || opts.details.type;
+    if (opts.termCollectionSelectionMode === "fraction" && memberType === "numeric") {
+      pickCollectionFraction({
+        holder: opts.holder,
+        term: makeTerm(opts.details, termlst, opts.usecase),
+        callback: (tw) => opts.callback(tw)
+      });
+      return;
+    }
+    const tableDiv = opts.holder.append("div");
+    renderTable({
+      columns: [{ label: "VARIABLES" }],
+      rows: termlst.map((t) => {
+        return [{ value: t.name }];
+      }),
+      div: tableDiv,
+      maxWidth: "30vw",
+      maxHeight: "40vh",
+      // the button is disabled while the selection cannot be submitted
+      noButtonCallback: () => updateSelectBtn(),
+      striped: false,
+      showHeader: true,
+      //false,
+      selectAll: true,
+      columnButtons: void 0,
+      //Leave until table.js is typed
+      buttons: void 0
+    });
+    let categoryTable;
+    let ckSource = [];
+    if (opts.details.categoryKeys) {
+      ckSource = opts.details.categoryKeys;
+      const categoryDiv = opts.holder.append("div").style("margin-top", "15px");
+      const values = opts.details.termlst[0].values || {};
+      categoryTable = categoryDiv.append("div");
+      renderTable({
+        columns: [{ label: "CATEGORIES" }],
+        rows: ckSource.map((ck) => {
+          return [{ value: values[ck.key]?.label ?? ck.key, checked: ck.shown }];
+        }),
+        div: categoryTable,
+        maxWidth: "30vw",
+        maxHeight: "40vh",
+        noButtonCallback: () => updateSelectBtn(),
+        striped: false,
+        showHeader: true,
+        //false,
+        selectAll: true,
+        columnButtons: void 0,
+        //Leave until table.js is typed
+        buttons: void 0
+      });
+    }
+    function getRowChecks(div) {
+      const trs = div.select("table").select("tbody").node().querySelectorAll("tr");
+      return [...trs].map((tr) => tr.querySelectorAll("td")[1]?.querySelector("input")?.checked === true);
+    }
+    function getSelectedTermlst() {
+      const checked = getRowChecks(tableDiv);
+      return termlst.filter((term, i) => checked[i]);
+    }
+    function getCategoryKeys() {
+      if (!categoryTable) return void 0;
+      const checked = getRowChecks(categoryTable);
+      return ckSource.map((ck, i) => ({ key: ck.key, shown: checked[i] }));
+    }
+    function getSelectionError() {
+      if (getSelectedTermlst().length < 2) return "Select at least two variables.";
+      if (getCategoryKeys()?.every((ck) => !ck.shown)) return "Select at least one category.";
+      return void 0;
+    }
+    function updateSelectBtn() {
+      if (!selectBtn) return;
+      const error = getSelectionError();
+      selectBtn.property("disabled", Boolean(error)).attr("title", error || null);
+    }
+    const selectBtn = opts.holder.append("div").style("float", "right").style("padding", "6px 20px").append("button").attr("data-testid", "sjpp-term-collection-select").text("Select").on("click", () => {
+      opts.callback({
+        // makeTerm() extracts propsByTermId (color, etc) for the selected terms
+        ...makeTerm(opts.details, getSelectedTermlst(), opts.usecase),
+        categoryKeys: getCategoryKeys()
+      });
+    });
+    updateSelectBtn();
+  }
+};
+function makeTerm(details, termlst, usecase) {
+  const propsByTermId = {};
+  if (details.propsByTermId) {
+    for (const term of termlst) {
+      if (details.propsByTermId[term.id]) propsByTermId[term.id] = details.propsByTermId[term.id];
+    }
+  }
+  return {
+    type: "termCollection",
+    termIds: termlst.map((term) => term.id),
+    termlst,
+    name: details.name,
+    valueTransform: details.valueTransformByPlots?.[usecase?.target],
+    // memberType = ds.cohort.termdb.termCollections[].type for client code
+    memberType: details.memberType || details.type,
+    categoryKeys: details.categoryKeys,
+    isleaf: true,
+    propsByTermId
+  };
+}
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-IMKIDF2H.js.map

package/dist/chunk-ITKMNOLR.js

@@ -0,0 +1,37 @@
+import {
+  addGeneSearchbox,
+  getGEunit
+} from "./chunk-73PFJ2VF.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  TermTypes
+} from "./chunk-GEQUQ3GG.js";
+
+// termdb/handlers/geneExpression.ts
+var SearchHandler = class {
+  init(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)
+    });
+  }
+  async selectGene(gene) {
+    const unit = getGEunit(this.app.vocabApi);
+    const name = `${gene} ${unit}`;
+    if (!gene) throw new Error("No gene selected");
+    this.callback({ gene, name, type: TermTypes.GENE_EXPRESSION });
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-ITKMNOLR.js.map