@sjcrh/proteinpaint-client 2.181.0 → 2.182.1

package/dist/chunk-6VLA5NEW.js

@@ -0,0 +1,335 @@
+import {
+  storeInit
+} from "./chunk-ZTKQLABY.js";
+import {
+  summaryInit
+} from "./chunk-LRMV5DNW.js";
+import {
+  navInit
+} from "./chunk-NV5XWADG.js";
+import {
+  AppBase,
+  downloadSVGsAsPdf,
+  filterRxCompInit,
+  newSandboxDiv,
+  sayerror,
+  vocabInit
+} from "./chunk-NVB7MQLH.js";
+import {
+  importPlot
+} from "./chunk-4JON7TLI.js";
+import {
+  Menu
+} from "./chunk-A6TQGNDQ.js";
+import {
+  AppApi,
+  getCompInit,
+  multiInit
+} from "./chunk-MVTCBVSX.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.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)
+      promises.filter = filterRxCompInit({
+        app: this.app,
+        vocabApi: this.app.vocabApi,
+        parentId: this.id,
+        holder: this.dom.filterDiv,
+        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")
+    };
+    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.trace("Trace from MassApp.printError() call");
+  }
+  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-6VLA5NEW.js.map

package/dist/chunk-6VLA5NEW.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\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: this.dom.filterDiv,\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\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 { 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\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\tif (this.opts?.debug) console.trace('Trace from MassApp.printError() call')\n\t}\n\n\tskipPrevActionAbort(action) {\n\t\t// may skip aborting previously dispatched actions in AppApi.dispatch()\n\t\t// if the new dispatched action doesn't affect all components; this will\n\t\t// allow plots and control menus to continue rendering while creating,\n\t\t// editing, or deleting another plot\n\t\tif (!action) return false\n\t\tif (action.type.startsWith('filter')) return false\n\t\tif (action.type.startsWith('cohort')) return false\n\t\tif (action.type == 'app_refresh') {\n\t\t\tif (action.subactions) {\n\t\t\t\treturn action.subactions.find(a => a.type.startsWith('filter') || a.type.startsWith('cohort')) ? false : true\n\t\t\t}\n\t\t}\n\t\treturn true\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"],
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+  "names": []
+}

package/dist/chunk-7FKIAQ4K.js

@@ -0,0 +1,17 @@
+// ../shared/types/src/routes/termdb.violinBox.ts
+function isErrorResponse(response) {
+  return "error" in response && "status" in response;
+}
+
+// ../shared/types/src/routes/samplewsimages.ts
+var WSImage = class {
+  constructor(filename) {
+    this.filename = filename;
+  }
+};
+
+export {
+  WSImage,
+  isErrorResponse
+};
+//# sourceMappingURL=chunk-7FKIAQ4K.js.map

package/dist/chunk-7FKIAQ4K.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/types/src/routes/termdb.violinBox.ts", "../../shared/types/src/routes/samplewsimages.ts"],
+  "sourcesContent": ["import type { RoutePayload } from './routeApi.js'\nimport type { TermWrapper } from '../terms/tw.ts'\nimport type { Filter } from '../filter.ts'\nimport type { ErrorResponse } from './errorResponse.ts'\nimport type { DescrStats } from './termdb.descrstats.ts'\n\n/** Common properties shared by both violin and box plots */\ntype CommonProps = {\n\t/** numeric tw to fetch numeric data. tw.q.mode must be continuous */\n\ttw: TermWrapper\n\tdslabel: string\n\tgenome: string\n\t/** overlay tw for multiple violins/boxplots */\n\toverlayTw?: TermWrapper\n\t/** tw to divide to multiple charts */\n\tdivideTw?: TermWrapper\n\t/** mass filter */\n\tfilter?: Filter\n\t/** read-only invisible filter */\n\tfilter0?: any\n\t/** TODO: Needs description FIXME delete */\n\tcurrentGeneNames?: string[]\n\t/** if true, use log scale; if false or undefined, use linear scale */\n\tisLogScale?: boolean\n}\n\n/** Request type for violin plots with required violin-specific parameters */\nexport type ViolinRequest = CommonProps & {\n\t/** Indicates the type of chart to render */\n\tplotType: 'violin'\n\t/** A number representing the dimension perpendicular to the violin spread */\n\taxisHeight?: number\n\t/** A string representing the type of symbol used on the plot */\n\tdatasymbol?: string\n\t/** A number representing the device's pixel ratio */\n\tdevicePixelRatio: number\n\t/** If true, uses KDE method to build plot */\n\tisKDE?: boolean\n\t/** A string with two possible values: 'horizontal' or 'vertical' */\n\torientation: string\n\t/** A number representing the radius of the data symbols */\n\tradius: number\n\t/** A number representing the right margin */\n\trightMargin?: number\n\t/** Term may be scaled from regression analysis */\n\tscale?: any\n\t/** A number representing the width of the stroke */\n\tstrokeWidth?: number\n\t/** A number representing the width of the SVG box */\n\tsvgw: number\n\t/** Number of bins to build the plot. Default is 20. */\n\tticks?: number\n}\n\n/** Request type for box plots with required box-specific parameters */\nexport type BoxRequest = CommonProps & {\n\t/** Indicates the type of chart to render */\n\tplotType: 'box'\n\t/** sort plots by median value */\n\torderByMedian?: boolean\n\t/** Remove outliers from the plot */\n\tremoveOutliers?: boolean\n\t/** If true, show association tests table */\n\tshowAssocTests?: boolean\n}\n\n/**Unified request type for violin and boxplot - union of ViolinRequest and BoxRequest */\nexport type ViolinBoxRequest = ViolinRequest | BoxRequest\n\nexport type ViolinBoxResponse = ViolinResponse | BoxPlotResponse | ErrorResponse\n\n/** Type guard to check if response is an ErrorResponse */\nexport function isErrorResponse(response: ViolinBoxResponse): response is ErrorResponse {\n\treturn 'error' in response && 'status' in response\n}\n\n/** Type guard to check if response is a BoxPlotResponse */\nexport function isBoxPlotResponse(response: ViolinBoxResponse): response is BoxPlotResponse {\n\treturn !isErrorResponse(response) && 'charts' in response && 'descrStats' in response\n}\n\n/** Type guard to check if response is a ViolinResponse */\nexport function isViolinResponse(response: ViolinBoxResponse): response is ViolinResponse {\n\treturn !isErrorResponse(response) && 'min' in response && 'max' in response\n}\n\n/** Violin response types */\ninterface BinsEntries {\n\tx0: number\n\tx1: number\n\tdensity: number\n}\n\ninterface ValuesEntries {\n\tid: string\n\tlabel: string\n\tvalue: number\n}\n\ninterface PValueEntries {\n\tvalue?: string\n\thtml?: string\n}\n\ntype ViolinDensity = {\n\tbins: BinsEntries[]\n\tdensityMax: number\n\tdensityMin: number\n}\n\nexport type ViolinPlotEntry = {\n\tcolor: string\n\tchartId: string\n\tdensity: ViolinDensity\n\tlabel: string\n\tplotValueCount: number\n\tseriesId: string\n\tsrc: string\n\tsummaryStats: ValuesEntries[]\n}\n\nexport type ViolinResponse = {\n\tbins: { [index: string]: any }\n\tcharts: {\n\t\t[index: string]: {\n\t\t\tchartId: string\n\t\t\tplots: ViolinPlotEntry[]\n\t\t\tpvalues?: PValueEntries[][]\n\t\t}\n\t}\n\tmin: number\n\tmax: number\n\tuncomputableValues: { [index: string]: number }[] | null\n\tdescrStats?: DescrStats\n}\n\n/** Boxplot response types */\nexport type BoxPlotData = {\n\tw1: number | undefined\n\tw2: number | undefined\n\tp05: number\n\tp25: number\n\tp50: number\n\tp75: number\n\tp95: number\n\tiqr: number\n\tout: { value: number }[]\n}\n\nexport type BoxPlotEntry = {\n\tboxplot: BoxPlotData & { label: string }\n\tcolor?: string\n\tdescrStats: DescrStats\n\tisHidden?: boolean\n\tkey: string\n\tseriesId?: string\n}\n\nexport type BoxPlotChartEntry = {\n\tchartId: string\n\tplots: BoxPlotEntry[]\n\tsampleCount: number\n\twilcoxon?: [{ value: string }, { value: string }, { html: string }][]\n}\n\nexport type BoxPlotResponse = {\n\tabsMin?: number\n\tabsMax?: number\n\tbins?: {\n\t\t[index: string]: any\n\t}\n\tcharts: {\n\t\t[chartId: string]: BoxPlotChartEntry\n\t}\n\tdescrStats: DescrStats\n\tuncomputableValues: { label: string; value: number }[] | null\n}\n\nexport const violinBoxPayload: RoutePayload = {\n\trequest: {\n\t\ttypeId: 'ViolinBoxRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'ViolinBoxResponse'\n\t},\n\texamples: [\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tplotType: 'violin',\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\ttw: {\n\t\t\t\t\t\tterm: { id: 'aaclassic_5', type: 'float' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tdevicePixelRatio: 2,\n\t\t\t\t\tsvgw: 200,\n\t\t\t\t\torientation: 'horizontal',\n\t\t\t\t\tdatasymbol: 'rug',\n\t\t\t\t\tradius: 5,\n\t\t\t\t\tisLogScale: false\n\t\t\t\t}\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tplotType: 'box',\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\ttw: {\n\t\t\t\t\t\tterm: { id: 'agedx', type: 'float' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\toverlayTw: {\n\t\t\t\t\t\tterm: { id: 'sex', type: 'categorical' }\n\t\t\t\t\t},\n\t\t\t\t\torderByMedian: true\n\t\t\t\t}\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t}\n\t]\n}\n", "import type { RoutePayload } from './routeApi.ts'\nimport type { WSIClass } from '../dataset.ts'\nimport type { Annotation, Prediction } from './aiProjectSelectedWSImages.ts'\n\nexport type SampleWSImagesRequest = {\n\tgenome: string\n\tdslabel: string\n\tsample_id: string\n\twsimage: string\n}\n\nexport type SampleWSImagesResponse = {\n\tsampleWSImages: WSImage[]\n}\n\nexport class WSImage {\n\tid?: number\n\tfilename: string\n\tmetadata?: string\n\tpredictionLayers?: Array<string>\n\tannotations?: Array<Annotation>\n\tpredictions?: Array<Prediction>\n\tclasses?: Array<WSIClass>\n\t/** ds defined uncertainity labels and colors */\n\tuncertainty?: any\n\t/** Color to highlight active patches */\n\tactivePatchColor?: string\n\t/** Tile size in pixels needed for AI scripts */\n\ttileSize?: number\n\n\tconstructor(filename: string) {\n\t\tthis.filename = filename\n\t}\n}\n\nexport const sampleWSImagesPayload: RoutePayload = {\n\trequest: {\n\t\ttypeId: 'SampleWSImagesRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'SampleWSImagesResponse'\n\t}\n\t// examples: []\n}\n"],
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+}