@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/chunk-DBKNWR4J.js

@@ -1,1561 +0,0 @@
-import {
-  recoverInit
-} from "./chunk-4KY4XKJV.js";
-import {
-  parentCorsMessage
-} from "./chunk-PRZWSBMA.js";
-import {
-  chartsInit,
-  fillTermWrapper,
-  filterRxCompInit,
-  first_genetrack_tolist,
-  getDNAMethUnit,
-  getFilterItemByTag,
-  groupsInit,
-  keyupEnter,
-  renderTable,
-  sayerror,
-  to_textfile
-} from "./chunk-5VOPABBA.js";
-import {
-  importPlot
-} from "./chunk-Z5U6HOE4.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  icons
-} from "./chunk-IIT367QZ.js";
-import {
-  dofetch3
-} from "./chunk-M6EF3WVV.js";
-import {
-  getCompInit,
-  multiInit
-} from "./chunk-M3J4MINX.js";
-import {
-  DNA_METHYLATION
-} from "./chunk-I6WR4CG7.js";
-import {
-  dtcnv,
-  dtfusionrna,
-  dtsnvindel,
-  dtsv
-} from "./chunk-2X6W4E3W.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// mass/sessionBtn.js
-var MassSessionBtn = class _MassSessionBtn {
-  static type = "sessionBtn";
-  constructor() {
-    this.type = _MassSessionBtn.type;
-    this.route = "termdb";
-    this.embedderOrigin = window.location.origin;
-    this.hostURL = sessionStorage.getItem("hostURL") || this.embedderOrigin;
-  }
-  async init(appState) {
-    const tip = new Menu({ padding: "0px" });
-    const copytip = new Menu({ padding: "5px" });
-    this.dom = {
-      button: this.opts.button,
-      tip,
-      copytip
-    };
-    this.dom.button.on("click", (event2) => {
-      event2.stopPropagation();
-      this.dom.tip.clear();
-      this.showMenu();
-    });
-    this.dslabel = appState.vocab.dslabel;
-    this.savedSessions = JSON.parse(localStorage.getItem("savedMassSessions") || `{}`);
-    this.requiredAuth = appState.termdbConfig?.requiredAuth?.find((a) => a.route == this.route && a.type == "jwt");
-  }
-  async showMenu() {
-    this.dom.tip.clear().d.style("padding", 0);
-    this.dom.tip.d.attr("id", "sjpp-session-menu");
-    const gt = `<span style='margin-left: 24px; float: right'>&gt;</span>`;
-    const options = [
-      { label: `Open`, title: "Recover a saved session", callback: this.open },
-      { label: `Save`, title: "Save the current view", callback: this.save },
-      { label: `Share`, title: "Share the current view", callback: this.getSessionUrl }
-    ];
-    if (!this.serverCachedSessions) await this.setServerCachedSessions();
-    if (Object.keys(this.savedSessions).length || Object.keys(this.serverCachedSessions).length) {
-      options.push({ label: `Delete`, title: "Delete a saved session", callback: this.delete });
-    }
-    this.dom.tip.clear().d.selectAll(".sja_menuoption sja_sharp_border").data(options).enter().append("div").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", (d) => `sjpp-session-btn-${d.label.toLowerCase().replace(/\s/g, "-")}`).attr("aria-label", (d) => d.title).html((d) => d.label).on("click", (event2, d) => {
-      this.dom.tip.clear().d.style("padding", "10px");
-      event2.stopPropagation();
-      this.showBackBtn();
-      d.callback.call(this);
-    });
-    this.dom.tip.showunder(this.dom.button.node());
-  }
-  async open() {
-    const radioName = `sjpp-session-open-radio-` + Math.random().toString().slice(-6);
-    this.dom.tip.d.append("div").style("display", "none").style("padding", "3px 9px").html(`
-			<b>Open in</b>
-			<label>
-				<input type='radio' name='${radioName}' value='new' style='margin-right: 0; vertical-align: bottom'/>
-				<span>a new tab</span>
-			</label>
-			<label style='margin-left: 5px'>
-				<input type='radio' name='${radioName}' value='current' checked=checked style='margin-right: 0; vertical-align: bottom'/>
-				<span>current tab</span>
-			</label>
-		`);
-    const t = await this.listSessions({
-      trClickHandler: async (event2, d) => {
-        const { loc, id: id2 } = d;
-        if (!id2) return;
-        if (loc.includes("browser")) {
-          this.sessionName = id2;
-          const state = structuredClone(this.savedSessions[id2]);
-          await preprocessState(state, this.app);
-          const targetWindow = this.dom.tip.d.node().querySelector(`[name="${radioName}"]:checked`).value;
-          if (targetWindow == "current") {
-            this.app.dispatch({ type: "app_refresh", state });
-          } else if (window.location.origin == this.hostURL) {
-            window.open(`/?mass-session-id=${id2}&src=browser`);
-          } else {
-            if (state.embedder) parentCorsMessage({ state });
-            else {
-              const { protocol, host, search, origin, href } = window.location;
-              const embedder = { protocol, host, search, origin, href };
-              parentCorsMessage({ state: Object.assign({ embedder }, state) });
-            }
-          }
-          this.dom.tip.hide();
-        } else if (loc == "server") {
-          const headers = await this.app.vocabApi.mayGetAuthHeaders(this.route);
-          const body = { id: id2, route: this.route, dslabel: this.dslabel, embedder: window.location.hostname };
-          const res = await dofetch3(`/massSession?`, { headers, body });
-          if (!res.state) throw res.error || "unable to get the cached session from the server";
-          await preprocessState(res.state, this.app);
-          this.savedSessions[id2] = res.state;
-          const targetWindow = this.dom.tip.d.node().querySelector(`[name="${radioName}"]:checked`).value;
-          if (targetWindow == "current") {
-            this.app.dispatch({ type: "app_refresh", state: res.state });
-          } else if (window.location.origin == this.hostURL) {
-            window.open(`/?mass-session-id=${id2}&src=cred&dslabel=${this.dslabel}&route=${this.route}`);
-          } else {
-            parentCorsMessage(res);
-          }
-          this.dom.tip.hide();
-        }
-      }
-    });
-    t.headtr.select("th").html("Open from");
-    const tr1 = t.tbody.insert("tr", "tr");
-    tr1.append("td").style("text-align", "center").style("padding", "3px 9px").html("Local file");
-    const label = tr1.append("td").style("text-align", "left").append("label");
-    label.append("span").style("padding", "3px 9px").style("text-decoration", "underline").style("cursor", "pointer").html("Choose File");
-    label.append("input").attr("type", "file").attr("placeholder", "file name").style("opacity", 0).style("width", "0.1px").style("height", "0.1px").style("position", "absolute").on("change", async () => {
-      const file = event.target.files.item(0);
-      const json = await file.text();
-      let sessionName = file.name;
-      if (this.savedSessions[sessionName]) {
-        sessionName = prompt(
-          `Leave as-is to overwrite a session with the same name, or enter a different session name.`,
-          sessionName
-        );
-      }
-      this.sessionName = sessionName;
-      const state = JSON.parse(json);
-      await preprocessState(state, this.app);
-      this.savedSessions[sessionName] = state;
-      localStorage.setItem("savedMassSessions", JSON.stringify(this.savedSessions));
-      const targetWindow = this.dom.tip.d.node().querySelector(`[name="${radioName}"]:checked`).value;
-      if (targetWindow == "current") {
-        this.app.dispatch({ type: "app_refresh", state });
-      } else if (window.location.origin == this.hostURL) {
-        window.open(`/?mass-session-id=${sessionName}&src=browser`);
-      } else {
-        if (state.embedder) parentCorsMessage({ state });
-        else {
-          const { protocol, host, search, origin, href } = window.location;
-          const embedder = { protocol, host, search, origin, href };
-          parentCorsMessage({ state: Object.assign({ embedder }, state) });
-        }
-      }
-      this.dom.tip.hide();
-    });
-  }
-  async listSessions(opts = {}) {
-    const table = this.dom.tip.d.append("table").attr("class", "sjpp-controls-table");
-    const headtr = table.append("thead").append("tr");
-    headtr.selectAll("th").data(["Cache Location", "Session ID"]).enter().append("th").style("text-align", (d, i) => i === 0 ? "center" : "left").style("padding", "3px 9px").html((d) => d);
-    const sessionIds = Object.keys(this.savedSessions).map((id2) => ({ loc: "browser", id: id2 }));
-    if (!this.serverCachedSessions) await this.setServerCachedSessions();
-    sessionIds.push(...this.serverCachedSessions.map((id2) => ({ loc: "server", id: id2 })));
-    const tbody = table.append("tbody");
-    const trs = tbody.selectAll("tr").data(sessionIds).enter().append("tr").on("click", opts.trClickHandler || null);
-    trs.selectAll("td").data((d) => [d, d]).enter().append("td").style("text-align", (d, i) => i === 0 ? "center" : "left").style("padding", "3px 9px").style("cursor", "pointer").html((d, i) => i === 0 ? d.loc : d.id);
-    if (!this.serverCachedSessions.length && this.requiredAuth && !this.app.vocabApi.hasVerifiedToken()) {
-      const tbody2 = table.append("tbody").append("tr").selectAll("td").data(["server", "requires sign-in"]).enter().append("td").style("text-align", (d, i) => i === 0 ? "center" : "left").style("padding", "3px 9px").html((d) => d);
-    }
-    return { table, headtr, tbody, trs };
-  }
-  async setServerCachedSessions() {
-    const state = this.app.getState();
-    this.requiredAuth = state.termdbConfig?.requiredAuth?.find((a) => a.route == this.route && a.type == "jwt");
-    if (!this.requiredAuth) {
-      this.serverCachedSessions = [];
-      return;
-    }
-    const headers = this.app.vocabApi.mayGetAuthHeaders(this.route);
-    const body = { route: this.route, dslabel: this.dslabel, embedder: window.location.hostname };
-    const res = await dofetch3("/sessionIds", { headers, body });
-    this.serverCachedSessions = res.sessionIds || [];
-  }
-  async save(d) {
-    const div = this.dom.tip.d;
-    const inputDiv = div.append("div");
-    inputDiv.append("span").html("Save as");
-    const sessionNames = Object.keys(this.savedSessions);
-    if (!this.serverCachedSessions) await this.setServerCachedSessions();
-    sessionNames.push(...this.serverCachedSessions.filter((d2) => !sessionNames.includes(d2)));
-    const placeholder = this.sessionName || "unnamed-session";
-    const input = inputDiv.append("input").attr("type", "text").attr("placeholder", placeholder).style("width", "220px").on("input", () => {
-      searchResultDiv.selectAll("*").remove();
-      const value = input.property("value");
-      const exactMatch = sessionNames.filter((s) => s === value);
-      const startsWith = sessionNames.filter((s) => s.startsWith(value));
-      const includes = sessionNames.filter((s) => s.includes(value) && s !== value && !startsWith.includes(s));
-      searchResultDiv.selectAll("div").data([...exactMatch, ...startsWith, ...includes]).enter().append("div").attr("class", "sja_menuoption").attr("data-testid", `sjpp-save-session-option`).html((d2) => d2).on("click", (event2, d2) => {
-        input.property("value", d2);
-        searchResultDiv.selectAll("*").remove();
-      });
-    });
-    const searchResultDiv = div.append("div");
-    const submitDiv = div.append("div");
-    submitDiv.append("span").html("Save to&nbsp;");
-    submitDiv.append("button").style("min-width", "80px").html("Browser").attr(
-      "title",
-      `Save the session in your current browser's cache. The session can be easily recovered, but not shared among your other devices`
-    ).on("click", () => {
-      this.sessionName = input.property("value") || placeholder;
-      this.savedSessions[this.sessionName] = this.app.getState();
-      localStorage.setItem("savedMassSessions", JSON.stringify(this.savedSessions));
-      this.confirmAction(`Cached '<b>${this.sessionName}</b>' in browser`);
-    });
-    submitDiv.append("button").style("min-width", "80px").html("File").attr(
-      "title",
-      `Save the session into a local file. The session can be easily recoved using the 'Open from local file' option.`
-    ).on("click", () => {
-      const name = input.property("value") || placeholder;
-      this.savedSessions[name] = this.app.getState();
-      this.download(name);
-      this.confirmAction(`Downloaded '<b>${name}</b>'`);
-    });
-    if (this.requiredAuth) {
-      const requiresSignIn = this.app.vocabApi.hasVerifiedToken() ? "" : "Requires sign-in. ";
-      submitDiv.append("button").style("min-width", "80px").html("Server").attr(
-        "title",
-        `${requiresSignIn}Save the session into a remote server. The session can be easily shared across your different devices and recovered using the 'Open from server' option.`
-      ).property("disabled", !this.app.vocabApi.hasVerifiedToken()).on("click", async () => {
-        if (!this.app.vocabApi.hasVerifiedToken()) {
-          alert("Requires sign-in");
-          return;
-        }
-        const name = input.property("value") || placeholder;
-        this.savedSessions[name] = this.app.getState();
-        const res = await this.getSessionUrl(name);
-        if (res.id != name) throw `error saving ${name}`;
-        this.confirmAction(`Saved '<b>${name}</b>' on the server`);
-      });
-    }
-  }
-  download(name = "") {
-    const sessionName = name || this.sessionName;
-    const ext = sessionName?.endsWith(".txt") ? "" : ".txt";
-    const filename = `${sessionName}${ext}`;
-    to_textfile(filename, JSON.stringify(this.savedSessions[sessionName]));
-  }
-  async getSessionUrl(filename = "") {
-    const headers = await this.app.vocabApi.mayGetAuthHeaders("termdb");
-    const state = structuredClone(this.app.getState());
-    const { protocol, host, search, origin, href } = window.location;
-    state.embedder = { protocol, host, search, origin, href };
-    if (filename) {
-      state.__sessionFor__ = {
-        route: this.route,
-        filename,
-        dslabel: this.dslabel,
-        embedder: window.location.hostname
-      };
-    }
-    const res = await dofetch3("/massSession", {
-      headers,
-      method: "POST",
-      body: JSON.stringify(state)
-    });
-    if (filename) {
-      return res;
-    } else {
-      const url = `${this.hostURL}/?mass-session-id=${res.id}&noheader=1`;
-      this.dom.tip.showunder(this.dom.button.node());
-      const linkDiv = this.dom.tip.d.append("div").style("margin", "10px");
-      linkDiv.append("div").style("display", "flex").style("margin-bottom", "12px").html(`Open or copy the session link.`);
-      const a = linkDiv.append("a").style("display", "none").attr("href", url).attr("target", "_blank").html(res.id);
-      linkDiv.append("button").style("cursor", "pointer").text("Open link").on("click", () => {
-        a.node().click();
-      });
-      linkDiv.append("button").style("cursor", "pointer").style("margin-left", "10px").text("Copy link").on("click", async (event2) => {
-        await navigator.clipboard.writeText(url);
-        this.dom.copytip.clear().showunder(event2.target);
-        this.dom.copytip.d.append("div").html("&#10003;");
-        setTimeout(() => {
-          this.dom.copytip.hide();
-        }, 1e3);
-      });
-      if (this.hostURL != window.location.origin) {
-        a.on("click", (event2) => {
-          event2.preventDefault();
-          parentCorsMessage({ state }, "noredirect");
-          return false;
-        });
-      }
-      linkDiv.append("div").html(`
-					<br>
-					<div style="max-width: 400px; font-size: 1em; opacity:.6">
-					<span>NOTES</span>
-					<ul>
-					<li>A recovered session may hide data or views to users that are not authorized to access the saved datasets or features.</li>
-					<li>This session will be saved for ${this.opts.massSessionDuration} days.</li>
-					</ul>
-					</div>`);
-      setTimeout(() => {
-        this.dom.button.property("disabled", false);
-      }, 1e3);
-    }
-  }
-  async delete() {
-    const t = await this.listSessions({
-      trClickHandler: function(event2) {
-        const input = this.lastChild.querySelector("input");
-        const checked = event2.target == input ? input.checked : !input.checked;
-        select_default(this).style("text-decoration", checked ? "line-through" : "");
-        if (event2.target != input) input.checked = checked;
-        const checkedRows = t.table.node().querySelectorAll("input:checked");
-        submitBtn.property("disabled", checkedRows.length ? false : true);
-      }
-    });
-    t.headtr.append("th").html("Delete");
-    t.trs.each(function(d) {
-      select_default(this).append("td").style("text-align", "center").append("input").attr("type", "checkbox").attr("value", d.id);
-    });
-    const submitBtn = this.dom.tip.d.append("div").style("text-align", "center").append("button").html("Delete selected sessions").property("disabled", true).on("click", async () => {
-      const inputs = t.table.node().querySelectorAll("input");
-      const sessionIdsDeletedFromServer = [];
-      for (const input of inputs) {
-        if (select_default(input).property("checked")) {
-          const d = input.parentNode.parentNode.__data__;
-          if (d.loc == "browser") {
-            delete this.savedSessions[input.value];
-          } else if (d.loc == "server") {
-            delete this.serverCachedSessions[input.value];
-            sessionIdsDeletedFromServer.push(input.value);
-          } else throw `unknown cache location=${d.loc}`;
-        }
-      }
-      localStorage.setItem("savedMassSessions", JSON.stringify(this.savedSessions));
-      try {
-        const headers = await this.app.vocabApi.mayGetAuthHeaders("termdb");
-        const body = {
-          ids: sessionIdsDeletedFromServer,
-          route: this.route,
-          dslabel: this.dslabel,
-          embedder: window.location.hostname
-        };
-        const res = dofetch3(`/massSession?`, { method: "DELETE", headers, body });
-      } catch (e) {
-        throw e;
-      }
-      this.dom.tip.hide();
-    });
-  }
-  showBackBtn() {
-    this.dom.tip.d.append("div").attr("class", "sja_clbtext2").style("margin-bottom", "10px").style("cursor", "pointer").html(`&lt; Session Menu`).on("click", () => this.showMenu());
-  }
-  confirmAction(html) {
-    this.dom.tip.clear().d.append("div").html(html).transition().delay(3e3).duration(1e3).style("opacity", 0);
-    setTimeout(() => {
-      this.dom.tip.hide();
-    }, 3500);
-  }
-};
-async function preprocessState(state, app) {
-  delete state.termdbConfig;
-  if (state.plots) {
-    const promises = [];
-    for (const plot of state.plots) {
-      promises.push(
-        (async () => {
-          const _ = await importPlot(plot.chartType);
-          return await _.getPlotConfig(plot, app);
-        })()
-      );
-    }
-    try {
-      await Promise.all(promises);
-    } catch (e) {
-      console.log(e);
-      app.printError(e);
-    }
-  }
-}
-var sessionBtnInit = getCompInit(MassSessionBtn);
-
-// mass/about.ts
-var cohortTableActiveColor = "yellow";
-var MassAbout = class _MassAbout {
-  constructor(opts) {
-    this.initCohort = (appState) => {
-      if (this.selectCohort == null) return;
-      if (!this.selectCohort.values) return;
-      const instanceNum2 = this.instanceNum;
-      const activeCohort = appState.activeCohort;
-      const app = this.app;
-      this.dom.cohortOpts.append("table").attr("data-testid", "sjpp-about-cohort-options-table").selectAll("tr").data(this.selectCohort.values).enter().append("tr").each(function(d, i, nodes) {
-        const tr = select_default(nodes[i]);
-        const td0 = tr.append("td");
-        const radioName = "sja-termdb-cohort-" + instanceNum2;
-        const radioId = radioName + "-" + i;
-        td0.append("input").style("scale", "1.2").attr("type", "radio").attr("name", radioName).attr("id", radioId).attr("value", i).property("checked", i === activeCohort).style("margin-right", "5px").style("margin-left", "0px").on("click", async (event2) => {
-          const state = app.getState();
-          const clearOnChange = state.termdbConfig.selectCohort.clearOnChange;
-          if (clearOnChange) {
-            const subactions = [];
-            const toBeCleared = [];
-            const plots = state.plots;
-            const filter = state.termfilter.filter.lst.find((f) => f.tag == "filterUiRoot")?.lst;
-            const groups = state.groups;
-            if (clearOnChange.plots && plots?.length) toBeCleared.push("plots");
-            for (const plot of plots) {
-              subactions.push({
-                type: "plot_delete",
-                id: plot.id
-              });
-            }
-            if (clearOnChange.filter && filter?.length) toBeCleared.push("filters");
-            subactions.push({
-              type: "filter_replace",
-              filter: {
-                type: "tvslst",
-                in: true,
-                join: "",
-                tag: "filterUiRoot",
-                lst: []
-              }
-            });
-            if (clearOnChange.groups && groups?.length) {
-              toBeCleared.push("groups");
-              for (const group of groups) {
-                subactions.push({
-                  type: "delete_group",
-                  name: group.name
-                });
-              }
-              for (const term of state.customTerms) {
-                subactions.push({
-                  type: "delete_customTerm",
-                  name: term.name
-                });
-              }
-            }
-            subactions.push({ type: "cohort_set", activeCohort: i });
-            if (toBeCleared.length) {
-              const confirm = window.confirm(
-                `Changing the cohort will clear all ${joinByComma(
-                  toBeCleared
-                )}. To proceed, click "OK". To save the session, click "Cancel" and then click the "Session" button at the top of the page.`
-              );
-              if (!confirm) {
-                event2.preventDefault();
-                return;
-              }
-            }
-            app.dispatch({
-              type: "app_refresh",
-              subactions
-            });
-          } else app.dispatch({ type: "cohort_set", activeCohort: i });
-        });
-        td0.append("label").style("font-size", "1.4em").attr("for", radioId).attr("colspan", 2).style("cursor", "pointer").html((d2) => d2.label);
-        tr.selectAll("td").style("max-width", "600px").style("padding-bottom", "10px").style("padding-right", "20px").style("vertical-align", "top");
-      });
-      this.dom.cohortTable = this.subheader.append("div").attr("data-testid", "sjpp-about-cohort-table").style("margin-left", "12px");
-      if (this.selectCohort.asterisk) {
-        this.dom.cohortAsterisk = this.subheader.append("div").attr("data-testid", "sjpp-about-cohort-asterisk").style("margin", "10px").style("font-size", ".8em").text(this.selectCohort.asterisk);
-      }
-    };
-    this.renderCohortsTable = async () => {
-      if (!this.dom.cohortTable) return;
-      this.dom.cohortTable.selectAll("*").remove();
-      const columns = [{ label: "Feature" }];
-      const rows = [];
-      const result = await this.app.vocabApi.getCohortsData();
-      if ("error" in result) throw result.error;
-      if (this.selectCohort?.values) {
-        const values = this.selectCohort.values;
-        result.cohorts.sort((a, b) => {
-          const aIndex = values.findIndex((v) => v.keys.toString() == a.cohort);
-          const bIndex = values.findIndex((v) => v.keys.toString() == b.cohort);
-          if (aIndex < bIndex) return -1;
-          if (aIndex > bIndex) return 1;
-          return 0;
-        });
-      }
-      if (!result.cfeatures.length) return;
-      for (const feature of result.features) rows.push([{ value: feature.name }]);
-      for (const cohort of result.cohorts) {
-        if (cohort.subcohorts?.length) continue;
-        columns.push({ label: cohort.name });
-        for (const [i, feature] of result.features.entries()) {
-          const cf = result.cfeatures.find((cf2) => cf2.idfeature === feature.idfeature && cf2.cohort === cohort.cohort);
-          if (cf) rows[i].push({ value: cf.value });
-        }
-      }
-      renderTable({
-        rows,
-        columns,
-        div: this.dom.cohortTable,
-        showLines: false,
-        maxHeight: "60vh",
-        header: { style: { "font-size": "1.2em", "font-weight": "bold" } }
-      });
-      this.dom.cohortTable.select("table").style("border-collapse", "collapse");
-      this.dom.cohortTable.selectAll(`tbody > tr > td`).style("background-color", "transparent").style("padding", "6px");
-      const state = this.app.getState();
-      const selectCohort = state.termdbConfig.selectCohort;
-      const activeCohort = state.activeCohort;
-      const keys = selectCohort.values[activeCohort].keys;
-      let selector = `tbody > tr > td:nth-child(${activeCohort + 2})`;
-      const combined = keys.length > 1;
-      if (combined) {
-        selector = "";
-        for (const key of keys) {
-          const i = result.cohorts.map((c) => c.cohort).indexOf(key);
-          if (selector !== "") selector += ",";
-          selector += `tbody > tr > td:nth-child(${i + 2})`;
-        }
-      }
-      const activeColumns = this.dom.cohortTable.selectAll(selector);
-      const color = state.termdbConfig.massNav?.activeColor || cohortTableActiveColor;
-      activeColumns.style("background-color", color);
-    };
-    this.initCustomHtml = () => {
-      if (this.selectCohort != null) return;
-      if (!this.aboutOverrides?.html) return;
-      this.subheader.append("div").attr("data-testid", "sjpp-custom-about-content").style("padding", "10px").html(this.aboutOverrides.html);
-    };
-    // render the world map (from termdbConfig.geomap) directly on the landing tab when the dataset opts in.
-    // the renderer (and its ~170KB world.json basemap) is dynamically imported so it never loads for
-    // datasets that don't enable the map.
-    this.initGeomap = async (appState) => {
-      if (!this.aboutOverrides?.showGeomap) return;
-      const geomap = appState.termdbConfig?.geomap;
-      if (!geomap?.sites?.length) return;
-      const holder = this.subheader.append("div").attr("data-testid", "sjpp-about-geomap").style("padding", "10px");
-      const { renderGeomap } = await import("./render-N5FOF247.js");
-      renderGeomap(holder, geomap);
-    };
-    this.initActiveItems = () => {
-      if (!this.aboutOverrides?.activeItems) return;
-      const div = this.subheader.append("div").attr("data-testid", "sjpp-custom-about-activeItems").style("padding", "0px 0px 10px 20px");
-      for (const item of this.aboutOverrides.activeItems.items) {
-        div.append("div").style("display", "inline-block").style("margin", "5px").attr("class", "sja_menuoption").attr("data-testid", "sjpp-custom-active-item-btn").html(item.title).on("click", async () => {
-          await this.app.dispatch({
-            type: "tab_set",
-            activeTab: 1
-          });
-          this.app.dispatch({
-            type: "plot_create",
-            id: getId(),
-            config: structuredClone(item.plot)
-          });
-        });
-      }
-    };
-    this.initDisclaimer = () => {
-      const d = this.aboutOverrides?.disclaimer;
-      if (!d) return;
-      const div = this.subheader.append("div").attr("data-testid", "sjpp-custom-about-disclaimer").style("margin", "10px 0 20px 10px").style("opacity", 0.7).style("padding", "10px").style("background-color", "#f8f9fa").style("border-left", "4px solid #6c757d").style("font-size", "0.8em");
-      div.append("div").style("margin-bottom", "8px").style("font-weight", "bold").text("DISCLAIMER");
-      div.append("div").text(d.text);
-    };
-    this.showServerInfo = () => {
-      const state = this.app.getState();
-      const about = state.termdbConfig.massNav?.tabs?.about;
-      if (!about && !this.app.opts.pkgver && !this.app.opts.launchDate) return;
-      const dataRelease = about?.dataRelease;
-      const additionalInfo = about?.additionalInfo;
-      const div = this.subheader.append("div").attr("data-testid", "sjpp-about-server-info").style("margin", "10px").style("font-size", ".8em");
-      const htmlArr = [];
-      if (dataRelease) {
-        htmlArr.push(`Data Release: <a href=${dataRelease.link} target=_blank>${dataRelease.version}</a>`);
-      }
-      if (this.app.opts.pkgver) {
-        htmlArr.push(
-          `Software Release: <a href=https://github.com/stjude/proteinpaint/pkgs/container/ppfull target=_blank>${this.app.opts.pkgver}</a>`
-        );
-      }
-      if (this.app.opts.launchDate) {
-        htmlArr.push(`Server Launched: ${this.app.opts.launchDate}`);
-      }
-      if (additionalInfo) {
-        htmlArr.push(additionalInfo);
-      }
-      div.append("div").html(htmlArr.join("; "));
-    };
-    this.opts = opts;
-    this.type = _MassAbout.type;
-    this.app = opts.app;
-    this.subheader = opts.subheader;
-    this.instanceNum = opts.instanceNum;
-    this.aboutOverrides = opts.aboutOverrides;
-    this.selectCohort = opts.selectCohort;
-    this.dom = {
-      cohortDescription: this.subheader.append("div").attr("data-testid", "sjpp-about-cohort-desc").style("margin-left", "10px")
-    };
-    if (opts?.selectCohort?.title) {
-      this.dom.cohortTitle = opts.subheader.append("h2").attr("data-testid", "sjpp-about-cohort-title").style("margin-left", "10px").text(opts.selectCohort.title);
-    }
-    if (opts.selectCohort?.prompt) {
-      this.dom.cohortPrompt = this.subheader.append("div").attr("data-testid", "sjpp-about-cohort-prompt").style("margin-left", "10px").style("padding-top", "30px").style("padding-bottom", "10px").style("font-weight", "bold").style("font-size", "1.2em").text(opts.selectCohort.prompt);
-    }
-    if (opts.selectCohort) {
-      this.dom.cohortOpts = this.subheader.append("div").style("margin-bottom", "30px").style("margin-left", "10px");
-    }
-  }
-  static {
-    this.type = "about";
-  }
-  /* render all contents into this.subheader
-  do it through init() means that contents are rendered just once on launching mass ui and won't be rerendered or updated
-  since there's no reason to update about tab contents while user is interacting with mass ui
-  */
-  init(appState) {
-    this.initCohort(appState);
-    this.initCustomHtml();
-    this.initGeomap(appState);
-    this.initActiveItems();
-    this.initDisclaimer();
-    this.showServerInfo();
-  }
-  async main() {
-    if (this.state.nav.activeTab !== 0) return;
-    await this.renderCohortsTable();
-    if (this.opts.selectCohort) {
-      if (this.opts.selectCohort.description) {
-        this.dom.cohortDescription.html(this.opts.selectCohort.description);
-      } else if (this.opts.selectCohort.descriptionByCohort) {
-        this.dom.cohortDescription.html(
-          this.opts.selectCohort.descriptionByCohort[this.state.termdbConfig.selectCohort.values[this.state.activeCohort].keys.join(",")]
-        );
-      }
-    }
-  }
-};
-var aboutInit = getCompInit(MassAbout);
-function joinByComma(arr) {
-  if (!arr.length) return "";
-  else if (arr.length == 1) return arr[0];
-  else if (arr.length == 2) return arr.join(" and ");
-  else return `${arr.slice(0, -1).join(", ")}, and ${arr.slice(-1)}`;
-}
-
-// mass/search.ts
-var MIN_PROMPT_LENGTH_FOR_OMNISEARCH = 3;
-var MAX_PROMPT_LENGTH_FOR_OMNISEARCH = 20;
-function makeMethylationRegionTerm(opts, vocabApi) {
-  const { chr, start, stop } = opts;
-  if (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error("invalid coordinate");
-  return {
-    chr,
-    start,
-    stop,
-    type: DNA_METHYLATION,
-    unit: getDNAMethUnit("region", vocabApi),
-    genomicFeatureType: "region"
-  };
-}
-async function embedMethylationRegionPicker(opts) {
-  const { holder, genomeObj, vocabApi, chr, start, stop, callback } = opts;
-  if (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error("unable to retrieve gene coordinate");
-  holder.selectAll("*").remove();
-  holder.style("display", "block");
-  holder.append("div").style("opacity", 0.6).text("Navigate genome browser to desired region");
-  const arg = {
-    holder,
-    genome: genomeObj,
-    // genome obj
-    chr,
-    start,
-    stop,
-    tklst: [],
-    nobox: true,
-    width: 500,
-    hidegenelegend: true,
-    debugmode: opts.debug
-  };
-  first_genetrack_tolist(genomeObj, arg.tklst);
-  const _ = await import("./block-NBTCOT3H.js");
-  const blockInstance = new _.Block(arg);
-  holder.append("div").attr("data-testid", "sjpp-dnaMethylation-submitDiv").style("margin", "10px 0px").append("button").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").text("Submit Region").on("click", async () => {
-    const { chr: chr2, start: start2, stop: stop2 } = blockInstance.rglst[0];
-    await callback(makeMethylationRegionTerm({ chr: chr2, start: start2, stop: stop2 }, vocabApi));
-  });
-  return blockInstance;
-}
-function parseCoordCandidates(prompt2) {
-  const m = /^\s*(\w+)\s*:\s*([\d,]+)\s*-\s*([\d,]+)\s*$/.exec(prompt2);
-  if (!m) return null;
-  const [, chrToken, start, stop] = m;
-  const chrCandidates = /^chr/i.test(chrToken) ? [chrToken, chrToken.replace(/^chr/i, "")] : [chrToken, "chr" + chrToken];
-  return chrCandidates.map((chr) => `${chr}:${start}-${stop}`);
-}
-async function handleOmnisearchKeyup(self, event2) {
-  if (keyupEnter(event2)) return;
-  const prompt2 = event2.target.value.trim();
-  if (!prompt2) {
-    self.dom.noMatchShown = false;
-    self.clear({ hide: true });
-    return;
-  }
-  const coordCandidates = parseCoordCandidates(prompt2);
-  if (coordCandidates || MIN_PROMPT_LENGTH_FOR_OMNISEARCH <= prompt2.length && prompt2.length <= MAX_PROMPT_LENGTH_FOR_OMNISEARCH) {
-    try {
-      await doSearch(self, prompt2, coordCandidates);
-    } catch (e) {
-      if (e.stack) console.log(e.stack);
-      sayerror(self.dom.resultDiv, "Error: " + (e.message || e));
-    }
-  } else {
-    self.dom.noMatchShown = false;
-    self.clear({ hide: true });
-  }
-}
-async function fetchOmnisearch(opts) {
-  const data = await dofetch3("termdb/chat", {
-    body: {
-      genome: opts.genome,
-      dslabel: opts.dslabel,
-      omnisearch: true,
-      prompt: opts.prompt,
-      cohortStr: opts.cohortStr,
-      usecase: opts.usecase,
-      treeFilter: opts.treeFilter,
-      coordCandidates: opts.coordCandidates || void 0
-    }
-  });
-  if (data.error) throw data.error;
-  return data;
-}
-function renderOmnisearchResults(self, data) {
-  const coord = data.coord || null;
-  const lst = Array.isArray(data.dictionaryTerms) ? data.dictionaryTerms : [];
-  const genes = Array.isArray(data.genes) ? data.genes : [];
-  const dictNames = new Set(lst.map((t) => t.name?.toUpperCase()));
-  const geneMap = /* @__PURE__ */ new Map();
-  for (const g of genes) {
-    const gene = g?.gene;
-    if (!gene || dictNames.has(gene.toUpperCase())) continue;
-    const dt = g.dataTypes || {};
-    const geneVariantTypes = [];
-    if (dt.snvindel) geneVariantTypes.push({ label: "SNV/indel", testid: "snvindel", dtCandidates: [dtsnvindel] });
-    if (dt.cnv) geneVariantTypes.push({ label: "CNV", testid: "cnv", dtCandidates: [dtcnv] });
-    if (dt.svfusion)
-      geneVariantTypes.push({ label: "SV/fusion", testid: "svfusion", dtCandidates: [dtsv, dtfusionrna] });
-    const entry = { name: gene, gene, isGene: true };
-    if (dt.geneExpression) entry.isGeneExpression = true;
-    if (geneVariantTypes.length) {
-      entry.isGeneVariant = true;
-      entry.geneVariantTypes = geneVariantTypes;
-    }
-    if (dt.genomeBrowser) {
-      entry.isGenomeBrowser = true;
-      entry.coord = g.coord;
-    }
-    if (dt.dnaMethylation) {
-      entry.isMethylation = true;
-      entry.coord = g.coord;
-    }
-    if (entry.isGeneExpression || entry.isGeneVariant || entry.isGenomeBrowser || entry.isMethylation) {
-      geneMap.set(gene.toUpperCase(), entry);
-    }
-  }
-  for (const entry of geneMap.values()) lst.push(entry);
-  if (coord) {
-    lst.push({
-      isCoord: true,
-      name: `${coord.chr}:${coord.start.toLocaleString()}-${coord.stop.toLocaleString()}`,
-      coord
-    });
-  }
-  if (!lst.length) {
-    if (!self.dom.noMatchShown) {
-      self.dom.noMatchShown = true;
-      self.noResult();
-    }
-  } else {
-    self.dom.noMatchShown = false;
-    self.showTerms({ lst });
-  }
-}
-async function doSearch(self, prompt2, coordCandidates) {
-  if (!prompt2) {
-    self.clear({ hide: true });
-    return;
-  }
-  const data = await fetchOmnisearch({
-    genome: self.app.vocabApi.vocab.genome,
-    dslabel: self.app.vocabApi.vocab.dslabel,
-    prompt: prompt2,
-    cohortStr: self.getState(self.app.getState()).cohortStr,
-    usecase: self.opts.usecase,
-    treeFilter: self.app.vocabApi.state?.treeFilter,
-    coordCandidates
-  });
-  renderOmnisearchResults(self, data);
-}
-function setSearchRenderers(self) {
-  let text = "No match";
-  if (self.isChat) {
-    text = "No match. Using the chatbot...";
-  }
-  self.noResult = () => {
-    self.clear();
-    self.dom.resultDiv.append("div").text(text).style("padding", "3px 3px 3px 0px").style("opacity", 0.5);
-    setTimeout(() => {
-      self.clear({ hide: true });
-    }, 1500);
-  };
-  self.showTerms = (data) => {
-    if (self.opts.disable_terms)
-      data.lst.forEach((t) => {
-        if (t.disabled) self.opts.disable_terms.push(t);
-      });
-    self.clear({ hide: !data.lst.length });
-    if (data.lst.length) {
-      self.dom.resultDiv.append("table").selectAll().data(data.lst).enter().append("tr").each(self.showTerm);
-    }
-  };
-  self.launchPlot = async (config) => {
-    if (self.state?.nav?.activeTab == 0) {
-      await self.app.dispatch({ type: "tab_set", activeTab: 1 });
-    }
-    self.app.dispatch({ type: "plot_create", config });
-    self.dom.inputNode.value = "";
-    self.clear({ hide: true });
-  };
-  self.launchGeneVariantPlot = async (gene, dtCandidates) => {
-    let tw;
-    let lastErr;
-    for (const dt of dtCandidates) {
-      const candidate = {
-        term: {
-          id: gene,
-          name: gene,
-          genes: [{ kind: "gene", id: gene, gene, name: gene, type: "geneVariant" }],
-          type: "geneVariant"
-        },
-        q: { type: "predefined-groupset", dtLst: [dt] }
-      };
-      try {
-        await fillTermWrapper(candidate, self.app.vocabApi);
-        tw = candidate;
-        break;
-      } catch (e) {
-        lastErr = e;
-      }
-    }
-    if (!tw) throw lastErr;
-    await self.launchPlot({ chartType: "summary", term: tw });
-  };
-  self.launchGenomeBrowserView = async (mode, opts) => {
-    if (mode == "protein") {
-      if (!opts.gene) throw new Error("gene symbol required for protein view");
-      await self.launchPlot({
-        chartType: "genomeBrowser",
-        geneSearchResult: { geneSymbol: opts.gene },
-        blockIsProteinMode: true
-      });
-      return;
-    }
-    if (!opts.coord) throw new Error("coordinate required for genomic view");
-    await self.launchPlot({
-      chartType: "genomeBrowser",
-      geneSearchResult: { chr: opts.coord.chr, start: opts.coord.start, stop: opts.coord.stop },
-      blockIsProteinMode: false
-    });
-  };
-  self.launchGenomeBrowser = async (gene, coord) => {
-    const gbRestrictMode = self.app.getState().termdbConfig?.queries?.gbRestrictMode;
-    if (gbRestrictMode == "protein") {
-      await self.launchGenomeBrowserView("protein", { gene });
-      return;
-    }
-    if (gbRestrictMode == "genomic") {
-      if (!coord) throw new Error(`Unable to resolve genomic coordinates for gene "${gene}".`);
-      await self.launchGenomeBrowserView("genomic", { coord });
-      return;
-    }
-    self.dom.tip.clear();
-    self.dom.tip.showunder(self.dom.inputNode);
-    const holder = self.dom.resultDiv.append("div").style("margin", "10px");
-    holder.append("div").style("margin-bottom", "5px").text(gene);
-    const btndiv = holder.append("div");
-    const addViewBtn = (label, testid, mode) => {
-      btndiv.append("button").attr("data-testid", testid).style("margin-right", "10px").text(label).on(
-        "click",
-        () => void self.launchGenomeBrowserView(mode, { gene, coord }).catch((e) => sayerror(self.dom.resultDiv, "Error: " + (e?.message || e)))
-      );
-    };
-    addViewBtn(`Protein view of ${gene}`, `sjpp-mass-chat-gb-protein-${gene}`, "protein");
-    if (coord) addViewBtn(`Genomic view of ${gene}`, `sjpp-mass-chat-gb-genomic-${gene}`, "genomic");
-  };
-  self.launchMethylationPlot = async (gene, coord) => {
-    if (!coord) throw new Error(`Could not resolve coordinates for gene "${gene}"`);
-    self.dom.tip.clear();
-    self.dom.tip.showunder(self.dom.inputNode);
-    const holder = self.dom.resultDiv.append("div").style("margin", "10px");
-    holder.append("div").style("margin-bottom", "5px").text(gene);
-    await embedMethylationRegionPicker({
-      holder: holder.append("div"),
-      genomeObj: self.app.opts.genome,
-      vocabApi: self.app.vocabApi,
-      chr: coord.chr,
-      start: coord.start,
-      stop: coord.stop,
-      callback: async (term) => {
-        await self.launchPlot({ chartType: "summary", term: { term } });
-      }
-    });
-  };
-  self.showTerm = function(term) {
-    const tr = select_default(this);
-    if (term.isCoord) {
-      tr.append("td").text(term.name).style("padding", "5px 10px");
-      tr.append("td").append("span").attr("class", "sja_menuoption").attr("data-testid", "sjpp-mass-chat-coord-genomebrowser").style("display", "inline-block").style("margin", "0px 3px").style("padding", "5px 10px").style("border-radius", "5px").style("cursor", "pointer").text("Genome Browser").on(
-        "click",
-        () => void self.launchGenomeBrowserView("genomic", { coord: term.coord }).catch((e) => sayerror(self.dom.resultDiv, "Error: " + (e?.message || e)))
-      );
-      return;
-    }
-    if (term.isGene) {
-      tr.append("td").text(term.name).style("padding", "5px 10px");
-      const btnTd = tr.append("td");
-      const addBtn = (label, testid, onClick) => {
-        btnTd.append("span").attr("class", "sja_menuoption").attr("data-testid", testid).style("display", "inline-block").style("margin", "0px 3px").style("padding", "5px 10px").style("border-radius", "5px").style("cursor", "pointer").text(label).on("click", () => void onClick().catch((e) => sayerror(self.dom.resultDiv, "Error: " + (e?.message || e))));
-      };
-      if (term.isGeneExpression) {
-        addBtn("Gene expression", `sjpp-mass-chat-gene-exp-${term.gene}`, async () => {
-          await self.launchPlot({
-            chartType: "summary",
-            term: { term: { gene: term.gene, name: term.name, type: "geneExpression" } }
-          });
-        });
-      }
-      if (term.isGeneVariant) {
-        for (const vt of term.geneVariantTypes || []) {
-          addBtn(vt.label, `sjpp-mass-chat-gene-${vt.testid}-${term.gene}`, async () => {
-            await self.launchGeneVariantPlot(term.gene, vt.dtCandidates);
-          });
-        }
-      }
-      if (term.isGenomeBrowser) {
-        addBtn("Genome Browser", `sjpp-mass-chat-gene-genomebrowser-${term.gene}`, async () => {
-          await self.launchGenomeBrowser(term.gene, term.coord);
-        });
-      }
-      if (term.isMethylation) {
-        addBtn("DNA methylation", `sjpp-mass-chat-gene-methylation-${term.gene}`, async () => {
-          await self.launchMethylationPlot(term.gene, term.coord);
-        });
-      }
-      return;
-    }
-    const button = tr.append("td").text(term.name);
-    if (term.type) {
-      button.style("cursor", "pointer").attr("class", "sja_menuoption").attr("data-testid", `sjpp-mass-chat-term-${term.id}`).on("click", async () => {
-        await self.launchPlot({
-          chartType: term.type == "survival" ? "survival" : "summary",
-          term: { term }
-        });
-      });
-    } else {
-      button.style("padding", "5px 10px").style("opacity", 0.5);
-    }
-    tr.append("td").text((term.__ancestorNames || []).join(" > ")).style("opacity", 0.5).style("font-size", ".7em");
-  };
-  self.clear = (opts = {}) => {
-    self.dom.tip.clear();
-    if (opts.hide) self.dom.tip.hide();
-    else self.dom.tip.showunder(self.dom.inputNode);
-  };
-}
-
-// mass/chat.ts
-var MIN_PROMPT_LENGTH_FOR_CHAT = 5;
-var MassAiChatBot = class _MassAiChatBot {
-  static {
-    this.type = "chat";
-  }
-  constructor(opts) {
-    this.type = _MassAiChatBot.type;
-    this.opts = opts;
-    this.app = opts.app;
-    this.opts.usecase = this.opts.usecase || { target: "dictionary", detail: "term" };
-    this.opts.targetType = this.opts.targetType ? this.opts.targetType : "Dictionary Variables";
-    this.isChat = this.app.getState().termdbConfig?.queries?.chat;
-    setSearchRenderers(this);
-  }
-  getState(appState) {
-    return {
-      cohortStr: appState.activeCohort == -1 || !appState.termdbConfig.selectCohort ? "" : appState.termdbConfig.selectCohort.values[appState.activeCohort].keys.slice().sort().join(","),
-      search: appState.search,
-      nav: appState.nav
-    };
-  }
-  async init() {
-    this.initDom();
-  }
-  initDom() {
-    let text = "Search an item";
-    let height = "1px";
-    if (this.isChat) {
-      text = "Ask a question";
-      height = "200px";
-    }
-    this.dom = {
-      tip: new Menu({ padding: "5px" }),
-      div: this.opts.subheader,
-      error: this.opts.subheader.append("div").attr("id", "sjpp-corrVolcano-error").style("opacity", 0.75),
-      bubbleDiv: this.opts.subheader.append("div").attr("class", "sjpp_show_scrollbar").style("margin", "5px 20px 0px 20px").style("height", height).style("overflow", "auto").style("scroll-behavior", "smooth")
-    };
-    const inputSel = this.dom.div.append("input").attr("type", "search").attr("data-testid", "sjpp-mass-omnisearch-input").style("margin", "15px").style("padding", "17px").style("border-radius", "34px").attr("size", 70).attr("placeholder", text);
-    this.dom.inputNode = inputSel.node();
-    this.dom.resultDiv = this.dom.tip.d.style("border-left", "solid 1px rgb(133,182,225)").style("padding-left", "5px").attr("tabindex", -1);
-    inputSel.on("keyup.search", (event2) => handleOmnisearchKeyup(this, event2)).on("keyup.submit", async (event2) => {
-      if (!keyupEnter(event2)) return;
-      if (!this.isChat) {
-        return;
-      }
-      const prompt2 = event2.target.value.trim();
-      if (!prompt2) return;
-      this.addBubble({ msg: escapeHtml(prompt2), me: 1 });
-      event2.target.value = "";
-      const serverBubble = this.addBubble({ msg: "..." });
-      if (prompt2.length <= MIN_PROMPT_LENGTH_FOR_CHAT) {
-        serverBubble.text("Your prompt is too short. Enter a longer prompt.");
-        return;
-      }
-      const body = {
-        genome: this.app.vocabApi.vocab.genome,
-        dslabel: this.app.vocabApi.vocab.dslabel,
-        filter: this.app.vocabApi.state.termfilter?.filter,
-        prompt: prompt2
-      };
-      try {
-        const data = await dofetch3("termdb/chat", { body });
-        if (data.error) throw data.error;
-        const result = data;
-        if (result.type === "text") {
-          serverBubble.text(result.text);
-        } else if (result.type === "html") {
-          serverBubble.html(result.html);
-        } else if (result.type === "plot") {
-          const optionField = findPossibleOptionsField(result.plot);
-          if (optionField) {
-            this.showPossibleOptions(serverBubble, result.plot, optionField, result.msg);
-          } else {
-            this.app.dispatch({
-              type: "plot_create",
-              config: result.plot
-            });
-            serverBubble.text(`${result.msg ? result.msg + ". " : ""}Please refer to the plot generated below.`);
-          }
-        }
-      } catch (e) {
-        if (e.stack) console.log(e.stack);
-        serverBubble.html(`Error: ${e.message || e}`);
-      }
-    }).node().focus();
-  }
-  addBubble(arg) {
-    const bubble = this.dom.bubbleDiv.append("div").style("padding", "10px").html(`${arg.me ? '<span style="font-size:.7em">[ME]</span> ' : ""}${arg.msg}`);
-    if (arg.me) bubble.style("background", "#f1f1f1");
-    const n = this.dom.bubbleDiv.node();
-    n.scrollTop = n.scrollHeight;
-    return bubble;
-  }
-  // Render click boxes for an incomplete plot state. `fieldKey` is the field of `plot` whose
-  // value holds `possible_options`. Clicking a box completes the plot state and dispatches plot_create.
-  // Each option completes the plot in one of two ways:
-  //  - opt.config: a config patch merged into the plot (the incomplete field is dropped). Used when the
-  //    choice sets other fields, e.g. the genome browser view sets blockIsProteinMode: true|false.
-  //  - otherwise: the incomplete field is set to { id: opt.id }, e.g. survival term selection -> term:{id}.
-  showPossibleOptions(bubble, plot, fieldKey, msg) {
-    const options = plot[fieldKey].possible_options || [];
-    bubble.text(`${msg ? msg + ". " : ""}Multiple options are available. Please select one:`);
-    const boxDiv = bubble.append("div").style("margin-top", "5px");
-    for (const opt of options) {
-      boxDiv.append("div").attr("class", "sja_menuoption").attr("data-testid", `sjpp-mass-chat-option-${opt.id}`).style("display", "inline-block").style("margin", "3px").style("padding", "5px 10px").style("border-radius", "5px").style("cursor", "pointer").text(opt.name).on("click", () => {
-        const config = JSON.parse(JSON.stringify(plot));
-        if (opt.config) {
-          delete config[fieldKey];
-          Object.assign(config, opt.config);
-        } else {
-          config[fieldKey] = { id: opt.id };
-        }
-        this.app.dispatch({
-          type: "plot_create",
-          config
-        });
-        bubble.selectAll("*").remove();
-        bubble.text(`Selected "${opt.name}". Please refer to the plot generated below.`);
-      });
-    }
-  }
-  main() {
-    if (this.opts.subheader.style("display") == "none") {
-      this.dom.inputNode.blur();
-      return;
-    }
-    if (this.opts?.focus != "off") this.dom.inputNode.focus();
-  }
-};
-var chatInit = getCompInit(MassAiChatBot);
-function escapeHtml(s) {
-  return s.replace(/&/g, "&amp;").replace(/</g, "&lt;").replace(/>/g, "&gt;").replace(/"/g, "&quot;").replace(/'/g, "&#39;");
-}
-function findPossibleOptionsField(plot) {
-  if (!plot || typeof plot !== "object") return null;
-  for (const key of Object.keys(plot)) {
-    const val = plot[key];
-    if (val && typeof val === "object" && Array.isArray(val.possible_options)) return key;
-  }
-  return null;
-}
-
-// mass/nav.js
-var activeTabBgColor = "#ececec";
-var activeTabBgColorHover = "#e0e0e0";
-var activeTabTextColor = "black";
-var inactiveTabBgColorHover = "#fcfced";
-var inactiveTabTextColor = "gray";
-var instanceNum = 0;
-var idPrefix = "_MASS_AUTOID_" + Math.random().toString().slice(-6);
-var id = (+/* @__PURE__ */ new Date()).toString().slice(-8);
-var headtip = new Menu({ padding: "0px", offsetX: 0, offsetY: 0 });
-headtip.d.style("z-index", 5555);
-var aboutTab = { top: "ABOUT", mid: "", btm: "", subheader: "about" };
-var chartTab = { top: "CHARTS", mid: "NONE", btm: "", subheader: "charts" };
-var groupsTab = { top: "GROUPS", mid: "NONE", btm: "", subheader: "groups" };
-var filterTab = { top: "FILTER", mid: "NONE", btm: "", subheader: "filter" };
-function getId() {
-  return idPrefix + "_" + id++;
-}
-var TdbNav = class _TdbNav {
-  static type = "nav";
-  constructor(opts) {
-    this.type = _TdbNav.type;
-    this.instanceNum = instanceNum++;
-    this.tabs = [];
-    this.activeTab = 0;
-    this.activeCohort = 0;
-    this.samplecounts = {};
-    this.searching = false;
-    this.massSessionDuration = opts.massSessionDuration;
-    this.sessionDaysLeft = opts.app.opts.sessionDaysLeft || null;
-    this.sessionId = opts.app.opts.sessionId || null;
-    this.pkgver = opts.pkgver || null;
-    setInteractivity(this);
-    setRenderers(this);
-  }
-  async init(appState) {
-    try {
-      this.cohortFilter = getFilterItemByTag(appState.termfilter.filter, "cohortFilter");
-      this.initUI(appState);
-      if (appState?.termdbConfig?.selectCohort) {
-        this.dom.tds.filter((d) => d.colNum === 0).style("display", "");
-        this.cohortNames = appState.termdbConfig.selectCohort.values.map((d) => d.keys.slice().sort().join(","));
-      }
-      this.components = await multiInit({
-        filter: filterRxCompInit({
-          app: this.app,
-          vocabApi: this.app.vocabApi,
-          holder: this.dom.subheader.filter.append("div").style("margin", "5px"),
-          hideLabel: this.opts.header_mode === "with_tabs",
-          emptyLabel: "+Add new filter",
-          callback: (filter) => {
-            this.app.dispatch({
-              type: "filter_replace",
-              filter
-            });
-          }
-        }),
-        charts: chartsInit({
-          app: this.app,
-          holder: this.dom.subheader.charts,
-          vocab: this.opts.vocab
-        }),
-        groups: groupsInit({
-          app: this.app,
-          holder: this.dom.subheader.groups,
-          vocab: this.opts.vocab
-        }),
-        recover: recoverInit({
-          app: this.app,
-          holder: this.dom.recoverDiv,
-          // TODO: ???? may limit the tracked state to only the filter, activeCohort ???
-          getState: (appState2) => appState2,
-          reactsTo: (action) => action.type != "plot_edit",
-          maxHistoryLen: 5
-        }),
-        sessionBtn: sessionBtnInit({
-          app: this.app,
-          button: this.dom.saveBtn,
-          massSessionDuration: this.opts.massSessionDuration,
-          sessionDaysLeft: this.app.opts.sessionDaysLeft || null
-        }),
-        about: aboutInit({
-          app: this.app,
-          subheader: this.dom.subheader.about,
-          instanceNum: this.instanceNum,
-          aboutOverrides: appState?.termdbConfig?.massNav?.tabs?.about || null,
-          selectCohort: appState?.termdbConfig?.selectCohort || null
-        }),
-        chat: chatInit({
-          app: this.app,
-          subheader: this.dom.subheader.chat
-        })
-      });
-      this.mayShowMessage_sessionDaysLeft();
-    } catch (e) {
-      throw e;
-    }
-  }
-  reactsTo(action) {
-    if (action.type.includes("cache_termq")) return true;
-    if (action.type.startsWith("filter")) return true;
-    if (action.type.startsWith("cohort")) return true;
-    if (action.type.startsWith("tab")) return true;
-    if (action.type == "plot_prep") return true;
-    if (action.type == "plot_create") return true;
-    if (action.type == "plot_delete") return true;
-    if (action.type == "app_refresh") return true;
-    if (action.type.endsWith("_customTerm")) return true;
-    if (action.type.endsWith("_group")) return true;
-  }
-  getState(appState) {
-    return {
-      searching: this.searching,
-      // for detection of internal state change
-      nav: appState.nav,
-      activeCohort: appState.activeCohort,
-      termdbConfig: appState.termdbConfig,
-      filter: appState.termfilter.filter,
-      plots: appState.plots,
-      groups: appState.groups
-    };
-  }
-  async main() {
-    this.dom.tabDiv.style("display", this.state.nav.header_mode === "with_tabs" ? "inline-block" : "none");
-    this.dom.tip.hide();
-    this.activeTab = this.state.nav.activeTab;
-    this.prevCohort = this.activeCohort;
-    this.activeCohort = +this.state.activeCohort;
-    this.filterUiRoot = getFilterItemByTag(this.state.filter, "filterUiRoot");
-    this.cohortFilter = getFilterItemByTag(this.state.filter, "cohortFilter");
-    if (this.cohortNames) {
-      this.activeCohortName = this.cohortNames[this.activeCohort];
-      if (this.activeCohort !== -1)
-        this.activeCohortLabel = this.state.termdbConfig.selectCohort.values[this.activeCohort].shortLabel;
-    }
-    this.filterJSON = JSON.stringify(this.state.filter);
-    this.cohortsData = await this.app.vocabApi.getCohortsData();
-    if (this.state.nav.header_mode === "with_tabs") {
-      if (!(this.activeCohort in this.samplecounts)) {
-        this.samplecounts[this.activeCohort] = await this.app.vocabApi.getCohortSampleCount(this.activeCohortName);
-      }
-      if (!(this.filterJSON in this.samplecounts)) {
-        if (!this.filterUiRoot || !this.filterUiRoot.lst.length) {
-          this.samplecounts[this.filterJSON] = this.samplecounts[this.activeCohort];
-        } else {
-          const n = await this.app.vocabApi.getFilteredSampleCount(this.filterJSON);
-          this.samplecounts[this.filterJSON] = n;
-        }
-      }
-    }
-    this.updateUI();
-  }
-};
-var navInit = getCompInit(TdbNav);
-function setRenderers(self) {
-  self.initUI = (appState) => {
-    const verifiedToken = self.app.vocabApi.verifiedToken;
-    const invalidTokenErrorHandling = appState.termdbConfig.invalidTokenErrorHandling;
-    if (!verifiedToken && invalidTokenErrorHandling?.affectedCharts?.includes("*"))
-      throw new Error(appState.termdbConfig.invalidTokenErrorHandling.errorMessage);
-    const header = self.opts.holder.append("div").style("white-space", "nowrap");
-    const massNav = appState.termdbConfig?.massNav || {};
-    let titleDiv = header.append("div").style("display", "inline-block").style("float", "right").style("font-size", "1.1em").style("margin", "50px 10px 0 0").text(massNav?.title?.text);
-    const tabDiv = header.append("div").style("display", "none").style("vertical-align", "bottom");
-    const controlsDiv = header.append("div").style("vertical-align", "top").style("margin", "10px").style("display", "inline-block").style("float", "right");
-    if (self.opts.header_mode === "only_buttons") {
-      tabDiv.style("display", "none");
-      titleDiv.style("display", "none");
-      controlsDiv.style("display", "none");
-    }
-    self.opts.holder.attr("class", "sjpp-nav");
-    self.dom = {
-      holder: self.opts.holder,
-      header,
-      tabDiv,
-      controlsDiv,
-      searchDiv: controlsDiv.append("div").style("margin", "10px"),
-      sessionDiv: controlsDiv.append("div").style("display", "inline-block"),
-      recoverDiv: controlsDiv.append("div").style("display", "inline-block"),
-      pdfDiv: controlsDiv.append("div").style("display", "inline-block").style("padding", "4px").style("vertical-align", "middle"),
-      deleteAllDiv: controlsDiv.append("div").style("display", "inline-block").style("padding", "4px").style("vertical-align", "middle"),
-      helpDiv: controlsDiv.append("div").style("display", "none"),
-      sessionElapsedMessageDiv: controlsDiv.append("div").style("display", "none"),
-      subheaderDiv: self.opts.holder.append("div").style("display", "block").style("border-bottom", "1px solid #000"),
-      messageDiv: self.opts.holder.append("div").style("margin", "30px").style("display", "none"),
-      titleDiv,
-      tip: new Menu({ padding: "5px" })
-    };
-    icons["trash"](self.dom.deleteAllDiv, {
-      handler: self.deletePlots,
-      title: "Delete all plots. To revert, click Undo button"
-    });
-    icons["pdf"](self.dom.pdfDiv, {
-      handler: self.opts.downloadPlots,
-      title: "Generate a PDF of all the plots opened"
-    });
-    if (self.opts.header_mode === "with_cohortHtmlSelect") {
-      self.dom.cohortStandaloneDiv = header.append("div").style("display", "inline-block").style("margin", "10px").style("vertical-align", "top");
-      self.dom.cohortStandaloneDiv.append("label").html("Cohort: ");
-      self.dom.cohortSelect = self.dom.cohortStandaloneDiv.append("select").on("change", async function() {
-        self.app.dispatch({ type: "cohort_set", activeCohort: +this.value });
-      });
-      self.dom.cohortSelect.selectAll("option").data(appState.termdbConfig.selectCohort.values).enter().append("option").attr("value", (d, i) => i).property("selected", (d, i) => i === appState.activeCohort).html((d) => d.shortLabel);
-    }
-    self.dom.subheader = Object.freeze({
-      // For either the COHORT or ABOUT tab
-      about: self.dom.subheaderDiv.append("div").attr("data-testid", "sjpp-mass-nav-subheader-about").style("display", "none"),
-      search: self.dom.subheaderDiv.append("div").attr("data-testid", "sjpp-mass-nav-subheader-search").style("display", "none"),
-      groups: self.dom.subheaderDiv.append("div").attr("data-testid", "sjpp-mass-nav-subheader-groups").style("display", "none"),
-      charts: self.dom.subheaderDiv.append("div").attr("data-testid", "sjpp-mass-nav-subheader-charts").style("display", "none"),
-      filter: self.dom.subheaderDiv.append("div").attr("data-testid", "sjpp-mass-nav-subheader-filter").style("display", "none"),
-      chat: self.dom.subheaderDiv.append("div").attr("data-testid", "sjpp-mass-nav-subheader-chat").style("display", "none")
-      // cart: self.dom.subheaderDiv.append('div').style('display', 'none').html('<br/>Cart feature under construction - work in progress<br/>&nbsp;<br/>'),
-    });
-    if (!massNav.tabs?.about?.hide) {
-      self.tabs.push(aboutTab);
-      const override = Object.assign({}, massNav.tabs?.about);
-      if (appState.termdbConfig?.selectCohort) {
-        if (!override.top) override.top = "COHORT";
-      } else {
-        if (!override.mid) override.mid = self.pickDatasetLabel(appState);
-      }
-      Object.assign(aboutTab, override);
-    }
-    if (!massNav.tabs?.charts?.hide) {
-      self.tabs.push(chartTab);
-      Object.assign(chartTab, massNav.tabs?.charts);
-    }
-    if (!massNav.tabs?.groups?.hide) {
-      self.tabs.push(groupsTab);
-      Object.assign(groupsTab, massNav.tabs?.groups);
-    }
-    if (!massNav.tabs?.filter?.hide) {
-      self.tabs.push(filterTab);
-      Object.assign(filterTab, massNav.tabs?.filter);
-    }
-    if (!massNav.tabs?.chat?.hide) {
-      if (appState.termdbConfig?.queries?.chat) {
-        const chatTab = { top: "CHAT", mid: "", btm: "", subheader: "chat" };
-        Object.assign(chatTab, massNav.tabs?.chat);
-        chatTab.top = "CHAT";
-        self.tabs.push(chatTab);
-      } else {
-        const searchTab = { top: "SEARCH", mid: "", btm: "", subheader: "chat" };
-        Object.assign(searchTab, massNav.tabs?.chat);
-        searchTab.top = "SEARCH";
-        self.tabs.push(searchTab);
-      }
-    }
-    const table = self.dom.tabDiv.append("table").attr("data-testid", "sjpp-nav-tabs-table").style("border-collapse", "collapse");
-    table.selectAll("tr").data(["top", "mid", "btm"]).enter().append("tr").attr("class", (d, i) => `sjpp-nav-tabs-row-${i}`).style("font-size", (d, i) => i == 1 ? "20px" : "12px").selectAll("td").data(
-      (key, i) => self.tabs.map((row, colNum) => {
-        return {
-          rowNum: i,
-          key,
-          colNum,
-          label: row[key],
-          subheader: row.subheader,
-          disabled: row.disabled,
-          disabledMessage: row.disabledMessage
-        };
-      })
-    ).enter().append("td").attr("class", (d) => `sjpp-nav-tab-col-${d.colNum}`).style("display", "none").style("width", "100px").style("padding", (d) => d.rowNum === 0 ? "12px 12px 3px 12px" : "3px 12px").style("text-align", "center").style("border-left", "1px solid #ccc").style("border-right", "1px solid #ccc").style("color", "#aaa").style("opacity", (d) => d.disabled ? 0.5 : 1).style("cursor", (d) => d.disabled ? "not-allowed" : "pointer").attr("title", (d) => d.disabledMessage || "").html((d) => d.label).on("click", (event2, d) => {
-      self.setTab(event2, d);
-    }).on("mouseover", (event2, d) => {
-      self.mouseover(event2, d);
-    }).on("mouseout", () => {
-      self.mouseout();
-    });
-    self.dom.trs = table.selectAll("tr");
-    self.dom.tds = table.selectAll("td");
-    self.subheaderKeys = self.tabs.map((d) => d.subheader);
-    self.dom.saveBtn = self.dom.sessionDiv.append("button").attr("data-testid", "sjpp-nav-session-btn").style("margin", "10px").text("Session \u25BC");
-    if (self.sessionDaysLeft != null) {
-      self.dom.fileBtn = self.dom.sessionDiv.append("button").attr("data-testid", "sjpp-nav-file-btn").style("margin", "10px").text("Export Session").on("click", (event2) => {
-        self.getSessionFile(event2);
-      });
-    }
-  };
-  self.deletePlots = () => {
-    const state = self.app.getState();
-    const subactions = [];
-    for (const plot of state.plots) subactions.push({ type: "plot_delete", id: plot.id });
-    self.app.dispatch({ type: "app_refresh", subactions });
-  };
-  self.mayShowMessage_sessionDaysLeft = () => {
-    if (!Number.isFinite(self.sessionDaysLeft)) {
-      return;
-    }
-    self.dom.sessionElapsedMessageDiv.style("display", "block");
-    self.dom.remainingDaysMessage = self.dom.sessionElapsedMessageDiv.append("div").style("display", "block").style("opacity", "0.65").html(
-      `<u>${self.sessionDaysLeft} days</u> left until this session is removed. Click the "Session \u25BC" button and select "Save" option to create a new one.`
-    );
-  };
-  self.updateUI = async () => {
-    if (!self.dom.subheaderDiv) return;
-    if (self.activeTab && self.state.termdbConfig.selectCohort && self.activeCohort == -1) {
-      self.dom.subheaderDiv.style("display", "none");
-      self.dom.messageDiv.selectAll("text").remove();
-      self.dom.messageDiv.style("display", "").text('No cohort selected. Please select a cohort in the "COHORT" tab.');
-    } else {
-      if (self.dom.subheaderDiv) self.dom.subheaderDiv.style("display", self.activeTab != -1 ? "block" : "none");
-      if (self.dom.messageDiv) self.dom.messageDiv.style("display", "none");
-    }
-    const selectCohort = self.state.termdbConfig.selectCohort;
-    const massNav = self.state.termdbConfig.massNav;
-    self.dom.searchDiv.style("display", selectCohort && self.activeCohort == -1 ? "none" : "inline-block");
-    self.dom.header.style("border-bottom", self.state.nav.header_mode === "with_tabs" ? "1px solid #000" : "");
-    self.dom.tds.style("display", "").style("color", (d) => d.colNum == self.activeTab ? activeTabTextColor : inactiveTabTextColor).style(
-      "background-color",
-      (d) => d.colNum == self.activeTab && self.dom.subheaderDiv.style("display") != "none" ? self.state.termdbConfig.massNav?.activeColor || activeTabBgColor : "transparent"
-    ).html(function(d, i) {
-      if (d.key == "top") return this.innerHTML;
-      if (d.subheader == "groups") {
-        if (d.key == "mid") return self.state.groups.length || "NONE";
-        return "";
-      }
-      if (d.subheader === "charts") {
-        const n = self.state.plots.filter((p) => !p.parentId).length;
-        if (d.key == "mid") return !n ? "NONE" : n;
-        else return "";
-      } else if (d.subheader === "about") {
-        if (self.activeCohort != -1 && self.activeCohort in self.samplecounts) {
-          const aboutMap = {
-            top: this.innerHTML,
-            mid: self.activeCohortLabel,
-            btm: self.samplecounts[self.activeCohort]
-          };
-          return aboutMap[d.key] || "";
-        } else if (!selectCohort) {
-          const aboutMap = {
-            top: massNav?.tabs?.about?.top || "ABOUT",
-            mid: massNav?.tabs?.about?.mid || this.innerHTML,
-            btm: massNav?.tabs?.about?.btm || self.samplecounts[self.activeCohort]
-          };
-          return aboutMap[d.key] || "";
-        } else {
-          return d.key === "mid" ? "NONE" : this.innerHTML;
-        }
-      } else if (d.subheader === "filter") {
-        const filter = self.filterUiRoot ? self.filterUiRoot : { lst: [] };
-        if (filter.lst.length === 0) {
-          return d.key === "mid" ? "NONE" : "";
-        } else {
-          const n = self.samplecounts[self.filterJSON] != void 0 ? "" + self.samplecounts[self.filterJSON] : "";
-          return d.key === "mid" ? filter.lst.length : n;
-        }
-      } else {
-        return d.key === "mid" ? this.innerHTML : "&nbsp;";
-      }
-    });
-    for (const key in self.dom.subheader) {
-      self.dom.subheader[key].style(
-        "display",
-        self.activeTab == -1 ? "none" : self.tabs[self.activeTab].subheader === key ? "block" : "none"
-      );
-    }
-    if (self.opts.header_mode === "with_cohortHtmlSelect") {
-      self.dom.cohortSelect.selectAll("option").property("value", self.activeCohort);
-    }
-  };
-}
-function setInteractivity(self) {
-  self.setTab = async (event2, d) => {
-    if (d.disabled) return;
-    if (d.colNum === self.activeTab && !self.searching) {
-      if (self.activeTab == 0) return;
-      self.prevCohort = self.activeCohort;
-      await self.updateUI();
-      self.app.dispatch({ type: "tab_set", activeTab: -1 });
-      return;
-    }
-    self.activeTab = d.colNum;
-    self.searching = false;
-    self.app.dispatch({ type: "tab_set", activeTab: self.activeTab });
-    const chartsIdx = self.subheaderKeys.indexOf("charts");
-    if (self.activeTab == chartsIdx && self.activeCohort != -1 && !self.state.plots.length) {
-      const defaultChartType = self.state.termdbConfig.defaultChartType || "dictionary";
-      self.app.dispatch({
-        type: "plot_create",
-        id: getId(),
-        config: { chartType: defaultChartType }
-      });
-    }
-  };
-  self.mouseover = (event2, d) => {
-    const defaultActiveColor = self.state.termdbConfig.massNav?.activeColor || activeTabBgColor;
-    self.dom.tds.style("background-color", (t) => {
-      if (t.colNum === d.colNum)
-        return self.activeTab == t.colNum ? self.state.termdbConfig.massNav?.activeColorHover || activeTabBgColorHover : inactiveTabBgColorHover;
-      return self.activeTab == t.colNum ? defaultActiveColor : "transparent";
-    });
-  };
-  self.mouseout = () => {
-    const defaultActiveColor = self.state.termdbConfig.massNav?.activeColor || activeTabBgColor;
-    self.dom.tds.style("background-color", (t) => self.activeTab == t.colNum ? defaultActiveColor : "transparent");
-  };
-  self.getSessionFile = async (event2) => {
-    const res = await dofetch3(`/massSession?id=${self.sessionId}`);
-    const a = document.createElement("a");
-    const dataStr = "data:application/json;charset=utf-8," + encodeURIComponent(JSON.stringify(res.state));
-    a.setAttribute("href", dataStr);
-    a.download = `${self.sessionId}.json`;
-    a.click();
-    a.remove();
-  };
-  self.pickDatasetLabel = (appState) => {
-    const dslabel = appState.vocab.dslabel.toUpperCase();
-    return dslabel.length > 10 ? `${dslabel.slice(0, 10)}...` : dslabel;
-  };
-}
-
-export {
-  getId,
-  navInit
-};
-//# sourceMappingURL=chunk-DBKNWR4J.js.map