@sjcrh/proteinpaint-client 2.196.0 → 2.198.0

package/dist/chunk-DBKNWR4J.js

@@ -0,0 +1,1561 @@
+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