@sjcrh/proteinpaint-client 2.190.2 → 2.191.2

package/dist/AppHeader-4AZ76NN3.js

@@ -1,835 +0,0 @@
-import {
-  makeButton,
-  openSandbox
-} from "./chunk-IOQV2VX3.js";
-import {
-  get_tklst
-} from "./chunk-GERVYIL4.js";
-import "./chunk-5YF3LGLX.js";
-import "./chunk-76PGYH5J.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-MKAF2BHB.js";
-import {
-  urlmap_default
-} from "./chunk-WKNI3HRQ.js";
-import "./chunk-IWMWT7O7.js";
-import {
-  block_init_default
-} from "./chunk-WC62ZAWT.js";
-import {
-  InputSearch,
-  first_genetrack_tolist,
-  newSandboxDiv,
-  sayerror,
-  throwMsgWithFilePathAndFnName
-} from "./chunk-UK3PTE3P.js";
-import {
-  string2pos
-} from "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IFA3COXY.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5X6J6UAT.js";
-import "./chunk-3L32ZXRS.js";
-import "./chunk-GRNZWYOJ.js";
-import "./chunk-X27TRPIZ.js";
-import {
-  dofetch3
-} from "./chunk-STQU7XZV.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  StoreBase,
-  getAppInit,
-  getCompInit,
-  getStoreInit
-} from "./chunk-5V43Y2RC.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-B4VRYXOQ.js";
-import "./chunk-XOCO3LVN.js";
-import {
-  defaultcolor
-} from "./chunk-EBKERML3.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import {
-  rgb
-} from "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// src/header/omniSearch.js
-async function searchItems(app, tip, help, publications, jwt) {
-  const userInput = select_default("input").property("value").trim();
-  const data = [
-    {
-      title: "Genes",
-      default: true,
-      items: await findgenelst(userInput, app.selectgenome.property("value"), jwt),
-      color: "#F2F2F2",
-      callback: (d) => {
-        app.drawer.dispatch({ type: "is_apps_btn_active", value: false });
-        tip.hide();
-        findgene2paint(d, app, app.selectgenome.property("value"), jwt);
-      }
-    }
-  ];
-  await findAppDrawerElements(app, userInput, data, tip);
-  data.push({
-    title: "Help",
-    default: false,
-    items: help.filter((d) => d.label.toLowerCase().includes(userInput.toLowerCase())),
-    color: "#faebd9",
-    callback: (d) => {
-      window.open(d.link, d.label);
-    }
-  });
-  data.push({
-    title: "Publications",
-    default: false,
-    items: publications.filter(
-      (d) => d.title.toLowerCase().includes(userInput.toLowerCase()) || d.appHeaderTitle.toLowerCase().includes(userInput.toLowerCase())
-    ),
-    color: "#E6E6FA",
-    callback: (d) => {
-      const url = d.pmidURL || d.doi;
-      if (!url || !d.title) throw `Missing url or title for search selection`;
-      window.open(url, d.title);
-    }
-  });
-  return data;
-}
-async function findAppDrawerElements(app, input, data, tip) {
-  const re = await dofetch3(app.cardsPath + "/index.json");
-  if (re.error) throwMsgWithFilePathAndFnName(`Problem retrieving ../cards/index.json`);
-  const userInput = input.toLowerCase().trim();
-  const elements = [...re.elements];
-  let filteredElements;
-  if (userInput.length > 2) {
-    await getExampleNames(elements, app);
-    filteredElements = getFilteredElements(elements, userInput);
-  } else {
-    filteredElements = getFilteredElements(elements, userInput);
-  }
-  const opts = {
-    app: app.drawer.opts,
-    sandboxDiv: app.drawer.opts.sandboxDiv,
-    genomes: app.genomes,
-    fromApp: true
-  };
-  data.push(
-    {
-      title: "Tracks and Apps",
-      items: filteredElements.filter((c) => c.type == "card"),
-      color: "#e1edf7",
-      callback: (element) => {
-        app.drawer.dispatch({ type: "is_apps_btn_active", value: false });
-        tip.hide();
-        openSandbox(element, opts);
-      }
-    },
-    {
-      title: "Datasets",
-      items: filteredElements.filter((c) => c.type == "dsButton"),
-      color: "#e5f5e4",
-      callback: (element) => {
-        app.drawer.dispatch({ type: "is_apps_btn_active", value: false });
-        tip.hide();
-        openSandbox(element, opts);
-      }
-    }
-  );
-  return data;
-}
-async function getExampleNames(elements, app) {
-  const promises = elements.map(async (elem) => {
-    if (elem.hidden || elem.type != "card" || !elem.sandboxJson) return elem;
-    const exs = await dofetch3(app.cardsPath + `/${elem.sandboxJson}.json`);
-    if (exs?.ppcalls.length > 0) {
-      for (const c of exs.ppcalls) {
-        if (c.isUI) return;
-        if (c?.label) elem.searchterms.push(c.label);
-      }
-    }
-  });
-  await Promise.all(promises);
-}
-function getFilteredElements(elements, userInput) {
-  return elements.filter((elem) => {
-    if (elem.hidden) return false;
-    let searchTermFound = (elem.searchterms || []).reduce((searchTermFound2, searchTerm) => {
-      if (searchTermFound2) return true;
-      return searchTerm.toLowerCase().includes(userInput);
-    }, false);
-    return searchTermFound || elem.name.toLowerCase().includes(userInput);
-  }).sort((a, b) => a.name.localeCompare(b.name));
-}
-async function findgenelst(str, genome, jwt) {
-  if (str.length == 0) return;
-  try {
-    const data = await dofetch3("/genelookup", {
-      body: {
-        input: str,
-        genome,
-        jwt
-      }
-    });
-    if (data.error) throw data.error;
-    if (!data.hits) throw ".hits[] missing";
-    return data.hits;
-  } catch (err) {
-  }
-}
-async function findgene2paint(str, app, genomename, jwt) {
-  const g = app.genomes[genomename];
-  if (!g) {
-    console.error("unknown genome " + genomename);
-    return;
-  }
-  const sandbox_div = newSandboxDiv(app.drawer.opts.sandboxDiv);
-  sandbox_div.header.html(
-    '<div style="display:inline-block;">' + str + '</div><div class="sjpp-output-sandbox-title">' + genomename + "</div>"
-  );
-  const urlp = urlmap_default();
-  const tklst = await get_tklst(urlp, g);
-  const pos = string2pos(str, g);
-  if (pos) {
-    const par2 = {
-      hostURL: app.hostURL,
-      jwt,
-      holder: sandbox_div.body,
-      genome: g,
-      nobox: true,
-      chr: pos.chr,
-      start: pos.start - 1,
-      // entered positions are 1-based. block uses 0-based
-      stop: pos.stop - 1,
-      dogtag: genomename,
-      tklst,
-      debugmode: app.debugmode
-    };
-    first_genetrack_tolist(g, par2.tklst);
-    import("./block-OYSZ2JXC.js").then((b) => new b.Block(par2)).catch((err) => {
-      app.error0(err);
-    });
-    return;
-  }
-  const par = {
-    hostURL: app.hostURL,
-    jwt,
-    query: str,
-    genome: g,
-    holder: sandbox_div.body,
-    variantPageCall_snv: app.variantPageCall_snv,
-    samplecart: app.samplecart,
-    tklst,
-    debugmode: app.debugmode
-  };
-  const tmp = sessionStorage.getItem("urlp_mds");
-  if (tmp) {
-    const l = tmp.split(",");
-    if (l.length == 2) {
-      par.datasetqueries = [{ dataset: l[0], querykey: l[1] }];
-    }
-  }
-  await block_init_default(par);
-}
-
-// appdrawer/card.js
-var AppDrawerCard = class {
-  static type = "card";
-  // handles types 'card' and 'nestedCard'
-  constructor(opts) {
-    this.type = "card";
-    this.opts = this.validateOpts(opts);
-    this.holder = opts.holder;
-    this.dom = opts.dom;
-    this.sandboxDiv = opts.sandboxDiv;
-    setRenderers(this);
-  }
-  validateOpts(opts) {
-    if (!opts.element.name) throw `Card .name is missing`;
-    if (opts.element.type == "card") {
-      if (!opts.element.sandboxJson && !opts.element.sandboxHtml)
-        throw `Either .sandboxJson or .sandboxHtml is missing for card=${opts.element.name}`;
-    }
-    if (opts.element.type == "nestedCard") {
-      if (!opts.element.children || opts.element.children.length == 0)
-        throw `Missing .children for nested card = ${opts.element.name}`;
-    }
-    if (opts.element.ribbon) {
-      if (!opts.element.ribbon.text) throw `Missing ribbon .text for ${opts.element.type} = ${opts.element.name}`;
-      if ((opts.element.ribbon.text.toUpperCase() == "NEW" || opts.element.ribbon.text.toUpperCase() == "UPDATED") && !opts.element.ribbon.expireDate)
-        throw `${opts.element.type} = ${opts.element.name} ribbon is ${opts.element.ribbon.text.toUpperCase()} but .expireDate is missing. Please provide`;
-      if (opts.element.ribbon.expireDate) {
-        if (opts.element.ribbon.expireDate >= 0) {
-          throw `Flag for ${opts.element.type} = ${opts.element.name} is not a valid date`;
-        }
-      }
-    }
-    return opts;
-  }
-  main() {
-  }
-};
-var cardInit = getCompInit(AppDrawerCard);
-function setRenderers(self) {
-  const card = self.holder.append("li");
-  if (self.opts.element.type == "card") {
-    card.classed("sjpp-track", true).html(
-      `<div class="sjpp-track-h"><span style="font-size:14.5px;font-weight:500;">${self.opts.element.name}</span></div>
-				${self.opts.element.description ? `<span class="sjpp-track-blurb" style="cursor:default">${self.opts.element.description}</span></div>` : " "}
-				<span class="sjpp-track-image"><img src="${self.opts.element.image}" alt="${self.opts.element.description}"></img></span>
-				</div>`
-    );
-  } else if (self.opts.element.type == "nestedCard") {
-    card.classed("sjpp-app-drawer-card", true).html(
-      `<p style="margin-left: 12px; font-size:14.5px;font-weight:500; display: block;">${self.opts.element.name}</p>
-			<p style="display: block; font-size: 13px; font-weight: 300; margin-left: 20px; justify-content: center; font-style:oblique; color: #403f3f;">${self.opts.element.description}</p>`
-    );
-  }
-  self.makeRibbon = function(ribbon) {
-    const ribbonDiv = card.append("div").classed("sjpp-app-drawer-card-ribbon", true).style("align-items", "center").style("justify-content", "center");
-    const text = ribbon.text.toUpperCase();
-    const color = text == "BETA" ? "#418cb5" : text == "NEW" ? "#1ba176" : text == "UPDATED" ? "orange" : ribbon.color ? ribbon.color : "red";
-    ribbonDiv.append("span").text(text).style("color", "white").style("background-color", rgb(color).darker()).style("height", "auto").style("width", "100%").style("top", "15%").style("left", "-30%").style("font-size", "11.5px").style("text-transform", "uppercase").style("text-align", "center");
-  };
-  if (self.opts.element.ribbon) {
-    const today = /* @__PURE__ */ new Date();
-    const ribbonExpireDate = new Date(self.opts.element.ribbon.expireDate);
-    if (ribbonExpireDate > today || ribbonExpireDate == "Invalid Date") self.makeRibbon(self.opts.element.ribbon);
-  }
-  card.on("click", async (event) => {
-    event.stopPropagation();
-    await self.app.dispatch({
-      type: "is_apps_btn_active",
-      value: false
-    });
-    slideDrawer(self);
-    setTimeout(async () => {
-      await openSandbox(self.opts.element, self.opts);
-    }, self.state.duration + 5);
-  });
-}
-
-// appdrawer/dsButton.js
-var AppDrawerButton = class {
-  static type = "button";
-  constructor(opts) {
-    this.type = "button";
-    this.opts = this.validateOpts(opts);
-    this.holder = opts.holder;
-    this.dom = opts.dom;
-    this.sandboxDiv = opts.sandboxDiv;
-    setRenderers2(this);
-  }
-  validateOpts(opts) {
-    if (!opts.element.name) throw `Button name is missing`;
-    if (!opts.element.sandboxJson && !opts.element.sandboxHtml)
-      throw `Either .sandboxJson or .sandboxHtml is missing for button=${opts.element.name}`;
-    return opts;
-  }
-  main() {
-  }
-};
-var buttonInit = getCompInit(AppDrawerButton);
-function setRenderers2(self) {
-  const btn = makeButton({ div: self.holder, text: self.opts.element.name, margin: "20px 20px 0px" });
-  btn.attr("class", "sjpp-appdrawer-dataset-btn").on("click", async (event) => {
-    event.stopPropagation();
-    await self.app.dispatch({
-      type: "is_apps_btn_active",
-      value: false
-    });
-    slideDrawer(self);
-    await openSandbox(self.opts.element, self.opts);
-  });
-}
-
-// appdrawer/layout.js
-var AppDrawerLayoutComp = class {
-  static type = "layout";
-  constructor(opts) {
-    this.type = "layout";
-    this.dom = {
-      holder: opts.dom.drawerDiv,
-      wrapper: opts.dom.wrapper,
-      sandboxDiv: opts.dom.sandboxDiv
-    };
-    this.state = opts.state;
-    this.hasStatePreMain = true;
-  }
-  async validateIndexJson() {
-    const index = await this.getIndexJson();
-    if (!index.elements) throw `Missing elements array`;
-    if (!index.elements.length) throw `No element objects provided`;
-    if (index.columnsLayout) {
-      if (index.columnsLayout.length == 0) throw `Missing column objects`;
-      const allGridAreaValues = index.columnsLayout.map((s) => s.gridarea);
-      if (allGridAreaValues.length != new Set(allGridAreaValues).size) throw `Duplicate values for .gridarea found`;
-      const allSectionIdValues = [];
-      for (const col of index.columnsLayout) {
-        if (!col.gridarea) throw `Missing column .gridarea for column = ${col.name}`;
-        if (!col.sections || col.sections.length == 0) throw `Missing section objects for column = ${col.name}`;
-        for (const section of col.sections) {
-          if (!section.id)
-            throw `Missing section .id in ${section.name ? `section = ${section.name}` : `column = ${col.name} array`}`;
-          allSectionIdValues.push(section.id);
-        }
-        if (col.sections.length != new Set(col.sections).size) {
-          throw `Non-unique levels in line ${lineNum}: ${JSON.stringify(levelNames)}`;
-        }
-      }
-      if (allSectionIdValues.length != new Set(allSectionIdValues).size) throw `Duplicate values for section.id found`;
-      for (const element of index.elements) {
-        if (!element.section) throw `.section is missing for ${element.type} = ${element.name}`;
-        if (!allSectionIdValues.some((d) => d == element.section))
-          throw `section = ${element.section} for ${element.type} = ${element.name} is not a column section`;
-      }
-    }
-    return index;
-  }
-  async getIndexJson() {
-    const re = await dofetch3(this.app.cardsPath + "/index.json");
-    if (re.error) {
-      sayerror(this.dom.holder.append("div"), re.error);
-      return;
-    }
-    return re;
-  }
-  validateElements() {
-    const features = JSON.parse(sessionStorage.getItem("optionalFeatures")) || {};
-    this.elements = this.index.elements.filter((e) => !e.hidden && (!e.configFeature || features[e.configFeature]));
-  }
-  async init() {
-    this.index = await this.validateIndexJson();
-    this.elementsRendered = false;
-    setRenderers3(this);
-    this.validateElements();
-    this.layout = this.index.columnsLayout ? this.index.columnsLayout : null;
-    this.components = {
-      elements: []
-    };
-  }
-  async main() {
-    if (this.elementsRendered == true) return;
-    this.elementsRendered = true;
-    for (const element of this.elements) {
-      const holder = select_default(this.layout ? `#${element.section} > .sjpp-element-list` : `.sjpp-element-list`);
-      if (element.type == "card" || element.type == "nestedCard") {
-        this.components.elements.push(
-          await cardInit({
-            app: this.app,
-            holder: holder.style("display", "grid").style("grid-template-columns", "repeat(auto-fit, minmax(320px, 1fr))").style("gap", "10px").style("list-style", "none").style("margin", "15px 0px"),
-            element,
-            dom: this.opts.dom,
-            state: this.state,
-            sandboxDiv: this.dom.sandboxDiv
-          })
-        );
-      } else if (element.type == "dsButton") {
-        this.components.elements.push(
-          await buttonInit({
-            app: this.app,
-            holder,
-            element,
-            dom: this.opts.dom,
-            state: this.state,
-            sandboxDiv: this.dom.sandboxDiv
-          })
-        );
-      }
-    }
-  }
-};
-var layoutInit = getCompInit(AppDrawerLayoutComp);
-function setRenderers3(self) {
-  if (!self.index.columnsLayout) noDefinedLayout(self);
-  if (self.index.columnsLayout) columnsLayout(self);
-}
-function noDefinedLayout(self) {
-  const flexLayout = self.dom.wrapper.append("div").style("display", "flex").style("padding", "10px").classed("sjpp-element-list", true);
-  return flexLayout;
-}
-function columnsLayout(self) {
-  const parentGrid = self.dom.wrapper.append("div").style("display", "grid").style("grid-template-columns", "repeat(auto-fit, minmax(425px, 1fr))").style("gap", "10px").style("padding", "10px").style("text-align", "left");
-  const gridareas = [];
-  for (const column of self.index.columnsLayout) gridareas.push(column.gridarea);
-  parentGrid.style("grid-template-areas", `"${gridareas.toString().replace(",", " ")}"`);
-  for (const col of self.index.columnsLayout) {
-    const newCol = parentGrid.append("div").style("grid-area", col.gridarea).classed(".sjpp-track-cols", true);
-    for (const section of col.sections) addSection(section, newCol);
-  }
-  function addSection(section, newCol) {
-    const newSection = newCol.append("div").attr("id", section.id);
-    if (section.name)
-      newSection.append("h5").classed("sjpp-appdrawer-cols", true).style("color", rgb(defaultcolor).darker()).text(section.name);
-    newSection.append("div").classed("sjpp-element-list", true).style("padding", "10px");
-    return newSection;
-  }
-}
-
-// appdrawer/mainBtn.js
-var MainHeadboxBtn = class {
-  static type = "mainBtn";
-  constructor(opts) {
-    this.type = "mainBtn";
-    this.opts = this.validateOpts(opts);
-    this.dom = opts.dom;
-    this.state = opts.state;
-    this.hasStatePreMain = true;
-  }
-  validateOpts(opts) {
-    return opts.app.opts;
-  }
-  getState(appState) {
-    return {
-      appBtnActive: appState.appBtnActive,
-      duration: appState.duration,
-      arrowSize: appState.arrowSize,
-      arrowColor: appState.arrowColor,
-      hintWidth: appState.hintWidth,
-      hintPos: appState.hintPos
-    };
-  }
-  async init(appState) {
-    this.state = this.getState(appState);
-    setRenderers4(this);
-    this.btnRendered = false;
-    this.drawerFullHeight = "";
-    try {
-      if (window.location.pathname == "/" && !window.location.search.length)
-        await this.app.dispatch({ type: "is_apps_btn_active", value: true });
-      this.components = {
-        layout: []
-      };
-    } catch (e) {
-      throw e;
-    }
-  }
-  async main(appState) {
-    if (this.state.appBtnActive == true && this.btnRendered == false) {
-      this.dom.drawerDiv.style("background-color", "#f5f5f5");
-      this.components.layout.push(
-        await layoutInit({
-          app: this.app,
-          dom: this.dom,
-          state: this.state
-        })
-      );
-      setTimeout(() => {
-        this.drawerFullHeight = this.dom.drawerDiv.node().getBoundingClientRect().height + 5;
-      }, this.state.duration + 5);
-      slideDrawer(this);
-      this.btnRendered = true;
-    }
-    if (this.state.appBtnActive == false && this.btnRendered == true) slideDrawer(this);
-  }
-};
-var mainBtnInit = getCompInit(MainHeadboxBtn);
-function setRenderers4(self) {
-  self.dom.btnWrapper.style("background-color", self.state.appBtnActive ? "#b2b2b2" : "#f2f2f2").style("color", self.state.appBtnActive ? "#fff" : "#000").on("click", async (event) => {
-    event.stopPropagation();
-    await self.app.dispatch({ type: "is_apps_btn_active" });
-    slideDrawer(self);
-    if (self.state.appBtnActive) {
-      setTimeout(() => {
-        self.drawerFullHeight = self.dom.drawerDiv.node().getBoundingClientRect().height + 5;
-      }, self.state.duration + 5);
-    }
-  });
-  self.dom.btn.attr("class", "sja_menuoption").attr("data-testid", "sjpp-appDrawer-main-btn").style("display", "inline-block").style("background-color", "transparent").style("color", self.state.appBtnActive ? "#fff" : "#000").style("padding", self.opts.padw_sm).style("margin", "0px 5px").style("cursor", "pointer").text("Apps");
-  self.dom.drawerHint.style("position", "relative").style("display", "inline-block").style("height", self.state.arrowSize.closed + "px").style("width", self.state.appBtnActive ? self.state.hintWidth.open : self.state.hintWidth.closed).style("background-color", "transparent").style("text-align", "center").style("cursor", "pointer");
-  self.dom.drawerArrow.style("position", "absolute").style("font-size", self.state.arrowSize.closed + "px").style("right", self.state.hintPos.closed.rt + "px").style("bottom", self.state.hintPos.closed.btm + "px").style("background-color", "transparent").style("color", self.state.arrowColor.closed).style("opacity", self.state.appBtnActive ? 0 : 1).style("cursor", "pointer").html("&#9660;");
-  self.dom.drawerArrowOpen.style("position", "absolute").style("font-size", self.state.arrowSize.open + "px").style("left", self.state.hintPos.open.left + "px").style("bottom", self.state.hintPos.open.btm + "px").style("transform", "rotate(180deg)").style("background-color", "transparent").style("color", self.state.arrowColor.open).style("opacity", self.state.appBtnActive ? 1 : 0).style("cursor", "pointer").style("pointer-events", self.state.appBtnActive ? "auto" : "none").html("&#9660;");
-  self.drawerFullHeight = self.dom.drawerRow.node().getBoundingClientRect().height + 5;
-}
-async function slideDrawer(self) {
-  self.dom.btnWrapper.transition().duration(self.opts.state.duration).style("background-color", self.state.appBtnActive ? "#b2b2b2" : "#f2f2f2").style("color", self.state.appBtnActive ? "#fff" : "#000");
-  self.dom.btn.transition().duration(self.opts.state.duration).style("color", self.state.appBtnActive ? "#fff" : "#000");
-  self.dom.drawerDiv.style("display", "inline-block").transition().duration(self.opts.state.duration).style("top", self.state.appBtnActive ? "0px" : "-" + self.drawerFullHeight + "px");
-  self.dom.drawerRow.transition().duration(self.opts.state.duration).style("height", self.state.appBtnActive ? self.drawerFullHeight + "px" : "0px");
-  self.dom.drawerHint.transition().duration(self.opts.state.duration).style("width", self.state.appBtnActive ? self.opts.state.hintWidth.open : self.opts.state.hintWidth.closed);
-  self.dom.drawerArrow.transition().duration(self.opts.state.duration).style("opacity", self.state.appBtnActive ? 0 : 1);
-  self.dom.drawerArrowOpen.style("pointer-events", self.state.appBtnActive ? "auto" : "none").transition().duration(self.opts.state.duration).style("opacity", self.state.appBtnActive ? 1 : 0);
-}
-
-// appdrawer/store.js
-var AppDrawerStore = class _AppDrawerStore extends StoreBase {
-  static type = "store";
-  constructor(opts) {
-    super(opts);
-    this.type = _AppDrawerStore.type;
-    this.defaultState = {
-      // for apps drawer animation
-      duration: 500,
-      hintPos: {
-        open: { btm: -42, left: 13 },
-        closed: { btm: 3, rt: 5 }
-      },
-      hintWidth: { open: "0px", closed: "18px" },
-      arrowSize: { open: 42, closed: 20 },
-      arrowColor: { open: "rgb(242,242,242)", closed: "rgb(85,85,85)" },
-      appBtnActive: false
-    };
-  }
-  async init() {
-  }
-};
-var appDrawerStoreInit = getStoreInit(AppDrawerStore);
-AppDrawerStore.prototype.actions = {
-  is_apps_btn_active(action) {
-    this.state.appBtnActive = "value" in action ? action.value : !this.state.appBtnActive;
-  }
-};
-
-// appdrawer/app.js
-var AppDrawerApp = class _AppDrawerApp {
-  static type = "app";
-  constructor(opts) {
-    this.type = _AppDrawerApp.type;
-    const drawerDiv = opts.drawerRow.append("div").style("position", "relative").style("margin", "0 20px").style("padding", `0 ${opts.padw_sm}`).style("display", "inline-block").style("overflow", "hidden").style("border-radius", "0px 0px 5px 5px").style("width", "93vw").classed("sjpp-drawer-div", true);
-    const btnWrapper = opts.headbox.append("div").style("position", "relative").style("display", "inline-block").style("margin-left", "5px").style("margin-right", "5px").style("border-radius", "5px").classed("sjpp-apps-btn-wrapper", true);
-    this.dom = {
-      drawerRow: opts.drawerRow,
-      drawerDiv,
-      sandboxDiv: opts.sandboxDiv,
-      btnWrapper,
-      btn: btnWrapper.append("div"),
-      drawerHint: btnWrapper.append("div"),
-      drawerArrow: btnWrapper.append("div"),
-      drawerArrowOpen: btnWrapper.append("div"),
-      wrapper: drawerDiv.append("div")
-    };
-  }
-  preApiFreeze(api) {
-    api.cardsPath = this.opts.cardsPath;
-  }
-  async init() {
-    try {
-      this.store = await appDrawerStoreInit({ app: this.api, state: this.opts.state });
-      this.state = await this.store.copyState();
-      this.components = {
-        mainBtn: await mainBtnInit({
-          app: this.api,
-          dom: this.dom,
-          state: this.state,
-          indexJson: this.indexJson
-        })
-      };
-      await this.api.dispatch();
-    } catch (e) {
-      throw e;
-    }
-  }
-  main() {
-  }
-};
-var appDrawerInit = getAppInit(AppDrawerApp);
-
-// src/header/AppHeader.ts
-var AppHeader = class _AppHeader {
-  static {
-    /** Used in both the Help button and omni search
-     * .onlySearch is used to filter out items that should not appear in the Help button
-     */
-    this.help = [
-      {
-        label: "Embed in your website",
-        link: "https://github.com/stjude/proteinpaint/wiki/Embedding"
-      },
-      {
-        label: "URL parameters",
-        link: "https://github.com/stjude/proteinpaint/wiki/URL-parameters"
-      },
-      {
-        label: "All tutorials",
-        link: "https://github.com/stjude/proteinpaint/wiki/"
-      },
-      {
-        label: "User community",
-        link: "https://groups.google.com/g/proteinpaint"
-      },
-      {
-        label: "License ProteinPaint",
-        link: "https://www.stjude.org/research/why-st-jude/shared-resources/technology-licensing/technologies/proteinpaint-web-application-for-visualizing-genomic-data-sj-15-0021.html",
-        onlySearch: true
-      },
-      {
-        label: "Our Team",
-        link: "https://proteinpaint.stjude.org/team/",
-        onlySearch: true
-      }
-    ];
-  }
-  constructor(opts) {
-    this.headtip = opts.headtip;
-    this.app = opts.app;
-    this.data = opts.data;
-    this.jwt = opts.jwt;
-    this.publications = [];
-  }
-  async createPublicationsList() {
-    const re = await dofetch3(this.app.cardsPath + "/citations.json");
-    if (re.error) console.error(`Problem retrieving ../cards/citations.json`);
-    this.publications = re?.publications?.length ? re.publications.filter((d) => d.appHeaderTitle).sort((a, b) => b.year - a.year) : [];
-  }
-  async makeheader() {
-    await this.createPublicationsList();
-    const color = rgb(defaultcolor);
-    const padw_lg = "13px";
-    const padw_input = "5px 10px";
-    const padw_sm = "7px 10px";
-    const doc_width = document.documentElement.clientWidth;
-    const row = this.app.holder.append("div").style("white-space", "nowrap").style(
-      "border-bottom",
-      doc_width > 1600 ? "solid 1px rgba(" + color.r + "," + color.g + "," + color.b + ",.3)" : ""
-    );
-    const headbox = row.append("div").style("margin", "10px").style("padding", "8px").style("padding-bottom", "12px").style("display", doc_width < 1600 ? "block" : "inline-block").style(
-      "border-bottom",
-      doc_width < 1600 ? "solid 1px rgba(" + color.r + "," + color.g + "," + color.b + ",.3)" : ""
-    );
-    const headinfo = row.append("div").style("display", "inline-block").style("padding", padw_sm).style("padding-left", "25px").style("font-size", ".8em").style("color", rgb(defaultcolor).darker());
-    {
-      const row2 = headinfo.append("div").style("padding-left", "15px");
-      const link = `https://github.com/stjude/proteinpaint/pkgs/container/ppfull`;
-      const version = this.data.pkgver ? `Release version: <a href="${link}" target="${this.data.pkgver}">${this.data.pkgver}</a>` : `Code date: ${this.data.codedate}`;
-      row2.attr("id", "sjpp-serverstat").append("span").html(`${version}, server launched: ${this.data.launchdate || "??"}.`);
-      if (this.data.hasblat) {
-        row2.append("a").style("margin-left", "10px").text("Running BLAT").on("click", async (event) => {
-          this.headtip.clear().showunder(event.target);
-          const div = this.headtip.d.append("div").style("margin", "10px");
-          const wait = div.append("div").text("Loading...");
-          try {
-            const data = await dofetch3("blat?serverstat=1");
-            if (data.error) throw data.error;
-            if (!data.lst) throw "invalid response";
-            wait.remove();
-            for (const i of data.lst) {
-              div.append("div").text(i);
-            }
-          } catch (e) {
-            wait.text(e.message || e);
-            if (e.stack) console.error(e.stack);
-          }
-        });
-      }
-    }
-    if (this.data.headermessage) {
-      headinfo.append("div").html(this.data.headermessage);
-    }
-    headbox.append("div").text("ProteinPaint").style("display", "inline-block").style("padding", padw_lg).style("color", defaultcolor).style("font-size", "1.3em").style("font-weight", "bold");
-    const omniSearch = new InputSearch({
-      holder: headbox,
-      tip: this.headtip,
-      style: {
-        padding: padw_sm,
-        border: `'solid 1px ${defaultcolor}`
-      },
-      size: 32,
-      placeholder: "Gene, position, SNP, app, or dataset",
-      title: "Search by gene, SNP, position, app, or dataset",
-      searchItems: async () => {
-        return await searchItems(this.app, this.headtip, _AppHeader.help, this.publications, this.jwt);
-      }
-    });
-    omniSearch.initUI();
-    const genome_select_div = headbox.append("div").attr("class", "sjpp-genome-select-div").style("padding", padw_sm);
-    const get_placeholder = () => {
-      const currG = this.app.genomes[this.app.selectgenome.property("value")];
-      const opts2Show = ["Gene", "position", "app"];
-      if (currG.hasSNP) opts2Show.splice(2, 0, "SNP");
-      if (Object.keys(currG.datasets).length) opts2Show.push("dataset");
-      const str = opts2Show.join(", ").replace(/,(?=[^,]*$)/, ", or");
-      return str;
-    };
-    this.app.selectgenome = genome_select_div.append("select").attr("aria-label", "Select a genome").attr("class", "sjpp-genome-select").style("padding", padw_input).style("border", "solid 1px " + defaultcolor).on("change", () => {
-      this.update_genome_browser_btn(this.app);
-      omniSearch.updatePlaceholder(get_placeholder());
-    });
-    const filterGenomes = Object.values(this.app.genomes).filter((g) => !g.hideOnClient);
-    for (const n of filterGenomes) {
-      this.app.selectgenome.append("option").attr("n", n.name).text(`${n.species} ${n.name}`).property("value", n.name);
-    }
-    this.app.genome_browser_btn = this.make_genome_browser_btn(this.app, headbox, this.jwt);
-    this.app.drawer = await appDrawerInit({
-      holder: this.app.holder,
-      genomes: this.app.genomes,
-      drawerRow: this.app.holder.append("div").style("position", "relative").style("overflow-x", "visible").style("overflow-y", "hidden").classed("sjpp-drawer-row", true),
-      sandboxDiv: this.app.holder.append("div").style("margin-top", "15px").classed("sjpp-drawer-sandbox", true),
-      genome_browser_btn: this.app.genome_browser_btn,
-      debugmode: this.app.debugmode,
-      headbox,
-      padw_sm,
-      cardsPath: this.app.cardsPath
-    });
-    headbox.append("span").classed("sja_menuoption", true).attr("id", "sjpp-header-help-btn").style("padding", padw_sm).text("Help").on("click", async (event) => {
-      const p = event.target.getBoundingClientRect();
-      const div = this.headtip.clear().show(p.left - 0, p.top + p.height + 5);
-      await div.d.append("div").style("padding", "5px 20px").selectAll("p").data(_AppHeader.help.filter((d) => !d.onlySearch)).enter().append("p").html((d) => `<a href=${d.link} target=_blank>${d.label}</a>`);
-    });
-    if (this.publications.length > 0) {
-      headbox.append("span").classed("sja_menuoption", true).attr("id", "sjpp-header-publications-btn").style("padding", padw_sm).style("margin", "0px 5px").text("Publications").on("click", async (event) => {
-        const p = event.target.getBoundingClientRect();
-        const div = this.headtip.clear().show(p.left - 150, p.top + p.height + 5);
-        await div.d.append("div").style("padding", "5px 20px").selectAll("p").data(this.publications).enter().append("p").html(
-          (d) => `<a href=${d.pmidURL || d.doi} target=_blank>${d.appHeaderTitle}, ${d.journal}, ${d.year}</a>`
-        );
-      });
-    }
-  }
-  make_genome_browser_btn(app, headbox, jwt) {
-    if (app.selectgenome.node().options.length === 0) {
-      console.error(`No selected selectgenome options.`);
-      return;
-    }
-    const padw = "8px";
-    const genome_btn_div = headbox.append("span");
-    const genomename = app.selectgenome.node().options[app.selectgenome.property("selectedIndex")].value;
-    const g_browser_btn = genome_btn_div.attr("class", "sja_menuoption").attr("id", "genome_btn").style("padding", padw).datum(genomename).text(genomename + " genome browser").on("click", () => {
-      const genomeSelected = app.selectgenome.node().value;
-      const g = app.genomes[genomeSelected];
-      if (!g) {
-        alert("Invalid genome name: " + genomeSelected);
-        return;
-      }
-      const sandbox_div = newSandboxDiv(app.drawer.opts.sandboxDiv);
-      sandbox_div.header.text(genomeSelected + " genome browser");
-      const par = {
-        hostURL: app.hostURL,
-        jwt,
-        holder: sandbox_div.body,
-        genome: g,
-        chr: g.defaultcoord.chr,
-        start: g.defaultcoord.start,
-        stop: g.defaultcoord.stop,
-        nobox: true,
-        tklst: [],
-        debugmode: app.debugmode
-      };
-      first_genetrack_tolist(g, par.tklst);
-      import("./block-OYSZ2JXC.js").then((b) => new b.Block(par));
-      app.drawer.dispatch({ type: "is_apps_btn_active", value: false });
-    });
-    return g_browser_btn;
-  }
-  update_genome_browser_btn(app) {
-    app.genome_browser_btn.text(app.selectgenome.node().value + " genome browser");
-    app.genome_browser_btn.datum(app.selectgenome.node().value);
-  }
-};
-export {
-  AppHeader
-};
-//# sourceMappingURL=AppHeader-4AZ76NN3.js.map