@sjcrh/proteinpaint-client 2.180.0 → 2.180.1

package/dist/AppHeader-7TNVJJA7.js

@@ -0,0 +1,833 @@
+import {
+  makeButton,
+  openSandbox
+} from "./chunk-JGU7ERLS.js";
+import {
+  get_tklst
+} from "./chunk-YMY73A3W.js";
+import "./chunk-Z3BKMKQR.js";
+import "./chunk-HGHRMQQO.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-MKAF2BHB.js";
+import {
+  urlmap_default
+} from "./chunk-AQ4OP4GR.js";
+import "./chunk-O55HHVQS.js";
+import {
+  block_init_default
+} from "./chunk-DN52ILXL.js";
+import {
+  InputSearch,
+  first_genetrack_tolist,
+  newSandboxDiv,
+  sayerror,
+  throwMsgWithFilePathAndFnName
+} from "./chunk-SAHCLNNL.js";
+import {
+  string2pos
+} from "./chunk-HJ6L54YS.js";
+import "./chunk-XEBPIJHM.js";
+import "./chunk-CXMZYVZT.js";
+import {
+  dofetch3
+} from "./chunk-KDKY7S5G.js";
+import "./chunk-SSFOXHYJ.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-73VHTIHG.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import {
+  StoreBase,
+  getAppInit,
+  getCompInit,
+  getStoreInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-GM6H3CUI.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-SNMJEDHY.js";
+import "./chunk-XQMDLYEK.js";
+import "./chunk-72YYKDTX.js";
+import "./chunk-RTKRLATH.js";
+import {
+  defaultcolor
+} from "./chunk-SOYDFNWV.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-CTVZMQ5J.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-733PDAIR.js";
+import "./chunk-SEEYV6P2.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+import {
+  rgb
+} from "./chunk-OMR2DT66.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-PH3K3TGJ.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").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-PH3K3TGJ.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-7TNVJJA7.js.map