taxonium-component/dist/jb1ConfigLoad-DsWxhvl2.js

React component for exploring large phylogenetic trees in the browser

import { u as K, a4 as H } from "./JBrowsePanel-uJIA-L6s.js";
import { g as z } from "./index-dFotuATn.js";
/*!
 * isobject <https://github.com/jonschlinkert/isobject>
 *
 * Copyright (c) 2014-2017, Jon Schlinkert.
 * Released under the MIT License.
 */
var $, E;
function M() {
  return E || (E = 1, $ = function(t) {
    return t != null && typeof t == "object" && Array.isArray(t) === !1;
  }), $;
}
/*!
 * get-value <https://github.com/jonschlinkert/get-value>
 *
 * Copyright (c) 2014-2018, Jon Schlinkert.
 * Released under the MIT License.
 */
var J, V;
function N() {
  if (V) return J;
  V = 1;
  const e = M();
  J = function(n, l, u) {
    if (e(u) || (u = { default: u }), !i(n))
      return typeof u.default < "u" ? u.default : n;
    typeof l == "number" && (l = String(l));
    const y = Array.isArray(l), d = typeof l == "string", w = u.separator || ".", p = u.joinChar || (typeof w == "string" ? w : ".");
    if (!d && !y)
      return n;
    if (d && l in n)
      return s(l, n, u) ? n[l] : u.default;
    let c = y ? l : r(l, w, u), o = c.length, a = 0;
    do {
      let f = c[a];
      for (typeof f == "number" && (f = String(f)); f && f.slice(-1) === "\\"; )
        f = t([f.slice(0, -1), c[++a] || ""], p, u);
      if (f in n) {
        if (!s(f, n, u))
          return u.default;
        n = n[f];
      } else {
        let m = !1, h = a + 1;
        for (; h < o; )
          if (f = t([f, c[h++]], p, u), m = f in n) {
            if (!s(f, n, u))
              return u.default;
            n = n[f], a = h - 1;
            break;
          }
        if (!m)
          return u.default;
      }
    } while (++a < o && i(n));
    return a === o ? n : u.default;
  };
  function t(n, l, u) {
    return typeof u.join == "function" ? u.join(n) : n[0] + l + n[1];
  }
  function r(n, l, u) {
    return typeof u.split == "function" ? u.split(n) : n.split(l);
  }
  function s(n, l, u) {
    return typeof u.isValid == "function" ? u.isValid(n, l) : !0;
  }
  function i(n) {
    return e(n) || Array.isArray(n) || typeof n == "function";
  }
  return J;
}
var X = N();
const D = /* @__PURE__ */ z(X);
/*!
 * is-primitive <https://github.com/jonschlinkert/is-primitive>
 *
 * Copyright (c) 2014-present, Jon Schlinkert.
 * Released under the MIT License.
 */
var F, _;
function Y() {
  return _ || (_ = 1, F = function(t) {
    return typeof t == "object" ? t === null : typeof t != "function";
  }), F;
}
/*!
 * is-plain-object <https://github.com/jonschlinkert/is-plain-object>
 *
 * Copyright (c) 2014-2017, Jon Schlinkert.
 * Released under the MIT License.
 */
var A, L;
function Q() {
  if (L) return A;
  L = 1;
  var e = M();
  function t(r) {
    return e(r) === !0 && Object.prototype.toString.call(r) === "[object Object]";
  }
  return A = function(s) {
    var i, n;
    return !(t(s) === !1 || (i = s.constructor, typeof i != "function") || (n = i.prototype, t(n) === !1) || n.hasOwnProperty("isPrototypeOf") === !1);
  }, A;
}
/*!
 * set-value <https://github.com/jonschlinkert/set-value>
 *
 * Copyright (c) Jon Schlinkert (https://github.com/jonschlinkert).
 * Released under the MIT License.
 */
var x, T;
function Z() {
  if (T) return x;
  T = 1;
  const { deleteProperty: e } = Reflect, t = Y(), r = Q(), s = (o) => typeof o == "object" && o !== null || typeof o == "function", i = (o) => o === "__proto__" || o === "constructor" || o === "prototype", n = (o) => {
    if (!t(o))
      throw new TypeError("Object keys must be strings or symbols");
    if (i(o))
      throw new Error(`Cannot set unsafe key: "${o}"`);
  }, l = (o) => Array.isArray(o) ? o.flat().map(String).join(",") : o, u = (o, a) => {
    if (typeof o != "string" || !a) return o;
    let f = o + ";";
    return a.arrays !== void 0 && (f += `arrays=${a.arrays};`), a.separator !== void 0 && (f += `separator=${a.separator};`), a.split !== void 0 && (f += `split=${a.split};`), a.merge !== void 0 && (f += `merge=${a.merge};`), a.preservePaths !== void 0 && (f += `preservePaths=${a.preservePaths};`), f;
  }, y = (o, a, f) => {
    const m = l(a ? u(o, a) : o);
    n(m);
    const h = c.cache.get(m) || f();
    return c.cache.set(m, h), h;
  }, d = (o, a = {}) => {
    const f = a.separator || ".", m = f === "/" ? !1 : a.preservePaths;
    if (typeof o == "string" && m !== !1 && /\//.test(o))
      return [o];
    const h = [];
    let b = "";
    const k = (S) => {
      let j;
      S.trim() !== "" && Number.isInteger(j = Number(S)) ? h.push(j) : h.push(S);
    };
    for (let S = 0; S < o.length; S++) {
      const j = o[S];
      if (j === "\\") {
        b += o[++S];
        continue;
      }
      if (j === f) {
        k(b), b = "";
        continue;
      }
      b += j;
    }
    return b && k(b), h;
  }, w = (o, a) => a && typeof a.split == "function" ? a.split(o) : typeof o == "symbol" ? [o] : Array.isArray(o) ? o : y(o, a, () => d(o, a)), p = (o, a, f, m) => {
    if (n(a), f === void 0)
      e(o, a);
    else if (m && m.merge) {
      const h = m.merge === "function" ? m.merge : Object.assign;
      h && r(o[a]) && r(f) ? o[a] = h(o[a], f) : o[a] = f;
    } else
      o[a] = f;
    return o;
  }, c = (o, a, f, m) => {
    if (!a || !s(o)) return o;
    const h = w(a, m);
    let b = o;
    for (let k = 0; k < h.length; k++) {
      const S = h[k], j = h[k + 1];
      if (n(S), j === void 0) {
        p(b, S, f, m);
        break;
      }
      if (typeof j == "number" && !Array.isArray(b[S])) {
        b = b[S] = [];
        continue;
      }
      s(b[S]) || (b[S] = {}), b = b[S];
    }
    return o;
  };
  return c.split = w, c.cache = /* @__PURE__ */ new Map(), c.clear = () => {
    c.cache = /* @__PURE__ */ new Map();
  }, x = c, x;
}
var ee = Z();
const re = /* @__PURE__ */ z(ee);
function I(e) {
  return (e == null ? void 0 : e.label) && typeof e.label == "string";
}
function te(e) {
  return (e == null ? void 0 : e.url) && typeof e.url == "string";
}
function O(e, t) {
  for (const r of Object.keys(t))
    r in e && typeof t[r] == "object" && typeof e[r] == "object" ? O(e[r], t[r]) : (e[r] === void 0 || t[r] !== void 0) && (e[r] = t[r]);
  return e;
}
function se(e, t) {
  return e.replaceAll(/{([\s\w.]+)}/g, (r, s) => {
    s = s.replaceAll(/\s+/g, "");
    const i = D(t, s);
    if (i !== void 0)
      return typeof i == "function" ? i(s) : i;
    if (t.callback) {
      const n = t.callback.call(this, s);
      if (n !== void 0)
        return n;
    }
    return r;
  });
}
function ne(e, t) {
  if (typeof e == "string") {
    let r;
    try {
      r = JSON.parse(e);
    } catch (s) {
      throw new Error(`${s} when parsing configuration.`);
    }
    return g(r, t);
  }
  return g(e, t);
}
function ie(e, t) {
  let r;
  try {
    r = ae(e, t);
  } catch (s) {
    throw new Error(`${s} when parsing configuration.`);
  }
  return g(r, t);
}
function oe(e) {
  return e === "include";
}
function ae(e, t) {
  let r = [], s, i, n;
  const l = { tracks: {} };
  let u;
  function y() {
    if (n !== void 0) {
      let d;
      try {
        const w = /^json:(.+)/i.exec(n);
        if (w ? d = JSON.parse(w[1]) : /^[+-]?[\d.,]+([eE][-+]?\d+)?$/.test(n) ? d = Number.parseFloat(n.replaceAll(",", "")) : d = n, !s)
          throw new Error(`Error parsing in section ${r.join(" - ")}`);
        const p = [...r, ...s].join(".");
        if (i === "+=") {
          let c = D(l, p);
          c ? Array.isArray(c) || (c = [c]) : c = [], c.push(d), d = c;
        }
        d === "true" && (d = !0), d === "false" && (d = !1), re(l, p, d);
      } catch {
        throw new Error(`syntax error${t ? ` in ${t}` : ""}${u ? ` at line ${u - 1}` : ""}`);
      }
    }
  }
  for (const [d, w] of e.split(/\n|\r\n|\r/).entries()) {
    u = d + 1;
    const p = w.replace(/^\s*#.+/, "");
    let c;
    if (c = /^\s*\[([^\]]+)/.exec(p))
      y(), s = void 0, n = void 0, r = c[1].trim().split(/\s*\.\s*/), r.length === 1 && r[0].toLowerCase() === "general" && (r = []);
    else if (c = p.match(n === void 0 ? /^([^+=]+)(\+?=)(.*)/ : /^(\S[^+=]+)(\+?=)(.*)/))
      y(), s = c[1].trim().split(/\s*\.\s*/), [, , i] = c, oe([...r, ...s].join(".")) && (i = "+="), n = c[3].trim();
    else if (s !== void 0 && (c = /^\s{0,4}\+\s*(.+)/.exec(p)))
      y(), i = "+=", n = c[1].trim();
    else if (n !== void 0 && (c = /^\s+(\S.*)/.exec(p))) {
      const o = c[1];
      n += n.length ? ` ${o.trim()}` : o.trim();
    } else
      y(), s = void 0, n = void 0;
  }
  return y(), l;
}
function g(e, t) {
  if (e.tracks && !Array.isArray(e.tracks))
    if (I(e.tracks))
      e.tracks = [e.tracks];
    else {
      const s = [];
      for (const i of Object.keys(e.tracks)) {
        const n = e.tracks[i];
        I(n) ? s.push(n) : s.push({ label: i, ...n });
      }
      e.tracks = s;
    }
  const r = e.trackMetadata;
  if (r != null && r.sources) {
    if (typeof r.sources == "string" && (r.sources = [r.sources]), te(r.sources) && (r.sources = [r.sources]), !Array.isArray(r.sources)) {
      const s = [];
      for (const i of Object.keys(r.sources)) {
        const n = r.sources[i];
        "name" in n || (n.name = i), s.push(n);
      }
      r.sources = s;
    }
    r.sources = r.sources.map((s) => {
      if (typeof s == "string") {
        const i = { url: s }, n = /\.(\w+)$/.exec(s);
        return n && (i.type = n[1].toLowerCase()), i;
      }
      return s;
    });
  }
  if (e.sourceUrl = e.sourceUrl || t, e.sourceUrl.startsWith("/") && (e.sourceUrl = new URL(e.sourceUrl, window.location.href).href), e.baseUrl = e.baseUrl || new URL(".", e.sourceUrl).href, e.baseUrl.length && !e.baseUrl.endsWith("/") && (e.baseUrl += "/"), e.sourceUrl) {
    const s = [];
    e.tracks && s.push(...e.tracks), e.stores && s.push(...Object.values(e.stores)), e.names && s.push(e.names);
    for (const i of s)
      i.baseUrl || (i.baseUrl = e.baseUrl || "/");
    e.refSeqs && typeof e.refSeqs == "string" && (e.refSeqs = new URL(e.refSeqs, e.sourceUrl).href), e.nameUrl && (e.nameUrl = new URL(e.nameUrl, e.sourceUrl).href);
  }
  e.stores = e.stores || {};
  for (let s of e.tracks || []) {
    if (s.config) {
      const n = s.config;
      s.config = void 0, s = { ...n, ...s };
    }
    if (s.store)
      continue;
    let i;
    s.type === "FeatureTrack" ? i = "JBrowse/View/Track/HTMLFeatures" : s.type === "ImageTrack" ? i = "JBrowse/View/Track/FixedImage" : s.type === "ImageTrack.Wiggle" ? i = "JBrowse/View/Track/FixedImage/Wiggle" : s.type === "SequenceTrack" ? i = "JBrowse/View/Track/Sequence" : i = W("JBrowse/View/Track", s.type), s.type = i, R(e, s), s.histograms && (s.histograms.baseUrl || (s.histograms.baseUrl = s.baseUrl), R(e, s.histograms));
  }
  return e;
}
function W(e, t) {
  return t ? (t.includes("/") || (t = `${e}/${t}`), t = t.replace(/^\//, ""), t) : "";
}
function ue(e, t) {
  var r, s;
  return e ? !((r = e.type) === null || r === void 0) && r.includes("/FixedImage") ? `JBrowse/Store/TiledImage/Fixed${e.backendVersion === 0 ? "_v0" : ""}` : /\.jsonz?$/i.test(t) ? `JBrowse/Store/SeqFeature/NCList${e.backendVersion === 0 ? "_v0" : ""}` : /\.bam$/i.test(t) ? "JBrowse/Store/SeqFeature/BAM" : /\.cram$/i.test(t) ? "JBrowse/Store/SeqFeature/CRAM" : /\.gff3?$/i.test(t) ? "JBrowse/Store/SeqFeature/GFF3" : /\.bed$/i.test(t) ? "JBrowse/Store/SeqFeature/BED" : /\.vcf.b?gz$/i.test(t) ? "JBrowse/Store/SeqFeature/VCFTabix" : /\.gff3?.b?gz$/i.test(t) ? "JBrowse/Store/SeqFeature/GFF3Tabix" : /\.bed.b?gz$/i.test(t) ? "JBrowse/Store/SeqFeature/BEDTabix" : /\.(bw|bigwig)$/i.test(t) ? "JBrowse/Store/SeqFeature/BigWig" : /\.(bb|bigbed)$/i.test(t) ? "JBrowse/Store/SeqFeature/BigBed" : /\.(fa|fasta)$/i.test(t) ? "JBrowse/Store/SeqFeature/IndexedFasta" : /\.(fa|fasta)\.b?gz$/i.test(t) ? "JBrowse/Store/SeqFeature/BgzipIndexedFasta" : /\.2bit$/i.test(t) ? "JBrowse/Store/SeqFeature/TwoBit" : !((s = e.type) === null || s === void 0) && s.endsWith("/Sequence") ? "JBrowse/Store/Sequence/StaticChunked" : "" : "";
}
function R(e, t) {
  var r;
  const { urlTemplate: s = "" } = t, i = t.storeClass ? W("JBrowse/Store", t.storeClass) : ue(t, s);
  if (!i) {
    console.warn(`Unable to determine an appropriate data store to use with track '${t.label}', please explicitly specify a storeClass in the configuration.`);
    return;
  }
  const n = { ...t, type: i };
  n.name = (i === "JBrowse/Store/Sequence/StaticChunked" || i === "JBrowse/Store/Sequence/IndexedFasta" || i === "JBrowse/Store/SeqFeature/IndexedFasta" || i === "JBrowse/Store/SeqFeature/BgzipIndexedFasta" || i === "JBrowse/Store/SeqFeature/TwoBit" || i === "JBrowse/Store/Sequence/TwoBit" || t.useAsRefSeqStore) && !(!((r = e.stores) === null || r === void 0) && r.refseqs) ? "refseqs" : `store${K.objectHash(n)}`, e.stores || (e.stores = {}), e.stores[n.name] = n, t.store = n.name;
}
function v(e) {
  return e.uri !== void 0;
}
function U(e) {
  return e.localPath !== void 0;
}
async function Se(e = { uri: "", locationType: "UriLocation" }, t = {
  include: ["{dataRoot}/trackList.json", "{dataRoot}/tracks.conf"]
}, r = { uri: "", locationType: "UriLocation" }) {
  const s = "uri" in e ? "uri" : "localPath", i = JSON.parse(JSON.stringify(e));
  let n = "";
  if (v(e) && (n = e.uri), U(e) && (n = e.localPath), n.endsWith("/") && (i[s] = n.slice(0, -1)), v(r) && r.uri || U(r) && r.localPath) {
    const u = "uri" in r ? "uri" : "localPath";
    let y = "";
    v(r) && (y = r.uri), U(r) && (y = r.localPath), y.endsWith("/") && (y = y.slice(0, -1));
    let d = {};
    for (const w of ["jbrowse.conf", "jbrowse_conf.json"]) {
      let p = null;
      try {
        p = await G({
          [u]: `${y}/${w}`
        });
      } catch {
        console.error(`tried to access ${y}/${w}, but failed`);
      }
      d = B(d, p) || {};
    }
    return i[s] && (d.dataRoot = i[s]), C(d);
  }
  const l = g(t, window.location.href);
  return i[s] && (l.dataRoot = i[s]), C(l);
}
async function C(e, t = ye) {
  const r = O(structuredClone(t), e);
  let s = await ce(r);
  return s = B(s, e) || s, q(s, s), we(s), s;
}
async function G(e) {
  const t = await H.openLocation(e).readFile("utf8");
  return v(e) ? P(t, e.uri) : U(e) ? P(t, e.localPath) : P(t);
}
function P(e, t = "") {
  return e.trim().startsWith("{") ? ne(e, t) : ie(e, t);
}
function B(e, t) {
  if (t === null)
    return null;
  e === null && (e = {});
  for (const r of Object.keys(t))
    if (r === "tracks" && r in e) {
      const s = e[r] || [], i = t[r] || [];
      if (Array.isArray(s) && Array.isArray(i))
        e[r] = fe(s, i);
      else
        throw new Error(`Track config has not been properly regularized: ${s} ${i}`);
    } else !de(r) && r in e && typeof t[r] == "object" && typeof e[r] == "object" ? e[r] = O(e[r], t[r]) : r === "dataRoot" ? (e[r] === void 0 || e[r] === "data" && t[r] !== void 0) && (e[r] = t[r]) : (e[r] === void 0 || t[r] !== void 0) && (e[r] = t[r]);
  return e;
}
function fe(e, t) {
  if (!t.length)
    return e;
  const r = {};
  for (const [s, i] of e.entries())
    i.index = s, r[i.label] = i;
  for (const s of t) {
    const i = r[s.label];
    i ? B(i, s) : e.push(s);
  }
  return e;
}
async function ce(e) {
  e = structuredClone(e);
  async function t(r, s) {
    const i = r.sourceUrl || r.baseUrl;
    if (!i)
      throw new Error(`Could not determine source URL: ${JSON.stringify(r)}`);
    const n = B(structuredClone(s), r);
    if (!n)
      throw new Error("Problem merging configs");
    const l = q(le(r.include || []), n);
    r.include = void 0;
    const u = l.map(async (d) => {
      d.cacheBuster = e.cacheBuster;
      const w = await G({
        uri: new URL(d.url, i).href,
        locationType: "UriLocation"
      });
      return t(w, n);
    }), y = await Promise.all(u);
    for (const d of y)
      r = B(r, d) || r;
    return r;
  }
  return t(e, {});
}
function le(e) {
  return e ? (Array.isArray(e) || (e = [e]), e.map((t) => (typeof t == "string" && (t = { url: t }), "format" in t || (t.format = t.url.endsWith(".conf") ? "conf" : "JB_json"), t.format === "JB_json" && !("version" in t) && (t.version = 1), t))) : [];
}
function q(e, t) {
  if (!e)
    return e;
  if (Array.isArray(e))
    for (let r = 0; r < e.length; r += 1)
      e[r] = q(e[r], t);
  else if (typeof e == "object") {
    const r = e;
    for (const s of Object.keys(r))
      r[s] = q(r[s], t);
  } else if (typeof e == "string")
    return se(e, t);
  return e;
}
function de(e) {
  return e === "datasets";
}
const ye = {
  tracks: [],
  containerID: "GenomeBrowser",
  dataRoot: "data",
  show_tracklist: !0,
  show_nav: !0,
  show_menu: !0,
  show_overview: !0,
  show_fullviewlink: !0,
  update_browser_title: !0,
  updateBrowserURL: !0,
  refSeqs: "{dataRoot}/seq/refSeqs.json",
  include: ["jbrowse.conf", "jbrowse_conf.json"],
  nameUrl: "{dataRoot}/names/root.json",
  datasets: {
    _DEFAULT_EXAMPLES: !0,
    volvox: { url: "?data=sample_data/json/volvox", name: "Volvox Example" },
    modencode: {
      url: "?data=sample_data/json/modencode",
      name: "MODEncode Example"
    },
    yeast: { url: "?data=sample_data/json/yeast", name: "Yeast Example" }
  },
  highlightSearchedRegions: !1,
  highResolutionMode: "auto"
};
function we(e) {
  if (e.tracks || (e.tracks = []), !e.baseUrl)
    throw new Error("Must provide a `baseUrl` in configuration");
}
export {
  C as createFinalConfig,
  G as fetchConfigFile,
  Se as fetchJb1,
  P as parseJb1
};
//# sourceMappingURL=jb1ConfigLoad-DsWxhvl2.js.map