taxonium-component/dist/doConnect-BIGIRTf-.js

React component for exploring large phylogenetic trees in the browser

import { bZ as I, a4 as A, u as y, t as O, s as g } from "./JBrowsePanel-uJIA-L6s.js";
class L {
  constructor(e = [], c) {
    this.data = {};
    const { checkIndent: o = !0, skipValidation: d = !1 } = c ?? {}, s = typeof e == "string" ? e.trimEnd().split(/\r?\n/) : e;
    let i, t;
    for (const l of s) {
      if (l === "")
        throw new Error("Invalid stanza, contained blank lines");
      if (l.trim().startsWith("#"))
        continue;
      if (l.trimEnd().endsWith("\\")) {
        const f = l.trimEnd().slice(0, -1);
        t ? t += f.trimStart() : t = f;
        continue;
      }
      let m = l;
      if (t && (m = t + m.trimStart(), t = void 0), i ?? o) {
        const f = /^([ \t]+)/.exec(m);
        if (i === void 0)
          f ? [, i] = f : i = "";
        else if (i === "" && f !== null || i && f && i !== f[1])
          throw new Error("Inconsistent indentation of stanza");
      } else
        i = "";
      const n = m.trim(), h = n.indexOf(" ");
      if (h === -1) {
        if (!this.nameKey)
          throw new Error("First line in a stanza must have both a key and a value");
        if (this.data[n])
          continue;
        this.data[n] = "";
        continue;
      }
      const r = n.slice(0, h), u = n.slice(h + 1);
      if (this.data[r] && u !== this.data[r])
        throw new Error(`Got duplicate key with a different value in stanza: "${r}" key has both ${this.data[r]} and ${u}`);
      this.nameKey || (this.nameKey = r, this.name = n.slice(h + 1)), this.data[r] = u;
    }
    d || this.validate();
  }
  validate() {
  }
}
class C {
  constructor(e = [], c) {
    this.data = {};
    const { checkIndent: o = !0, skipValidation: d = !1 } = c ?? {}, s = typeof e == "string" ? e.trimEnd().split(/(?:[\t ]*\r?\n){2,}/) : e;
    for (const i of s) {
      if (i === "")
        throw new Error("Invalid stanza, was empty");
      if (i.startsWith("include") || i.trim().startsWith("#") && i.trimEnd().split(/\r?\n/).map((m) => m.trim()).every((m) => m.startsWith("#")))
        continue;
      const t = new L(i, { checkIndent: o });
      if (!this.nameKey)
        this.nameKey = t.nameKey;
      else if (t.nameKey !== this.nameKey)
        throw new Error(`The first line in each stanza must have the same key. Saw both ${this.nameKey} and ${t.nameKey}`);
      if (!t.name)
        throw new Error(`No stanza name: ${t.name}`);
      if (this.data[t.name])
        throw new Error(`Got duplicate stanza name: ${t.name}`);
      this.data[t.name] = t;
    }
    d || this.validate();
  }
  validate() {
  }
}
function T(a, e, c = "") {
  const o = [];
  for (const d of e)
    a.data[d] || o.push(d);
  if (o.length > 0)
    throw new Error(`${c} is missing required entr${o.length === 1 ? "y" : "ies"}: ${o.join(", ")}`);
}
class P extends C {
  constructor(e, c) {
    super(e, { ...c, checkIndent: !1 });
  }
  validate() {
    var e;
    if (this.nameKey !== "track")
      throw new Error(`trackDb has "${this.nameKey}" instead of "track" as the first line in each track`);
    for (const [c, o] of Object.entries(this.data)) {
      const d = Object.keys(o.data);
      T(o, ["track", "shortLabel"], `Track ${c}`);
      const s = /* @__PURE__ */ new Set([
        "superTrack",
        "compositeTrack",
        "container",
        "view"
      ]);
      if (!d.some((l) => s.has(l))) {
        if (!d.includes("bigDataUrl"))
          throw new Error(`Track ${c} is missing required key "bigDataUrl"`);
        if (!d.includes("type") && !Object.keys(this.settings(c)).includes("type"))
          throw new Error(`Neither track ${c} nor any of its parent tracks have the required key "type"`);
      }
      let i = c;
      do
        i = (e = this.data[i]) == null ? void 0 : e.parent, i && ([i] = i.split(" "));
      while (i);
      const t = this.data[c];
      t && (this.data[c] = t);
    }
  }
  /**
   * Gets all track entries including those of parent tracks, with closer
   * entries overriding more distant ones
   * @param {string} trackName The name of a track
   * @throws {Error} Throws if track name does not exist in the trackDb
   */
  settings(e) {
    var s;
    if (!this.data[e])
      throw new Error(`Track ${e} does not exist`);
    const c = [e];
    let o = e;
    do
      o = (s = this.data[o]) == null ? void 0 : s.parent, o && c.push(o);
    while (o);
    const d = {};
    c.reverse();
    for (const i of c) {
      const t = this.data[i];
      if (t)
        for (const [l, m] of Object.entries(t))
          d[l] = m;
    }
    return d;
  }
}
class G extends C {
  validate(e = ["genome", "trackDb"]) {
    if (this.nameKey !== "genome")
      throw new Error('Genomes file must begin with a line like "genome <genome_name>"');
    for (const [c, o] of Object.entries(this.data))
      T(o, e, `genome ${c}`);
  }
}
class W extends L {
  validate() {
    T(this, ["hub", "shortLabel", "longLabel", "genomesFile", "email"], "Hub file");
  }
}
class H {
  constructor(e) {
    const [c, o, ...d] = e.trimEnd().split(/(?:[\t ]*\r?\n){2,}/);
    this.hubData = new L(c), this.validateHub(), this.genome = new L(o), this.validateGenomeSection(), this.tracks = new P(d.join(`

`), {
      skipValidation: !1
    });
  }
  validateHub() {
    if (this.hubData.nameKey !== "hub")
      throw new Error('Hub file must begin with a line like "hub <hub_name>"');
    T(this.hubData, [
      "hub",
      "shortLabel",
      "longLabel",
      "email",
      "descriptionUrl"
    ]);
  }
  validateGenomeSection() {
    if (this.genome.nameKey !== "genome")
      throw new Error('Genomes file must begin with a line like "genome <genome_name>"');
  }
}
var R = I();
async function V(a) {
  const e = await A.openLocation(a).readFile("utf8");
  return new G(e);
}
async function _(a) {
  const e = await A.openLocation(a).readFile("utf8");
  return new P(e);
}
function U(a, e) {
  return {
    uri: new URL(a, new URL(e.uri, e.baseUri)).href,
    locationType: "UriLocation"
  };
}
function F(a, e, c) {
  return U(a || e, c);
}
function k(a, e) {
  return a ? {
    uri: a,
    locationType: "LocalPath"
  } : {
    uri: e,
    locationType: "UriLocation"
  };
}
function b(a, e) {
  return new URL(a, e).href;
}
function N({ trackDb: a, trackDbLoc: e, assemblyName: c, sequenceAdapter: o, baseUrl: d }) {
  const s = /* @__PURE__ */ new Set([
    "superTrack",
    "compositeTrack",
    "container",
    "view"
  ]);
  return Object.entries(a.data).map(([i, t]) => {
    var l;
    const { data: m } = t;
    if (!Object.keys(m).some((n) => s.has(n))) {
      const n = [];
      let h = i;
      do
        h = ((l = a.data[h]) === null || l === void 0 ? void 0 : l.data.parent) || "", h && (h = h.split(" ")[0], n.push(a.data[h]));
      while (h);
      return n.reverse(), {
        metadata: {
          ...t.data,
          ...t.data.html ? {
            html: `<a href="${b(t.data.html, d)}">${t.data.html}</a>`
          } : {}
        },
        category: [
          t.data.group,
          ...n.map((r) => r == null ? void 0 : r.data.group).filter((r) => !!r)
        ].filter((r) => !!r),
        ...M({
          track: t,
          trackDbLoc: e,
          trackDb: a,
          sequenceAdapter: o
        })
      };
    }
  }).filter(y.notEmpty).map((i) => ({
    ...i,
    trackId: `ucsc-trackhub-${y.objectHash(i)}`,
    assemblyNames: [c]
  }));
}
function M({ track: a, trackDbLoc: e, trackDb: c, sequenceAdapter: o }) {
  var d;
  const { data: s } = a, i = s.parent || "", t = s.bigDataUrl || "", l = s.bigDataIndex || "", m = s.type || ((d = c.data[i]) === null || d === void 0 ? void 0 : d.data.type) || "", n = (s.shortLabel || "") + (t.includes("xeno") ? " (xeno)" : ""), h = y.isUriLocation(e);
  let r = m.split(" ")[0] || "";
  r === "bam" && t.toLowerCase().endsWith("cram") && (r = "cram");
  const u = h ? U(t, e) : k(t);
  return r === "bam" ? {
    type: "AlignmentsTrack",
    name: n,
    description: s.longLabel,
    adapter: {
      type: "BamAdapter",
      bamLocation: u,
      index: {
        location: h ? F(l, `${t}.bai`, e) : k(l, `${t}.bai`)
      }
    }
  } : r === "cram" ? {
    type: "AlignmentsTrack",
    name: n,
    description: s.longLabel,
    adapter: {
      type: "CramAdapter",
      cramLocation: u,
      craiLocation: h ? F(l, `${t}.crai`, e) : k(l, `${t}.crai`),
      sequenceAdapter: o
    }
  } : r === "bigWig" ? {
    type: "QuantitativeTrack",
    name: n,
    description: s.longLabel,
    adapter: {
      type: "BigWigAdapter",
      bigWigLocation: u
    }
  } : r.startsWith("big") ? {
    type: "FeatureTrack",
    name: n,
    description: s.longLabel,
    adapter: {
      type: "BigBedAdapter",
      bigBedLocation: u
    }
  } : r === "vcfTabix" ? {
    type: "VariantTrack",
    name: n,
    description: s.longLabel,
    adapter: {
      type: "VcfTabixAdapter",
      vcfGzLocation: u,
      index: {
        location: h ? F(l, `${t}.tbi`, e) : k(l, `${t}.tbi`)
      }
    }
  } : r === "hic" ? {
    type: "HicTrack",
    name: n,
    description: s.longLabel,
    adapter: {
      type: "HicAdapter",
      hicLocation: u
    }
  } : O.generateUnknownTrackConf(n, r);
}
async function Z(a) {
  var e;
  const { pluginManager: c } = y.getEnv(a), o = y.getSession(a), d = [];
  try {
    const s = g.getConf(a, "hubTxtLocation"), i = await A.openLocation(s).readFile("utf8"), t = b(s.uri, s.baseUri), { assemblyManager: l } = o;
    if (i.includes("useOneFile on")) {
      const m = new H(i), { genome: n, tracks: h } = m, r = n.name, u = n.data.description;
      l.get(r) || o.addSessionAssembly({
        name: r,
        displayName: u,
        sequence: {
          type: "ReferenceSequenceTrack",
          metadata: {
            ...n.data,
            ...n.data.htmlPath ? {
              htmlPath: `<a href="${b(n.data.htmlPath, t)}">${n.data.htmlPath}</a>`
            } : {}
          },
          trackId: `${r}-${R.nanoid()}`,
          adapter: {
            type: "TwoBitAdapter",
            twoBitLocation: {
              uri: b(n.data.twoBitPath, t)
            },
            chromSizesLocation: {
              uri: b(n.data.chromSizes, t)
            }
          }
        },
        ...n.data.chromAliasBb ? {
          refNameAliases: {
            adapter: {
              type: "BigBedAdapter",
              uri: b(n.data.chromAliasBb, t)
            }
          }
        } : {}
      });
      const w = l.get(r), v = g.getConf(w, ["sequence", "adapter"]), $ = N({
        trackDb: h,
        trackDbLoc: s,
        assemblyName: r,
        sequenceAdapter: v,
        baseUrl: t
      });
      a.addTrackConfs($), c.evaluateExtensionPoint("LaunchView-LinearGenomeView", {
        session: o,
        assembly: r,
        tracklist: !0,
        loc: n.data.defaultPos
      });
    } else {
      const n = new W(i).data.genomesFile;
      if (!n)
        throw new Error("genomesFile not found on hub");
      const h = b(s.uri, s.baseUri), r = h ? {
        uri: b(n, h),
        locationType: "UriLocation"
      } : {
        localPath: n,
        locationType: "LocalPathLocation"
      }, u = await V(r), f = {};
      for (const [p, E] of Object.entries(u.data)) {
        const K = g.getConf(a, "assemblyNames");
        if (K.length > 0 && !K.includes(p))
          continue;
        const S = l.get(p);
        if (!S) {
          d.push(p);
          continue;
        }
        const x = E.data.trackDb;
        if (!x)
          throw new Error("genomesFile not found on hub");
        const B = new URL(n, h), z = h ? {
          uri: new URL(x, B).href,
          locationType: "UriLocation"
        } : {
          localPath: x,
          locationType: "LocalPathLocation"
        }, D = await _(z), q = g.getConf(S, ["sequence", "adapter"]), j = N({
          trackDb: D,
          trackDbLoc: z,
          assemblyName: p,
          sequenceAdapter: q,
          baseUrl: h
        });
        a.addTrackConfs(j), f[p] = j.length;
      }
      const w = Object.entries(f), v = w.length ? `Loaded data from these assemblies: ${w.map(([p, E]) => `${p} (${E} tracks)`).join(", ")}` : "", $ = d.length ? `Skipped data from these assemblies: ${d.join(", ")}` : "";
      o.notify([v, $].filter((p) => !!p).join(". "), "success");
    }
  } catch (s) {
    console.error(s), o.notifyError(`${g.getConf(a, "name")}: "${s}"`, s), (e = o.breakConnection) === null || e === void 0 || e.call(o, a.configuration);
  }
}
export {
  Z as doConnect
};
//# sourceMappingURL=doConnect-BIGIRTf-.js.map