@sjcrh/proteinpaint-client 2.181.0 → 2.183.0

package/dist/chunk-7RN3L2BX.js

@@ -0,0 +1,1788 @@
+import {
+  deepFreeze,
+  sleep
+} from "./chunk-MVTCBVSX.js";
+import {
+  ISOFORM_EXPRESSION,
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION,
+  TermTypes,
+  isNumericTerm
+} from "./chunk-6ITDJ5UR.js";
+import {
+  dtcnv,
+  dtfusionrna,
+  dtsnvindel as dtsnvindel2,
+  dtsv,
+  mclass,
+  mclassdeletion,
+  mclassinsertion,
+  mclassmnv,
+  mclassnonstandard as mclassnonstandard2,
+  mclasssnv,
+  morigingermline,
+  morigingermlinenonpathogenic,
+  morigingermlinepathogenic,
+  moriginrelapse,
+  moriginsomatic,
+  vepinfo
+} from "./chunk-XYFDBYOY.js";
+import {
+  isNumeric
+} from "./chunk-TV74I3Y5.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+
+// ../shared/utils/src/bulk.js
+function init_bulk_flag(genome) {
+  if (!genome) {
+    return null;
+  }
+  const mclasslabel2key2 = {};
+  for (const n in mclass) {
+    mclasslabel2key2[mclass[n].label.toUpperCase()] = n;
+  }
+  return {
+    genome,
+    mclasslabel2key: mclasslabel2key2,
+    data: {},
+    sample2disease: {},
+    // (proof) k: sample, v: disease
+    // will only record this when origin is used
+    patient2st: {},
+    // k: patient, v: { k: sampletype, v: sample }
+    // new sample names always override old
+    good: 0,
+    geneToUpper: true,
+    // option to not force uppercase on gene names
+    snv: {
+      loaded: false,
+      header: null,
+      badlines: [],
+      // jinghui: based on missense/silent ratio of entire dataset to decide whether to include silent when importing...
+      // hard-coded class codes
+      missense: 0,
+      silent: 0
+    },
+    svjson: {
+      loaded: false,
+      header: null,
+      badlines: []
+    },
+    fusion: {
+      loaded: false,
+      header: null,
+      badlines: [],
+      original: []
+    },
+    sv: {
+      loaded: false,
+      header: null,
+      badlines: [],
+      original: []
+    },
+    cnv: {
+      loaded: false,
+      header: null,
+      badlines: []
+    },
+    itd: {
+      loaded: false,
+      header: null,
+      badlines: []
+    },
+    del: {
+      loaded: false,
+      header: null,
+      badlines: []
+    },
+    truncation: {
+      loaded: false,
+      header: null,
+      badlines: []
+    }
+  };
+}
+function parsesample(m, flag, i2, lst, badline) {
+  let variantorigin = moriginsomatic;
+  if (m.sampletype) {
+    const s = m.sampletype.toLowerCase();
+    switch (s) {
+      case "relapse":
+        variantorigin = moriginrelapse;
+        break;
+      case "germline":
+        variantorigin = morigingermline;
+        break;
+      case "somatic":
+      case "diagnosis":
+        break;
+    }
+    if (m.sample) {
+      if (m.patient) {
+      } else {
+        m.patient = m.sample + " " + m.sampletype;
+      }
+    } else {
+      if (m.patient) {
+        m.sample = m.patient + " " + m.sampletype;
+      } else {
+      }
+    }
+  } else {
+    if (m.patient) {
+      if (m.sample) {
+        m.sampletype = m.sample;
+      } else {
+        m.sample = m.sampletype = m.patient;
+      }
+    } else {
+      if (m.sample) {
+        m.sampletype = m.sample;
+      } else {
+      }
+    }
+  }
+  if (m.origin) {
+    const s = m.origin.toLowerCase();
+    switch (s) {
+      case "r":
+      case "relapse":
+        variantorigin = moriginrelapse;
+        m.isrim2 = true;
+        break;
+      case "g":
+      case "germline":
+        variantorigin = morigingermline;
+        m.isrim1 = true;
+        break;
+      case "gp":
+      case "germline pathogenic":
+        variantorigin = morigingermlinepathogenic;
+        m.isrim1 = true;
+        break;
+      case "gnp":
+      case "germline nonpathogenic":
+      case "germline non-pathogenic":
+        variantorigin = morigingermlinenonpathogenic;
+        m.isrim1 = true;
+        break;
+      case "s":
+      case "somatic":
+      case "diagnosis":
+        variantorigin = moriginsomatic;
+        break;
+    }
+  }
+  m.origin = variantorigin;
+  if (!m.sample && !m.patient) {
+    return;
+  }
+  const nopatientname = "no patient/individual name";
+  let p;
+  if (m.patient) {
+    if (!flag.patient2st[m.patient]) {
+      flag.patient2st[m.patient] = {};
+    }
+    flag.patient2st[m.patient][m.sampletype] = m.sample;
+  } else {
+    if (!flag.patient2st[nopatientname]) {
+      flag.patient2st[nopatientname] = {};
+    }
+    flag.patient2st[nopatientname][m.sampletype] = m.sample;
+  }
+  if (m.sample) {
+    if (m.disease) {
+      if (m.sample in flag.sample2disease) {
+        if (m.disease != flag.sample2disease[m.sample]) {
+          flag.snv.badlines.push([
+            i2,
+            'conflict of disease types for sample "' + m.sample + '": ' + m.disease + ", " + flag.sample2disease[m.sample],
+            lst
+          ]);
+          return true;
+        }
+      } else {
+        flag.sample2disease[m.sample] = m.disease;
+      }
+    }
+  }
+  return false;
+}
+
+// ../shared/utils/src/clustering.js
+var clusterMethodLst = [
+  {
+    label: "Average",
+    value: "average",
+    title: `Cluster by average value`
+  },
+  {
+    label: `Complete`,
+    value: "complete",
+    title: `Use the complete clustering method`
+  },
+  {
+    label: `Single`,
+    value: "single",
+    title: `Use the single clustering method`
+  },
+  {
+    label: `Ward.D`,
+    value: "ward.D",
+    title: `Use the ward.D clustering method`
+  },
+  {
+    label: `Ward.D2`,
+    value: "ward.D2",
+    title: `Use the ward.D2 clustering method`
+  },
+  {
+    label: `Mcquitty`,
+    value: "mcquitty",
+    title: `Use the Mcquity clustering method`
+  }
+  /* These methods are currently disabled because the dendrogram lines tend to cross one another.
+  {
+  	label: `Centroid`,
+  	value: 'centroid',
+  	title: `Use the centroid clustering method`
+  },
+     	{
+  	label: `Median`,
+  	value: 'median',
+  	title: `Use the median clustering method`
+  }
+         */
+];
+var distanceMethodLst = [
+  {
+    label: "Euclidean",
+    value: "euclidean",
+    title: `Calculate distance using euclidean method`
+  },
+  {
+    label: "Maximum",
+    value: "maximum",
+    title: `Maximum distance between two components of x and y`
+  },
+  {
+    label: "Manhattan",
+    value: "manhattan",
+    title: `Calculate distance using the absolute distance between the two vectors`
+  },
+  {
+    label: "Canberra",
+    value: "canberra",
+    title: `Calculate distance using Canberra method`
+  }
+];
+
+// ../shared/utils/src/fileSize.js
+function fileSize(v) {
+  if (v > 1e9) return (v / 1e9).toFixed(2) + " GB";
+  if (v > 1e6) return (v / 1e6).toFixed(2) + " MB";
+  if (v > 1e3) return (v / 1e3).toFixed(2) + " KB";
+  return v + " Bytes";
+}
+
+// ../shared/utils/src/mds3tk.js
+var ssmIdFieldsSeparator = "__";
+function summarize_mclass(mlst) {
+  const m2c = /* @__PURE__ */ new Map();
+  const cnvs = [];
+  for (const m of mlst) {
+    if (m.dt == dtcnv) {
+      cnvs.push(m);
+      continue;
+    }
+    const key = m.class || m.dt;
+    m2c.set(key, 1 + (m2c.get(key) || 0));
+  }
+  if (cnvs.length) {
+    if (Number.isFinite(cnvs[0].value)) {
+      m2c.set(dtcnv, cnvs.length);
+    } else {
+      for (const c of cnvs) {
+        if (!c.class) continue;
+        m2c.set(c.class, 1 + (m2c.get(c.class) || 0));
+      }
+    }
+  }
+  return [...m2c].sort((i2, j) => j[1] - i2[1]);
+}
+function guessSsmid(ssmid) {
+  const l = ssmid.split(ssmIdFieldsSeparator);
+  if (l.length == 4) {
+    const [chr, tmp, ref, alt] = l;
+    const pos = Number(tmp);
+    if (Number.isNaN(pos)) throw "ssmid snvindel pos not integer";
+    return { dt: dtsnvindel2, l: [chr, pos, ref, alt] };
+  }
+  if (l.length == 5) {
+    const [chr, _start, _stop, _class, _value] = l;
+    const start = Number(_start), stop = Number(_stop), value = _value == "" ? null : Number(_value);
+    if (Number.isNaN(start) || Number.isNaN(stop))
+      throw "ssmid cnv start/stop not integer";
+    return { dt: dtcnv, l: [chr, start, stop, _class, value] };
+  }
+  if (l.length == 6) {
+    if (l[3] == "+" || l[3] == "-") {
+      const [_dt, chr2, _pos, strand, _pi, _mname] = l;
+      const mname = decodeURIComponent(_mname);
+      const dt = Number(_dt);
+      if (dt != dtsv && dt != dtfusionrna) throw "ssmid dt not sv/fusion";
+      const pos = Number(_pos);
+      if (Number.isNaN(pos)) throw "ssmid svfusion position not integer";
+      const pairlstIdx = Number(_pi);
+      if (Number.isNaN(pairlstIdx)) throw "ssmid pairlstIdx not integer";
+      return { dt, l: [dt, chr2, pos, strand, pairlstIdx, mname] };
+    }
+    const [chr, _start, _stop, _class, _value, sample] = l;
+    const start = Number(_start), stop = Number(_stop), value = _value == "" ? null : Number(_value);
+    if (Number.isNaN(start) || Number.isNaN(stop))
+      throw "ssmid cnv start/stop not integer";
+    return { dt: dtcnv, l: [chr, start, stop, _class, value, sample] };
+  }
+  throw "unknown ssmid";
+}
+
+// ../shared/utils/src/termdb.initbinconfig.js
+function initBinConfig(data, opts = {}) {
+  if (!data.length)
+    return {
+      mode: "discrete",
+      type: "regular-bin",
+      startinclusive: true,
+      bin_size: null,
+      first_bin: { stop: null }
+    };
+  if (data.find((d) => !Number.isFinite(d)))
+    throw new Error("non-numeric values found");
+  let binConfig;
+  const s = new Set(data);
+  if (s.size === 1) {
+    const value = [...s][0];
+    binConfig = {
+      type: "custom-bin",
+      lst: [
+        {
+          stop: value,
+          stopinclusive: false,
+          startunbounded: true,
+          label: "<" + value
+        },
+        {
+          start: value,
+          stop: value,
+          startinclusive: true,
+          stopinclusive: true,
+          label: "=" + value
+        },
+        {
+          start: value,
+          startinclusive: false,
+          stopunbounded: true,
+          label: ">" + value
+        }
+      ]
+    };
+  } else {
+    data.sort((a, b) => a - b);
+    const l = data.length;
+    const min = data[0];
+    const max = data[l - 1];
+    const p5idx = Math.ceil(l * 0.05) - 1;
+    const p98idx = Math.ceil(l * 0.98) - 1;
+    const p5 = data[p5idx];
+    const p98 = data[p98idx];
+    const binSize = p98 != p5 ? (p98 - p5) / 8 : (max - min) / 8;
+    const firstBinStop = Math.max(min + binSize, p5);
+    let [binSize_rnd, firstBinStop_rnd, lastBinStart_rnd, rounding] = roundBinVals(binSize, firstBinStop, max, min);
+    binConfig = {
+      type: "regular-bin",
+      startinclusive: true,
+      bin_size: binSize_rnd,
+      first_bin: { stop: firstBinStop_rnd }
+    };
+    if (lastBinStart_rnd) binConfig.last_bin = { start: lastBinStart_rnd };
+    if (rounding) binConfig.rounding = rounding;
+  }
+  if ("format" in opts) {
+    if (opts.format === "string") {
+      return JSON.stringify(binConfig);
+    } else {
+      throw "options are not in the correct format";
+    }
+  } else {
+    return binConfig;
+  }
+}
+function roundBinVals(binSize, firstBinStop, max, min) {
+  let binSize_rnd, firstBinStop_rnd, lastBinStart_rnd, rounding;
+  const log = Math.floor(Math.log10(binSize));
+  if (binSize >= 0.1 && binSize <= 2) {
+    binSize_rnd = Math.round(binSize / (1 * 10 ** log)) * (1 * 10 ** log);
+    firstBinStop_rnd = Math.round(firstBinStop / (1 * 10 ** log)) * (1 * 10 ** log);
+  } else {
+    binSize_rnd = Math.round(binSize / (5 * 10 ** log)) * (5 * 10 ** log);
+    firstBinStop_rnd = Math.round(firstBinStop / (5 * 10 ** log)) * (5 * 10 ** log);
+    if (binSize_rnd === 0) binSize_rnd = 1 * 10 ** log;
+    if (firstBinStop_rnd === 0) firstBinStop_rnd = 1 * 10 ** log;
+    if (binSize_rnd === 5 * 10 ** log && firstBinStop_rnd === 1 * 10 ** log)
+      firstBinStop_rnd = 5 * 10 ** log;
+  }
+  if (firstBinStop_rnd < min) firstBinStop_rnd = firstBinStop_rnd * 2;
+  const eighthBinStop_rnd = firstBinStop_rnd + binSize_rnd * 7;
+  if (max > eighthBinStop_rnd) {
+    lastBinStart_rnd = firstBinStop_rnd + binSize_rnd * 6;
+  }
+  if (binSize < 1) {
+    const digits = Math.abs(log);
+    binSize_rnd = Number(binSize_rnd.toFixed(digits));
+    firstBinStop_rnd = Number(firstBinStop_rnd.toFixed(digits));
+    if (lastBinStart_rnd)
+      lastBinStart_rnd = Number(lastBinStart_rnd.toFixed(digits));
+    rounding = "." + digits + "f";
+  }
+  if (Object.is(firstBinStop_rnd, -0)) firstBinStop_rnd = 0;
+  return [binSize_rnd, firstBinStop_rnd, lastBinStart_rnd, rounding];
+}
+
+// ../shared/utils/src/vcf.info.js
+function dissect_INFO(str) {
+  let findsemicolon = false;
+  let findequalorsemicolon = true;
+  let i2 = 0;
+  let idx = 0;
+  const k2v = {};
+  let lastkey;
+  while (i2 < str.length) {
+    const c = str[i2];
+    if (findequalorsemicolon) {
+      if (c == "=") {
+        findsemicolon = true;
+        findequalorsemicolon = false;
+        lastkey = str.substring(idx, i2);
+        idx = i2 + 1;
+      } else if (c == ";") {
+        k2v[str.substring(idx, i2)] = 1;
+        idx = i2 + 1;
+      }
+    } else if (findsemicolon && c == ";") {
+      findequalorsemicolon = true;
+      findsemicolon = false;
+      k2v[lastkey] = str.substring(idx, i2);
+      lastkey = null;
+      idx = i2 + 1;
+    }
+    i2++;
+  }
+  const remainstr = str.substr(idx, i2);
+  if (lastkey) {
+    k2v[lastkey] = remainstr;
+  } else {
+    k2v[remainstr] = 1;
+  }
+  return k2v;
+}
+
+// ../shared/utils/src/vcf.csq.js
+function parse_CSQ(str, header, m) {
+  if (!header) {
+    return null;
+  }
+  for (const thisannotation of str.split(",")) {
+    const lst = thisannotation.replace(/&/g, ",").split("|");
+    const o = {};
+    for (let i2 = 0; i2 < header.length; i2++) {
+      if (lst[i2]) {
+        o[header[i2].name] = lst[i2];
+      }
+    }
+    if (!o.Allele) {
+      continue;
+    }
+    let allele = null;
+    for (const a of m.mlst || m.alleles) {
+      if (a.allele_original == o.Allele) {
+        allele = a;
+        break;
+      }
+    }
+    if (!allele) {
+      if (o.Allele == "-") {
+        if (m.mlst) {
+          if (m.mlst.length == 1) {
+            allele = m.mlst[0];
+          }
+        } else if (m.alleles) {
+          if (m.alleles.length == 1) {
+            allele = m.alleles[0];
+          }
+        }
+      } else {
+        for (const a of m.mlst || m.alleles) {
+          if (a.allele_original.substr(1) == o.Allele) {
+            allele = a;
+            break;
+          }
+        }
+      }
+      if (!allele) {
+        continue;
+      }
+    }
+    if (!allele.csq) {
+      allele.csq = [];
+    }
+    allele.csq.push(o);
+    o._gene = o.SYMBOL || o.Gene;
+    if (o.Feature_type && o.Feature_type == "Transcript") {
+      o._isoform = o.Feature.split(".")[0];
+    } else {
+      o._isoform = o._gene;
+    }
+    if (o.Consequence) {
+      const [dt, cls, rank] = vepinfo(o.Consequence);
+      o._dt = dt;
+      o._class = cls;
+      o._csqrank = rank;
+    } else {
+      o._dt = dtsnvindel;
+      o._class = mclassnonstandard;
+    }
+    if (o.HGVSp) {
+      o._mname = decodeURIComponent(o.HGVSp.substr(o.HGVSp.indexOf(":") + 1));
+    } else if (o.Protein_position && o.Amino_acids) {
+      o._mname = decodeURIComponent(o.Protein_position + o.Amino_acids);
+    } else if (o.HGVSc) {
+      o._mname = o.HGVSc.substr(o.HGVSc.indexOf(":") + 1);
+    } else if (o.Existing_variation) {
+      o._name = o.Existing_variation;
+    } else {
+    }
+  }
+  return true;
+}
+
+// ../shared/utils/src/vcf.ann.js
+function parse_ANN(str, header, m) {
+  if (!header) {
+    return null;
+  }
+  for (const thisannotation of str.split(",")) {
+    const lst = thisannotation.replace(/&/g, ",").split("|");
+    const o = {};
+    for (let i2 = 0; i2 < header.length; i2++) {
+      if (lst[i2]) {
+        o[header[i2].name] = lst[i2];
+      }
+    }
+    if (!o.Allele) {
+      continue;
+    }
+    let allele = null;
+    for (const a of m.alleles) {
+      if (a.allele == o.Allele) {
+        allele = a;
+        break;
+      }
+    }
+    if (!allele) {
+      continue;
+    }
+    if (!allele.ann) {
+      allele.ann = [];
+    }
+    allele.ann.push(o);
+    o._gene = o.Gene_Name;
+    if (o.Feature_Type && o.Feature_Type == "transcript" && o.Feature_ID) {
+      o._isoform = o.Feature_ID.split(".")[0];
+    }
+    if (o.Annotation) {
+      const [dt, cls, rank] = vepinfo(o.Annotation);
+      o._dt = dt;
+      o._class = cls;
+      o._csqrank = rank;
+    } else {
+      o._dt = dtsnvindel;
+      o._class = mclassnonstandard;
+    }
+    if (o["HGVS.p"]) {
+      o._mname = o["HGVS.p"];
+    } else if (o["HGVS.c"]) {
+      o._mname = o["HGVS.c"];
+    } else {
+    }
+  }
+  return true;
+}
+
+// ../shared/utils/src/vcf.type.js
+function getVariantType(ref, alt) {
+  if (ref.length == 1 && alt.length == 1) {
+    if (alt == ".") {
+      return mclassdeletion;
+    }
+    return mclasssnv;
+  }
+  if (ref.length == alt.length) return mclassmnv;
+  if (ref.length < alt.length) return mclassinsertion;
+  if (ref.length > alt.length) return mclassdeletion;
+  return mclassnonstandard2;
+}
+
+// ../shared/utils/src/vcf.js
+var getallelename = new RegExp(/<(.+)>/);
+var mclasslabel2key = {};
+for (const k in mclass) {
+  mclasslabel2key[mclass[k].label.toUpperCase()] = k;
+}
+function vcfparsemeta(lines) {
+  let sample = [], errlst = [], info = {}, hasinfo = false, format = {}, hasformat = false;
+  for (const line of lines) {
+    if (!line.startsWith("#")) {
+      continue;
+    }
+    if (line.startsWith("#C")) {
+      sample = line.split("	").slice(9);
+      continue;
+    }
+    if (line.startsWith("##INFO")) {
+      const e = tohash(line.substring(8, line.length - 1), info);
+      if (e) {
+        errlst.push("INFO error: " + e);
+      } else {
+        hasinfo = true;
+      }
+      continue;
+    }
+    if (line.startsWith("##FORMAT")) {
+      const e = tohash(line.substring(10, line.length - 1), format);
+      if (e) {
+        errlst.push("FORMAT error: " + e);
+      } else {
+        hasformat = true;
+      }
+    }
+  }
+  const sampleobjlst = [];
+  for (const samplename of sample) {
+    const a = { name: samplename };
+    sampleobjlst.push(a);
+  }
+  if (info.CSQ) {
+    const lst = info.CSQ.Description.split(" Format: ");
+    if (lst[1]) {
+      const lst2 = lst[1].split("|");
+      if (lst2.length > 1) {
+        info.CSQ.csqheader = [];
+        for (const str of lst2) {
+          const attr = { name: str };
+          info.CSQ.csqheader.push(attr);
+        }
+      } else {
+        errlst.push("unknown format for CSQ header: " + info.CSQ.Description);
+      }
+    } else {
+      errlst.push("unknown format for CSQ header: " + info.CSQ.Description);
+    }
+  }
+  if (info.ANN) {
+    const lst = info.ANN.Description.split("'");
+    if (lst[1]) {
+      const lst2 = lst[1].split(" | ");
+      if (lst2.length) {
+        info.ANN.annheader = [];
+        for (const s of lst2) {
+          const attr = { name: s };
+          info.ANN.annheader.push(attr);
+        }
+      } else {
+        errlst.push(
+          'no " | " joined annotation fields for ANN (snpEff annotation): ' + info.ANN.Description
+        );
+      }
+    } else {
+      errlst.push(
+        "no single-quote enclosed annotation fields for ANN (snpEff annotation): " + info.ANN.Description
+      );
+    }
+  }
+  return [
+    hasinfo ? info : null,
+    hasformat ? format : null,
+    sampleobjlst,
+    errlst.length ? errlst : null
+  ];
+}
+function vcfparseline(line, vcf) {
+  const lst = line.split("	");
+  if (lst.length < 8) {
+    return ["line has less than 8 fields", null, null];
+  }
+  const rawpos = Number.parseInt(lst[2 - 1]);
+  if (!Number.isInteger(rawpos)) {
+    return ["invalid value for genomic position", null, null];
+  }
+  const refallele = lst[4 - 1];
+  const m = {
+    vcf_ID: lst[3 - 1],
+    chr: (vcf.nochr ? "chr" : "") + lst[1 - 1],
+    pos: rawpos - 1,
+    ref: refallele,
+    //refstr:refallele, // e.g. GA>GCC, ref:A, refstr:GA, "refstr" is required for matching in FORMAT
+    altstr: lst[5 - 1],
+    alleles: [
+      {
+        /*
+        ref allele only a placeholder, to be removed, this array only contains alt alleles
+        this is a must
+        also allows GT allele index to work
+        */
+        allele: refallele,
+        sampledata: []
+      }
+    ],
+    info: {},
+    // locus info, do not contain allele info
+    name: lst[3 - 1] == "." ? null : lst[3 - 1]
+  };
+  const altinvalid = [];
+  for (const alt of lst[5 - 1].split(",")) {
+    const a = {
+      ref: m.ref,
+      // may be corrected just below!
+      allele: alt,
+      // 5078356.TATCAGAGAA.GGGAGGA keep original allele for matching with csq which hardcodes original allele
+      allele_original: alt,
+      sampledata: [],
+      _m: m,
+      info: {}
+      // allele info, do not contain locus info
+    };
+    m.alleles.push(a);
+    if (alt[0] == "<") {
+      const tmp2 = alt.match(getallelename);
+      if (!tmp2) {
+        altinvalid.push(alt);
+        continue;
+      }
+      a.type = tmp2[1];
+      a.allele = tmp2[1];
+      a.issymbolicallele = true;
+    } else {
+      const [p, ref, alt2] = correctRefAlt(m.pos, m.ref, a.allele);
+      a.pos = p;
+      a.ref = ref;
+      a.allele = alt2;
+    }
+  }
+  if (lst[9 - 1] && lst[10 - 1]) {
+    parse_FORMAT2(lst, m, vcf);
+  }
+  m.alleles.shift();
+  const tmp = lst[8 - 1] == "." ? [] : dissect_INFO(lst[8 - 1]);
+  let badinfokeys = [];
+  if (vcf.info) {
+    badinfokeys = parse_INFO(tmp, m, vcf);
+  } else {
+    m.info = tmp;
+  }
+  const mlst = [];
+  for (const a of m.alleles) {
+    const m2 = {};
+    for (const k in m) {
+      if (k != "alleles") {
+        m2[k] = m[k];
+      }
+    }
+    for (const k in a) {
+      if (k == "allele") {
+        m2.alt = a[k];
+      } else if (k == "info") {
+        m2.altinfo = a[k];
+      } else {
+        m2[k] = a[k];
+      }
+    }
+    if (!m2.issymbolicallele && m2.alt != "NON_REF") {
+      m2.type = getVariantType(m2.ref, m2.alt);
+    }
+    mlst.push(m2);
+  }
+  return [
+    badinfokeys.length ? "unknown info keys: " + badinfokeys.join(",") : null,
+    mlst,
+    altinvalid.length > 0 ? altinvalid : null
+  ];
+}
+function correctRefAlt(p, ref, alt) {
+  while (ref.length > 1 && alt.length > 1 && ref[ref.length - 1] == alt[alt.length - 1]) {
+    ref = ref.substr(0, ref.length - 1);
+    alt = alt.substr(0, alt.length - 1);
+  }
+  while (ref.length > 1 && alt.length > 1 && ref[0] == alt[0]) {
+    ref = ref.substr(1);
+    alt = alt.substr(1);
+    p++;
+  }
+  return [p, ref, alt];
+}
+function parse_FORMAT2(lst, m, vcf) {
+  const formatfields = lst[9 - 1].split(":");
+  for (let _sampleidx = 9; _sampleidx < lst.length; _sampleidx++) {
+    const valuelst = lst[_sampleidx].split(":");
+    {
+      let none = true;
+      for (const v of valuelst) {
+        if (v != ".") {
+          none = false;
+          break;
+        }
+      }
+      if (none) {
+        continue;
+      }
+    }
+    const sampleidx = _sampleidx - 9;
+    for (let i2 = 1; i2 < m.alleles.length; i2++) {
+      const sobj = {};
+      if (vcf.samples && vcf.samples[sampleidx]) {
+        for (const k in vcf.samples[sampleidx]) {
+          sobj[k] = vcf.samples[sampleidx][k];
+        }
+      } else {
+        sobj.name = "missing_samplename_from_vcf_header";
+      }
+      m.alleles[i2].sampledata.push({
+        sampleobj: sobj
+      });
+    }
+    for (let fi = 0; fi < formatfields.length; fi++) {
+      const field = formatfields[fi];
+      const value = valuelst[fi];
+      if (value == ".") {
+        continue;
+      }
+      if (field == "GT") {
+        const splitter = value.indexOf("/") != -1 ? "/" : "|";
+        let gtsum = 0;
+        let unknowngt = false;
+        const gtalleles = [];
+        for (const i2 of value.split(splitter)) {
+          if (i2 == ".") {
+            unknowngt = true;
+            continue;
+          }
+          const j = Number.parseInt(i2);
+          if (Number.isNaN(j)) {
+            unknowngt = true;
+            continue;
+          }
+          gtsum += j;
+          const ale = m.alleles[j];
+          if (ale) {
+            gtalleles.push(ale.allele);
+          }
+        }
+        let gtallref = false;
+        if (!unknowngt) {
+          gtallref = gtsum == 0;
+        }
+        const genotype = gtalleles.join(splitter);
+        for (let i2 = 1; i2 < m.alleles.length; i2++) {
+          const ms = m.alleles[i2].sampledata[m.alleles[i2].sampledata.length - 1];
+          ms.GT = value;
+          ms.genotype = genotype;
+          if (gtallref) {
+            ms.gtallref = true;
+          }
+          ms.__gtalleles = gtalleles;
+        }
+        continue;
+      }
+      const formatdesc = vcf.format ? vcf.format[field] : null;
+      if (!formatdesc) {
+        for (let i2 = 1; i2 < m.alleles.length; i2++) {
+          m.alleles[i2].sampledata[m.alleles[i2].sampledata.length - 1][field] = value;
+        }
+        continue;
+      }
+      const isinteger = formatdesc.Type == "Integer";
+      const isfloat = formatdesc.Type == "Float";
+      if (formatdesc.Number && formatdesc.Number == "R" || field == "AD") {
+        const fvlst = value.split(",").map((i2) => {
+          if (isinteger) return Number.parseInt(i2);
+          if (isfloat) return Number.parseFloat(i2);
+          return i2;
+        });
+        for (let i2 = 1; i2 < m.alleles.length; i2++) {
+          if (fvlst[i2] != void 0) {
+            const m2 = m.alleles[i2];
+            const m2s = m2.sampledata[m2.sampledata.length - 1];
+            m2s[field] = {};
+            m2s[field][m2.ref] = fvlst[0];
+            m2s[field][m2.allele] = fvlst[i2];
+          }
+        }
+        continue;
+      }
+      if (formatdesc.Number && formatdesc.Number == "A") {
+        const fvlst = value.split(",").map((i2) => {
+          if (isinteger) return Number.parseInt(i2);
+          if (isfloat) return Number.parseFloat(i2);
+          return i2;
+        });
+        for (let i2 = 1; i2 < m.alleles.length; i2++) {
+          if (fvlst[i2 - 1] != void 0) {
+            const m2 = m.alleles[i2];
+            const m2s = m2.sampledata[m2.sampledata.length - 1];
+            m2s[field] = {};
+            m2s[field][m2.allele] = fvlst[i2 - 1];
+          }
+        }
+        continue;
+      }
+      for (let i2 = 1; i2 < m.alleles.length; i2++) {
+        m.alleles[i2].sampledata[m.alleles[i2].sampledata.length - 1][field] = value;
+      }
+    }
+  }
+  for (const a of m.alleles) {
+    for (const s of a.sampledata) {
+      if (s.AD) {
+        s.allele2readcount = {};
+        for (const k in s.AD) {
+          s.allele2readcount[k] = s.AD[k];
+        }
+      }
+    }
+  }
+}
+function tohash(s, hash2) {
+  const h = {}, err = [];
+  let prev = 0, prevdoublequote = false, k = null;
+  for (let i2 = 0; i2 < s.length; i2++) {
+    if (s[i2] == '"') {
+      i2++;
+      const thisstart = i2;
+      while (s[i2] != '"') {
+        i2++;
+      }
+      if (k) {
+        h[k] = s.substring(thisstart, i2);
+        k = null;
+      } else {
+        err.push("k undefined before double quotes");
+      }
+      prevdoublequote = true;
+      continue;
+    }
+    if (s[i2] == "=") {
+      k = s.substring(prev, i2);
+      prev = i2 + 1;
+      continue;
+    }
+    if (s[i2] == ",") {
+      if (prevdoublequote) {
+        prevdoublequote = false;
+      } else {
+        if (k) {
+          h[k] = s.substring(prev, i2);
+          k = null;
+        } else {
+          err.push("k undefined");
+        }
+      }
+      prev = i2 + 1;
+      continue;
+    }
+  }
+  if (k) {
+    h[k] = s.substring(prev, i);
+  }
+  if (h.ID) {
+    hash2[h.ID] = h;
+  } else {
+    return "no ID";
+  }
+  if (err.length) return err.join("\n");
+}
+function parse_INFO(tmp, m, vcf) {
+  const badinfokeys = [];
+  for (const key in tmp) {
+    if (vcf.info[key] == void 0) {
+      badinfokeys.push(key);
+      continue;
+    }
+    const value = tmp[key];
+    if (key == "CSQ") {
+      const okay = parse_CSQ(value, vcf.info.CSQ.csqheader, m);
+      if (!okay) {
+        m.info[key] = value;
+      }
+      continue;
+    }
+    if (key == "ANN") {
+      const okay = parse_ANN(value, vcf.info.ANN.annheader, m);
+      if (!okay) {
+        m.info[key] = value;
+      }
+      continue;
+    }
+    if (vcf.info[key].Type == "Flag") {
+      m.info[key] = key;
+      continue;
+    }
+    const __number = vcf.info[key].Number;
+    const isinteger = vcf.info[key].Type == "Integer";
+    const isfloat = vcf.info[key].Type == "Float";
+    if (__number == "0") {
+      m.info[key] = key;
+      continue;
+    }
+    if (__number == "A") {
+      const tt = value.split(",");
+      for (let j = 0; j < tt.length; j++) {
+        if (m.alleles[j]) {
+          m.alleles[j].info[key] = isinteger ? Number.parseInt(tt[j]) : isfloat ? Number.parseFloat(tt[j]) : tt[j];
+        }
+      }
+      continue;
+    }
+    if (__number == "R") {
+    }
+    if (__number == "1") {
+      m.info[key] = isinteger ? Number.parseInt(value) : isfloat ? Number.parseFloat(value) : value;
+      continue;
+    }
+    if (!value.split) {
+      continue;
+    }
+    const lst = value.split(",");
+    if (isinteger) {
+      m.info[key] = lst.map(Number.parseInt);
+    } else if (isfloat) {
+      m.info[key] = lst.map(Number.parseFloat);
+    } else {
+      m.info[key] = lst;
+    }
+  }
+  return badinfokeys;
+}
+
+// ../shared/utils/src/compute.percentile.js
+function computePercentile(values, percentile, sorted = false) {
+  if (!sorted) values.sort((a, b) => a - b);
+  const index = Math.abs(percentile / 100 * values.length - 1);
+  const value = Number.isInteger(index) ? (values[index] + values[index + 1]) / 2 : values[Math.ceil(index)];
+  return value;
+}
+
+// ../shared/utils/src/hash.js
+var encoder = new TextEncoder();
+async function hash(message) {
+  const msgUint8 = encoder.encode(message);
+  const hashBuffer = await crypto.subtle.digest("SHA-1", msgUint8);
+  const hashArray = Array.from(new Uint8Array(hashBuffer));
+  const hashHex = hashArray.map((b) => b.toString(16).padStart(2, "0")).join("");
+  return hexToBase64(hashHex).replace("=", "-");
+}
+function hexToBase64(hexStr) {
+  return btoa(
+    [...hexStr].reduce(
+      (acc, _, i2) => acc += !(i2 - 1 & 1) ? String.fromCharCode(parseInt(hexStr.substring(i2 - 1, i2 + 1), 16)) : "",
+      ""
+    )
+  );
+}
+
+// ../shared/utils/src/urljson.js
+var reserved = ["false", "true", "null", "undefined"];
+var delimiters = ['"', "{", "["];
+function encode(rawObject) {
+  const params = [];
+  for (const [key, value] of Object.entries(rawObject)) {
+    if (typeof value == "string" && !isNumeric(value) && !reserved.includes(value) && !delimiters.includes(value[0])) {
+      params.push(`${key}=${encodeURIComponent(value)}`);
+    } else if (value !== void 0) {
+      params.push(`${key}=${encodeURIComponent(JSON.stringify(value))}`);
+    }
+  }
+  return params.join("&");
+}
+
+// ../shared/utils/src/fetch-helpers.js
+async function processResponse(r) {
+  const ct = r.headers.get("content-type");
+  if (!ct) throw `missing response.header['content-type']`;
+  if (ct.includes("/json")) {
+    const payload = await r.json();
+    return payload;
+  }
+  if (ct.includes("/text") || ct.includes("text/")) {
+    return r.text();
+  }
+  if (ct.includes("multipart")) {
+    if (ct.startsWith("multipart/form-data")) return processFormData(r);
+    else throw `cannot handle response content-type: '${ct}'`;
+  }
+  if (ct == "application/x-ndjson-nestedkey") {
+    return processNDJSON_nestedKey(r);
+  }
+  return r.blob();
+}
+async function processFormData(res) {
+  const decoder = new TextDecoder();
+  const data = {};
+  try {
+    const form = await res.formData();
+    for (const [key, value] of form.entries()) {
+      if (value.type) {
+        data[key] = { headers: { "content-type": value.type }, body: value };
+      } else {
+        const body = !value ? [] : value.trim().split("\n").map(JSON.parse);
+        data[key] = { headers: { "content-type": "application/json" }, body };
+      }
+    }
+    return data;
+  } catch (e) {
+    throw e;
+  }
+}
+async function processNDJSON_nestedKey(r) {
+  const stream = r.body.pipeThrough(new TextDecoderStream());
+  const reader = stream.getReader();
+  let rootObj = {};
+  let buffer = "";
+  while (true) {
+    const { value, done } = await reader.read();
+    if (done) break;
+    buffer += value;
+    let parts = buffer.split("\n");
+    buffer = parts.pop();
+    for (const line of parts) {
+      if (line.trim()) {
+        const [keys, data] = JSON.parse(line);
+        if (!keys.length) rootObj = data;
+        else {
+          const lastKey = keys.pop();
+          let target = rootObj;
+          for (const k of keys) target = target[k];
+          target[lastKey] = data;
+        }
+      }
+    }
+  }
+  return rootObj;
+}
+var cacheLifetime = 1e3 * 60 * 5;
+async function getDataName(url, init) {
+  const dataName = url + " | " + init.method + " | " + init.body + " | " + JSON.stringify(init.headers);
+  return await hash(dataName);
+}
+
+// ../shared/utils/src/termdb.usecase.js
+var graphableTypes = /* @__PURE__ */ new Set([
+  "categorical",
+  "integer",
+  "float",
+  "condition",
+  "survival",
+  "snplst",
+  "snplocus",
+  "geneVariant",
+  "samplelst",
+  "geneExpression",
+  ISOFORM_EXPRESSION,
+  "dtcnv",
+  "dtsnvindel",
+  "dtfusion",
+  "dtsv",
+  "date",
+  TermTypes.SSGSEA,
+  TermTypes.DNA_METHYLATION,
+  TermTypes.METABOLITE_INTENSITY,
+  TermTypes.PROTEOME_ABUNDANCE,
+  SINGLECELL_GENE_EXPRESSION,
+  SINGLECELL_CELLTYPE,
+  TermTypes.SNP,
+  TermTypes.TERM_COLLECTION
+]);
+function isUsableTerm(term, _usecase, termdbConfig, ds) {
+  const usecase = _usecase || {};
+  if (typeof ds?.usecase?.[usecase.target] == "function") {
+    return ds.usecase[usecase.target](term, usecase);
+  }
+  const uses = /* @__PURE__ */ new Set();
+  const child_types = term.child_types || [];
+  switch (usecase.target) {
+    case "barchart":
+    case "violin":
+    case "boxplot":
+    case "summary":
+      if (term.type && term.type !== "survival") uses.add("plot");
+      if (hasAllowedChildTypes(child_types, ["survival"])) uses.add("branch");
+      return uses;
+    case "summaryInput":
+      if (usecase.detail === "term2" || usecase.detail == "term0") {
+        if (term.type && term.type !== "survival") uses.add("plot");
+        if (hasAllowedChildTypes(child_types, ["survival"])) uses.add("branch");
+        return uses;
+      } else {
+        if (graphableTypes.has(term.type)) uses.add("plot");
+        if (!term.isleaf) uses.add("branch");
+        return uses;
+      }
+    case "matrix":
+      if (term.type) uses.add("plot");
+      if (!term.isleaf) uses.add("branch");
+      return uses;
+    case "table":
+      if (usecase.detail == "term") uses.add("plot");
+      if (child_types.length > 1) uses.add("branch");
+      return uses;
+    case "sampleScatter":
+      if (usecase.detail == "numeric") {
+        if (isNumericTerm(term)) {
+          uses.add("plot");
+        }
+        if (hasNumericChild(child_types)) uses.add("branch");
+      } else {
+        if (graphableTypes.has(term.type)) uses.add("plot");
+        if (!term.isleaf) uses.add("branch");
+      }
+      return uses;
+    case "runChart2":
+      if (usecase.detail == "date" || usecase.detail == "xtw") {
+        if (term.type == "date") {
+          uses.add("plot");
+        }
+        if (child_types.includes("date")) uses.add("branch");
+      } else if (usecase.detail == "numeric") {
+        if (isNumericTerm(term) && term.type != "date") {
+          uses.add("plot");
+        }
+        if (hasNumericChild(child_types)) uses.add("branch");
+      } else {
+        if (graphableTypes.has(term.type)) uses.add("plot");
+        if (!term.isleaf) uses.add("branch");
+      }
+      return uses;
+    case "termCollections":
+      if (usecase.detail?.termIds?.includes(term.id)) uses.add("plot");
+      if (usecase.detail?.branchIds?.includes(term.id)) uses.add("branch");
+      return uses;
+    case "profileForms":
+      if (!term.isleaf) {
+        const ancestors = term.id.split("__").length;
+        if (ancestors == 3) {
+          uses.add("plot");
+        } else if (ancestors < 3) uses.add("branch");
+      }
+      return uses;
+    // case 'boxplot':
+    // 	if (term.type == 'float' || term.type == 'integer') uses.add('plot')
+    // 	if (usecase.detail === 'term2' && hasNumericChild(child_types)) uses.add('branch')
+    // 	return uses
+    case "cuminc":
+      if (usecase.detail == "term") {
+        if (term.type == "condition") uses.add("plot");
+        if (child_types.includes("condition")) uses.add("branch");
+        return uses;
+      }
+      if (usecase.detail === "term2" || usecase.detail == "term0") {
+        if (term.type && term.type != "condition" && term.type != "survival")
+          uses.add("plot");
+        if (hasAllowedChildTypes(child_types, ["condition", "survival"]))
+          uses.add("branch");
+        return uses;
+      }
+      return uses;
+    case "survival":
+      if (usecase.detail == "term") {
+        if (term.type == "survival") uses.add("plot");
+        if (child_types.includes("survival")) uses.add("branch");
+        return uses;
+      }
+      if (usecase.detail === "term2" || usecase.detail == "term0") {
+        if (term.type && term.type != "survival") uses.add("plot");
+        if (hasAllowedChildTypes(child_types, ["survival"])) uses.add("branch");
+        return uses;
+      }
+      return uses;
+    case "regression":
+      if (usecase.detail == "outcome") {
+        if (usecase.regressionType == "linear") {
+          if (term.type == "float" || term.type == "integer") uses.add("plot");
+          if (hasNumericChild(child_types)) uses.add("branch");
+          return uses;
+        }
+        if (usecase.regressionType == "logistic") {
+          if (term.type && term.type != "survival") uses.add("plot");
+          if (hasAllowedChildTypes(child_types, ["survival"]))
+            uses.add("branch");
+          return uses;
+        } else if (usecase.regressionType == "cox") {
+          if (term.type == "condition" || term.type == "survival")
+            uses.add("plot");
+          if (child_types.includes("condition") || child_types.includes("survival"))
+            uses.add("branch");
+          return uses;
+        }
+      }
+      if (usecase.detail == "independent") {
+        if (term.type == "float" || term.type == "integer" || term.type == "categorical" || term.type == "samplelst")
+          uses.add("plot");
+        if (hasChildTypes(child_types, ["categorical", "float", "integer"]))
+          uses.add("branch");
+        return uses;
+      }
+      return uses;
+    case "filter": {
+      const exlst = termdbConfig?.excludedTermtypeByTarget?.filter;
+      if (exlst) {
+        if (graphableTypes.has(term.type) && !exlst.includes(term.type))
+          uses.add("plot");
+        if (child_types.find((t) => !exlst.includes(t))) uses.add("branch");
+        return uses;
+      }
+      if (graphableTypes.has(term.type)) uses.add("plot");
+      if (!term.isleaf) uses.add("branch");
+      return uses;
+    }
+    case "correlationVolcano":
+      if (usecase.detail == "numeric") {
+        if (isNumericTerm(term)) {
+          uses.add("plot");
+        }
+        if (hasNumericChild(child_types)) uses.add("branch");
+      } else {
+        if (graphableTypes.has(term.type)) uses.add("plot");
+        if (!term.isleaf) uses.add("branch");
+      }
+      return uses;
+    case "proteinView":
+      if (term.type == TermTypes.PROTEOME_ABUNDANCE) uses.add("plot");
+      if (child_types.includes(TermTypes.PROTEOME_ABUNDANCE)) uses.add("branch");
+      return uses;
+    default:
+      if (graphableTypes.has(term.type)) uses.add("plot");
+      if (!term.isleaf) uses.add("branch");
+      return uses;
+  }
+}
+function hasAllowedChildTypes(child_types, excluded_types) {
+  if (!child_types.length) {
+    return false;
+  }
+  if (!excluded_types?.length) {
+    return true;
+  }
+  if (child_types.some((type) => !excluded_types.includes(type))) {
+    return true;
+  }
+}
+function hasNumericChild(child_types) {
+  return child_types.includes("float") || child_types.includes("integer");
+}
+function hasChildTypes(child_types, expected_types) {
+  for (const a of expected_types) {
+    if (child_types.includes(a)) return true;
+  }
+}
+
+// ../shared/utils/src/time.js
+function formatElapsedTime(ms, precision = 2) {
+  if (typeof ms !== "number" || isNaN(ms)) {
+    return typeof ms !== "number" ? "Invalid time: not a number" : "Invalid time: NaN";
+  }
+  if (!isFinite(ms)) {
+    return ms > 0 ? "Infinite time" : "-Infinite time";
+  }
+  const absMs = Math.abs(ms);
+  const sign = ms < 0 ? "-" : "";
+  if (absMs < 1e3) {
+    return `${sign}${absMs}ms`;
+  }
+  if (absMs < 6e4) {
+    return `${sign}${(absMs / 1e3).toFixed(precision)}s`;
+  }
+  const minutes = Math.floor(absMs / 6e4);
+  const seconds = (absMs % 6e4 / 1e3).toFixed(precision);
+  return `${sign}${minutes}m ${seconds}s`;
+}
+
+// common/auth.js
+var jwtByDsRouteStr = localStorage.getItem("jwtByDsRoute") || `{}`;
+var jwtByDsRoute = JSON.parse(jwtByDsRouteStr);
+function setTokenByDsRoute(dslabel, route, jwt) {
+  if (!jwtByDsRoute[dslabel]) jwtByDsRoute[dslabel] = {};
+  if (jwt) jwtByDsRoute[dslabel][route] = jwt;
+  else delete jwtByDsRoute[dslabel][route];
+  localStorage.setItem("jwtByDsRoute", JSON.stringify(jwtByDsRoute));
+}
+function getSavedToken(dslabel, route) {
+  return jwtByDsRoute[dslabel]?.[route] || jwtByDsRoute[dslabel]?.["/**"];
+}
+function mayAddJwtToRequest(init, body, url) {
+  if (init.headers.authorization) return;
+  let dslabel = body?.dslabel;
+  if (!dslabel) {
+    const param = url.split("?")[1]?.split("&").find((kv) => kv.includes("dslabel"));
+    if (!param) return;
+    let value = decodeURIComponent(param.split("=")[1]);
+    if (value.startsWith("{") && value.endsWith("}")) {
+      value = JSON.parse(value);
+      dslabel = value.dslabel || value.mass?.vocab.dslabel || value.tracks?.find((t) => t.dslabel)?.dslabel;
+    } else {
+      dslabel = value;
+    }
+  }
+  if (!dslabel || !jwtByDsRoute[dslabel]) return;
+  const h = url.split("//");
+  const postProtocolStr = h[1] || h[0];
+  const preQuestionMarkStr = postProtocolStr.split("?")[0];
+  const pathSegments = preQuestionMarkStr.split("/");
+  let route = pathSegments.find((p) => p != "" && !p.includes(":") && !p.includes("."));
+  const jwt = jwtByDsRoute[dslabel][route] || jwtByDsRoute[dslabel]["/**"];
+  if (jwt) init.headers.authorization = "Bearer " + btoa(jwt);
+}
+var dsAuthOk = /* @__PURE__ */ new Set();
+var dsAuth;
+var authUi;
+var authUiHolder;
+var includeEmbedder = false;
+async function setDsAuthOk(opts, dofetch32) {
+  dsAuth = opts.dsAuth;
+  authUi = opts.ui || defaultAuthUi;
+  authUiHolder = opts.holder || select_default("body");
+  for (const auth of dsAuth) {
+    if (auth.insession) dsAuthOk.add(auth);
+    else {
+      const { dslabel, route } = auth;
+      const jwt = getSavedToken(dslabel, route);
+      if (jwt) {
+        const payload = JSON.parse(atob(jwt.split(".")[1]));
+        if (payload.exp && Math.ceil(Date.now() / 1e3) > payload.exp) continue;
+        const data = await dofetch32("/jwt-status", {
+          method: "POST",
+          headers: {
+            //authorization: `Bearer ${btoa(jwt)}`
+            [auth.headerKey]: jwt
+          },
+          body: {
+            dslabel,
+            route,
+            embedder: location.hostname
+          }
+        });
+        if (data.ok || data.status == "ok") {
+          dsAuthOk.add(auth);
+          auth.insession = true;
+        }
+      }
+    }
+  }
+  includeEmbedder = opts.dsAuth?.length > 0 || false;
+}
+function getRequiredAuth(dslabel, route) {
+  if (!dsAuth || !Array.isArray(dsAuth)) return;
+  for (const a of dsAuth) {
+    if (a.dslabel == dslabel && (a.route == route || a.route == "*" || a.route == "/**")) return a;
+  }
+}
+function isInSession(dslabel, route) {
+  if (!dslabel) return false;
+  for (const a of dsAuthOk) {
+    if (a.dslabel == dslabel && (a.route == route || a.route == "/**")) return true;
+  }
+  return false;
+}
+async function mayShowAuthUi(init, path, opts = {}) {
+  const ok = { status: "ok" };
+  if (!dsAuth || path.endsWith("jwt-status")) return ok;
+  const body = JSON.parse(init.body || `{}`);
+  const params = (path.split("?")[1] || "").split("&").reduce((obj, kv) => {
+    const [key, value] = kv.split("=");
+    obj[key] = value;
+    return obj;
+  }, {});
+  const q = Object.assign({}, body, params);
+  const route = ((path.split("?")[0] || "").split("//")[1] || "").split("/").slice(1).join("/");
+  for (const a of dsAuth) {
+    if (q.dslabel == a.dslabel && (a.route == "/**" || route == a.route)) {
+      if (dsAuthOk.has(a)) return ok;
+      else if (a.route != "/**") return ok;
+      else if (a.type == "basic") return await authUi(a.dslabel, a, opts);
+      else if (a.type == "jwt") {
+      } else if (a.type == "forbidden") {
+        alert("Forbidden access");
+      } else throw `unsupported dsAuth type='${a.type}'`;
+    }
+  }
+  return ok;
+}
+async function defaultAuthUi(dslabel, auth, opts = {}) {
+  const mask = authUiHolder.append("div").style("position", "fixed").style("top", 0).style("left", 0).style("height", "100%").style("width", "100%").style("margin", 0).style("padding", "20px").style("background-color", "rgb(150,150,150)");
+  const form = mask.append("div").style("opacity", 1);
+  form.append("div").html(`Restricted dataset '${dslabel}'`);
+  form.append("span").html("Please enter password ");
+  const pwd = form.append("input").attr("type", "password");
+  pwd.node().focus();
+  const btn = form.append("button").html("Submit");
+  return new Promise((resolve, reject) => {
+    function login() {
+      fetch("/dslogin", {
+        method: "POST",
+        headers: {
+          authorization: `Basic ${btoa(pwd.property("value"))}`
+        },
+        body: JSON.stringify({ dslabel, route: auth.route, embedder: window.location.hostname })
+      }).then((res) => res.json()).then((res) => {
+        if (res.error) throw res.error;
+        mask.remove();
+        dsAuthOk.add(auth);
+        if (res.jwt) {
+          setTokenByDsRoute(dslabel, res.route, res.jwt);
+        }
+        if (!opts.setDomRefs) window.location.reload();
+        else resolve(dslabel);
+      }).catch((e) => {
+        alert("login error: " + e);
+      });
+    }
+    btn.on("click", login);
+    pwd.on("change", login);
+    if (opts.setDomRefs)
+      opts.setDomRefs({
+        pwd,
+        btn,
+        mask,
+        authUiHolder
+      });
+  });
+}
+
+// common/dofetch.js
+function dofetch(path, arg, opts = null) {
+  if (opts && typeof opts == "object") {
+    if (opts.serverData && typeof opts.serverData == "object") {
+      if (!dofetch.serverData) {
+        dofetch.serverData = opts.serverData;
+      } else if (!opts.serverData) {
+        opts.serverData = dofetch.serverData;
+      }
+    }
+    return dofetch2(
+      path,
+      {
+        method: "POST",
+        headers: {
+          "content-type": "application/json"
+        },
+        body: JSON.stringify(arg)
+      },
+      opts
+    );
+  } else {
+    if (path[0] == "/") {
+      path = path.slice(1);
+    }
+    const jwt = sessionStorage.getItem("jwt");
+    if (jwt) {
+      arg.jwt = jwt;
+    }
+    let url = path;
+    const host = sessionStorage.getItem("hostURL") || window.testHost || "";
+    if (host) {
+      if (host.endsWith("/")) {
+        url = host + path;
+      } else {
+        url = host + "/" + path;
+      }
+    }
+    return fetch(
+      new Request(url, {
+        method: "POST",
+        headers: {
+          "content-type": "application/json"
+        },
+        body: JSON.stringify(arg)
+      })
+    ).then((r) => r.json());
+  }
+}
+function dofetch2(path, init = {}, opts = {}) {
+  if (path[0] == "/") {
+    path = path.slice(1);
+  }
+  let url = path;
+  const host = sessionStorage.getItem("hostURL") || window.testHost || "";
+  if (host) {
+    if (host.endsWith("/")) {
+      url = host + path;
+    } else {
+      url = host + "/" + path;
+    }
+  }
+  const body = init.body || {};
+  url = mayAdjustRequest(url, init);
+  if (!init.headers) {
+    init.headers = {};
+  }
+  if (!init.headers["content-type"] && init.body) {
+    init.headers["content-type"] = "application/json";
+  }
+  const jwt = sessionStorage.getItem("jwt");
+  if (jwt) {
+    init.headers.authorization = "Bearer " + jwt;
+  }
+  return mayShowAuthUi(init, url).then(async () => {
+    if (!jwt) mayAddJwtToRequest(init, body, url);
+    if (opts.serverData) {
+      return namedFetch(url, init, opts);
+    } else {
+      return fetch(url, init).then(processResponse);
+    }
+  });
+}
+var optsServerDataNames2 = /* @__PURE__ */ new WeakMap();
+async function namedFetch(url, init, opts = {}) {
+  if (!opts.serverData) throw `use ezFetch() from fetch-helpers if a fetched response is not meant to be cached`;
+  if (typeof opts.serverData != "object") throw `opts.serverData is not an object`;
+  let result;
+  const dataName = await getDataName(url, init);
+  if (opts.serverData[dataName]) {
+    if (init.signal) {
+      await sleep(0);
+      if (init.signal.aborted) throw `stale sequenceId`;
+    }
+    result = structuredClone(opts.serverData[dataName]);
+  }
+  if (!result || typeof result != "object" && !(result instanceof Promise)) {
+    delete opts.serverData[dataName];
+    result = void 0;
+  }
+  if (!result) {
+    try {
+      const res = await fetch(url, init);
+      result = await processResponse(res);
+      if (typeof result == "object" && !(result instanceof Promise)) {
+        deepFreeze(result);
+        opts.serverData[dataName] = result;
+        result = structuredClone(result);
+      }
+    } catch (e) {
+      delete opts.serverData[dataName];
+      throw e;
+    }
+  }
+  if (!optsServerDataNames2.has(opts.serverData)) optsServerDataNames2.set(opts.serverData, []);
+  const keys = optsServerDataNames2.get(opts.serverData);
+  const i2 = keys.indexOf(dataName);
+  if (i2 > 0) {
+    keys.splice(i2, 1);
+  }
+  keys.unshift(dataName);
+  const maxKeys = 360;
+  while (keys.length > maxKeys) {
+    const oldestDataKey = keys.pop();
+    delete opts.serverData[oldestDataKey];
+  }
+  return result;
+}
+var defaultServerDataCache = {};
+function dofetch3(path, init = {}, opts = {}) {
+  if (!init.signal && typeof this?.app?.getAbortSignal == "function") init.signal = this.app.getAbortSignal();
+  opts.serverData = defaultServerDataCache;
+  return dofetch2(path, init, opts);
+}
+function clearServerDataCache(opts = {}) {
+  const cache = opts?.serverData || defaultServerDataCache;
+  if (!cache) return;
+  for (const k of Object.keys(cache)) {
+    delete cache[k];
+  }
+}
+var urlMaxLength = 2e3;
+function mayAdjustRequest(url, init) {
+  const hostname = window.location.hostname;
+  const method = init.method && init.method.toUpperCase() || "GET";
+  if (method == "POST") {
+    if (typeof init.body == "string") init.body = JSON.parse(init.body);
+    if (!init.body.embedder && includeEmbedder) init.body.embedder = hostname;
+    init.body = JSON.stringify(init.body);
+    return url;
+  }
+  if (method != "GET" && method != "DELETE" && method != "PUT") {
+    throw `unsupported init.method='${method}': must be undefined or GET or POST or DELETE or PUT`;
+  }
+  if (init.body) {
+    if (!init.body.embedder && includeEmbedder) init.body.embedder = hostname;
+    const params = encode(init.body);
+    if (!url.includes("?")) url += "?";
+    url += params;
+  }
+  if (!url.includes("embedder=") && includeEmbedder) {
+    const sep = url.includes("?") ? "&" : "?";
+    url += `${sep}embedder=${hostname}`;
+  }
+  if (url.length < urlMaxLength) {
+    if (init.body) delete init.body;
+    return url;
+  }
+  init.method = "POST";
+  const [hostpath, query] = url.split("?");
+  if (init.body) {
+    init.body = JSON.stringify(init.body);
+  } else {
+    const params = {};
+    if (query)
+      query.split("&").forEach((p) => {
+        const [k, v] = p.split("=");
+        const decodedVal = decodeURIComponent(v);
+        try {
+          params[k] = JSON.parse(decodedVal);
+        } catch {
+          params[k] = decodedVal;
+        }
+      });
+    if (!params.embedder && includeEmbedder) params.embedder = hostname;
+    init.body = JSON.stringify(params);
+  }
+  return hostpath;
+}
+function setAuth(opts) {
+  setDsAuthOk(opts, dofetch3);
+}
+
+export {
+  init_bulk_flag,
+  parsesample,
+  clusterMethodLst,
+  distanceMethodLst,
+  computePercentile,
+  fileSize,
+  ssmIdFieldsSeparator,
+  summarize_mclass,
+  guessSsmid,
+  initBinConfig,
+  isUsableTerm,
+  formatElapsedTime,
+  vcfparsemeta,
+  vcfparseline,
+  setTokenByDsRoute,
+  getSavedToken,
+  getRequiredAuth,
+  isInSession,
+  dofetch,
+  dofetch2,
+  dofetch3,
+  clearServerDataCache,
+  setAuth
+};
+//# sourceMappingURL=chunk-7RN3L2BX.js.map