@weng-lab/ui-components 1.3.3 → 2.0.1

package/dist/ui-components.es54.js

@@ -0,0 +1,165 @@
+import { j as l } from "./ui-components.es12.js";
+import { c as de } from "./ui-components.es13.js";
+import { Box as fe, Divider as me, Typography as ge, IconButton as pe, Tooltip as he, DialogTitle as ue, Checkbox as X, FormControlLabel as Y, DialogContent as xe, Stack as be, Button as Z, DialogActions as je, Dialog as Ce } from "@mui/material";
+import { useState as S } from "react";
+import { Download as _e } from "@mui/icons-material";
+import { ontologyDownloadMap as we } from "./ui-components.es75.js";
+import { formatFileSize as ee, fetchFileSize as le } from "./ui-components.es53.js";
+import { useDownloadContext as De } from "./ui-components.es52.js";
+const ke = (n) => {
+  const e = n.toLowerCase().replace(/\s+/g, "_");
+  return we[e] ?? [];
+}, Oe = (n) => {
+  const e = de.c(66), {
+    ontology: o
+  } = n, [I, F] = S(!1), [c, te] = S(!1), [r, oe] = S(!1), [D, ne] = S(null), [k, ie] = S(null), {
+    onDownload: A
+  } = De();
+  let t, i, E;
+  e[0] !== o ? (t = ke(o), i = t.find(ye)?.filename ?? void 0, E = t.find(Se)?.filename ?? void 0, e[0] = o, e[1] = t, e[2] = i, e[3] = E) : (t = e[1], i = e[2], E = e[3]);
+  const a = E;
+  let v;
+  e[4] !== a || e[5] !== k || e[6] !== i || e[7] !== D ? (v = () => {
+    i && !D && le(`https://downloads.wenglab.org/${i}`, ne), a && !k && le(`https://downloads.wenglab.org/${a}`, ie), F(!0);
+  }, e[4] = a, e[5] = k, e[6] = i, e[7] = D, e[8] = v) : v = e[8];
+  const U = v;
+  let $;
+  e[9] !== r || e[10] !== a || e[11] !== t || e[12] !== i || e[13] !== c || e[14] !== A || e[15] !== o ? ($ = () => {
+    if (!t || t.length === 0)
+      return;
+    const s = [];
+    c && i && s.push({
+      filename: i,
+      label: "excluding_cancer_cell_lines"
+    }), r && a && s.push({
+      filename: a,
+      label: "all_biosamples"
+    }), s.forEach((se, ae) => {
+      const {
+        filename: V,
+        label: ce
+      } = se, W = `https://downloads.wenglab.org/${V}`;
+      setTimeout(() => {
+        if (A) {
+          const re = `${o}_aggregate_ccres_${ce}`;
+          A(W, re);
+        }
+        const y = document.createElement("a");
+        y.href = W, y.download = V, document.body.appendChild(y), y.click(), document.body.removeChild(y);
+      }, ae * 500);
+    });
+  }, e[9] = r, e[10] = a, e[11] = t, e[12] = i, e[13] = c, e[14] = A, e[15] = o, e[16] = $) : $ = e[16];
+  const M = $;
+  let d;
+  e[17] !== t || e[18] !== o ? (d = t.length === 0 ? "No Aggregate cCRE Download Options" : /* @__PURE__ */ l.jsxs(fe, { children: [
+    "Download cCREs in ",
+    o.charAt(0).toUpperCase() + o.slice(1),
+    ":",
+    /* @__PURE__ */ l.jsx("ul", { style: {
+      margin: 0,
+      paddingLeft: 16
+    }, children: t.map(Fe) }),
+    "(Opens Download Dialog)"
+  ] }), e[17] = t, e[18] = o, e[19] = d) : d = e[19];
+  let f;
+  e[20] !== U ? (f = (s) => {
+    s.stopPropagation(), U();
+  }, e[20] = U, e[21] = f) : f = e[21];
+  const q = t.length === 0;
+  let R;
+  e[22] === Symbol.for("react.memo_cache_sentinel") ? (R = /* @__PURE__ */ l.jsx(_e, {}), e[22] = R) : R = e[22];
+  let m;
+  e[23] !== f || e[24] !== q ? (m = /* @__PURE__ */ l.jsx("span", { children: /* @__PURE__ */ l.jsx(pe, { onClick: f, disabled: q, children: R }) }), e[23] = f, e[24] = q, e[25] = m) : m = e[25];
+  let g;
+  e[26] !== d || e[27] !== m ? (g = /* @__PURE__ */ l.jsx(he, { title: d, placement: "left", arrow: !0, children: m }), e[26] = d, e[27] = m, e[28] = g) : g = e[28];
+  let T;
+  e[29] === Symbol.for("react.memo_cache_sentinel") ? (T = (s) => {
+    s.stopPropagation(), F(!1);
+  }, e[29] = T) : T = e[29];
+  let z;
+  e[30] === Symbol.for("react.memo_cache_sentinel") ? (z = {
+    backdrop: {
+      sx: {
+        backgroundColor: "rgba(255, 255, 255, 0.1)",
+        backdropFilter: "blur(2px)"
+      }
+    }
+  }, e[30] = z) : z = e[30];
+  let B;
+  e[31] !== o ? (B = o.charAt(0).toUpperCase(), e[31] = o, e[32] = B) : B = e[32];
+  const G = B + o.slice(1);
+  let p;
+  e[33] !== G ? (p = /* @__PURE__ */ l.jsxs(ue, { id: "export-dialog-title", children: [
+    "Download cCREs in ",
+    G,
+    ":"
+  ] }), e[33] = G, e[34] = p) : p = e[34];
+  let L;
+  e[35] === Symbol.for("react.memo_cache_sentinel") ? (L = (s) => oe(s.target.checked), e[35] = L) : L = e[35];
+  const H = !a;
+  let h;
+  e[36] !== r || e[37] !== H ? (h = /* @__PURE__ */ l.jsx(X, { checked: r, onChange: L, disabled: H }), e[36] = r, e[37] = H, e[38] = h) : h = e[38];
+  const J = `Aggregate cCREs (all biosamples)${k ? " - " + ee(k) : ""}`;
+  let u;
+  e[39] !== h || e[40] !== J ? (u = /* @__PURE__ */ l.jsx(Y, { control: h, label: J }), e[39] = h, e[40] = J, e[41] = u) : u = e[41];
+  let O;
+  e[42] === Symbol.for("react.memo_cache_sentinel") ? (O = (s) => te(s.target.checked), e[42] = O) : O = e[42];
+  const K = !i;
+  let x;
+  e[43] !== c || e[44] !== K ? (x = /* @__PURE__ */ l.jsx(X, { checked: c, onChange: O, disabled: K }), e[43] = c, e[44] = K, e[45] = x) : x = e[45];
+  const Q = `Aggregate cCREs (excluding cancer cell lines)${D ? " - " + ee(D) : ""}`;
+  let b;
+  e[46] !== x || e[47] !== Q ? (b = /* @__PURE__ */ l.jsx(Y, { control: x, label: Q }), e[46] = x, e[47] = Q, e[48] = b) : b = e[48];
+  let j;
+  e[49] !== t.length ? (j = t.length <= 1 && /* @__PURE__ */ l.jsxs(l.Fragment, { children: [
+    /* @__PURE__ */ l.jsx(me, { sx: {
+      marginTop: 1
+    } }),
+    /* @__PURE__ */ l.jsx(ge, { marginTop: 1, children: /* @__PURE__ */ l.jsx("strong", { children: "No cancerous cell lines available in this tissue" }) })
+  ] }), e[49] = t.length, e[50] = j) : j = e[50];
+  let C;
+  e[51] !== u || e[52] !== b || e[53] !== j ? (C = /* @__PURE__ */ l.jsx(xe, { children: /* @__PURE__ */ l.jsxs(be, { children: [
+    u,
+    b,
+    j
+  ] }) }), e[51] = u, e[52] = b, e[53] = j, e[54] = C) : C = e[54];
+  let N;
+  e[55] === Symbol.for("react.memo_cache_sentinel") ? (N = /* @__PURE__ */ l.jsx(Z, { onClick: () => {
+    F(!1);
+  }, children: "Cancel" }), e[55] = N) : N = e[55];
+  let _;
+  e[56] !== M ? (_ = /* @__PURE__ */ l.jsxs(je, { children: [
+    N,
+    /* @__PURE__ */ l.jsx(Z, { variant: "contained", onClick: () => {
+      M(), F(!1);
+    }, children: "Download" })
+  ] }), e[56] = M, e[57] = _) : _ = e[57];
+  let w;
+  e[58] !== I || e[59] !== p || e[60] !== C || e[61] !== _ ? (w = /* @__PURE__ */ l.jsxs(Ce, { open: I, onClose: T, "aria-labelledby": "export-dialog-title", disableScrollLock: !0, slotProps: z, onClick: Ae, children: [
+    p,
+    C,
+    _
+  ] }), e[58] = I, e[59] = p, e[60] = C, e[61] = _, e[62] = w) : w = e[62];
+  let P;
+  return e[63] !== w || e[64] !== g ? (P = /* @__PURE__ */ l.jsxs(l.Fragment, { children: [
+    g,
+    w
+  ] }), e[63] = w, e[64] = g, e[65] = P) : P = e[65], P;
+};
+function ye(n) {
+  return n.label === "Excluding Cancer Cell Lines";
+}
+function Se(n) {
+  return n.label === "All Biosamples";
+}
+function Fe(n) {
+  return /* @__PURE__ */ l.jsx("li", { children: n.label }, n.filename);
+}
+function Ae(n) {
+  return n.stopPropagation();
+}
+export {
+  Oe as AggregateDownloadButton,
+  ke as getAvailableFiles
+};
+//# sourceMappingURL=ui-components.es54.js.map

package/dist/ui-components.es54.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ui-components.es54.js","sources":["../src/components/BiosampleTable/AggregateDownload.tsx"],"sourcesContent":["import {\n  Button,\n  Tooltip,\n  Box,\n  Checkbox,\n  Dialog,\n  DialogActions,\n  DialogContent,\n  DialogTitle,\n  FormControlLabel,\n  Stack,\n  Typography,\n  Divider,\n  IconButton,\n} from \"@mui/material\";\nimport { useCallback, useMemo, useState } from \"react\";\nimport { Download } from \"@mui/icons-material\";\nimport { ontologyDownloadMap } from \"./ontologyDownloads\";\nimport { fetchFileSize, formatFileSize } from \"./helpers\";\nimport { useDownloadContext } from \"./DownloadContext\";\n\nexport type AggregateDownloadProps = {\n  ontology: string;\n};\n\n/**\n *\n * @param ontology\n * Finds available aggregate file urls for the given ontology in the form `[noccl, ccl]`\n */\n\nexport const getAvailableFiles = (ontology: string) => {\n  const key = ontology.toLowerCase().replace(/\\s+/g, \"_\");\n  return ontologyDownloadMap[key] ?? [];\n};\n\nexport const AggregateDownloadButton = ({ ontology }: AggregateDownloadProps) => {\n  const [isDialogOpen, setIsDialogOpen] = useState(false);\n  const [noccl, setNoccl] = useState(false);\n  const [all, setAll] = useState(false);\n  const [nocclFileSize, setNocclFileSize] = useState<number | null>(null);\n  const [allFileSize, setAllFileSize] = useState<number | null>(null);\n  const { onDownload } = useDownloadContext();\n\n  const availibleDownloads = getAvailableFiles(ontology);\n\n  const ncFile = availibleDownloads.find((d) => d.label === \"Excluding Cancer Cell Lines\")?.filename ?? undefined;\n  const allFile = availibleDownloads.find((d) => d.label === \"All Biosamples\")?.filename ?? undefined;\n\n  const handleOpenDialog = () => {\n    if (ncFile && !nocclFileSize) fetchFileSize(`https://downloads.wenglab.org/${ncFile}`, setNocclFileSize);\n    if (allFile && !allFileSize) fetchFileSize(`https://downloads.wenglab.org/${allFile}`, setAllFileSize);\n    setIsDialogOpen(true);\n  };\n\n  const handleDownload = useCallback(() => {\n    if (!availibleDownloads || availibleDownloads.length === 0) return;\n\n    const filesToDownload: { filename: string; label: string }[] = [];\n    if (noccl && ncFile) filesToDownload.push({ filename: ncFile, label: \"excluding_cancer_cell_lines\" });\n    if (all && allFile) filesToDownload.push({ filename: allFile, label: \"all_biosamples\" });\n\n    filesToDownload.forEach(({ filename, label }, index) => {\n      const url = `https://downloads.wenglab.org/${filename}`;\n\n      setTimeout(() => {\n        if (onDownload) {\n          // Use descriptive name: ontology_aggregate_ccres_label\n          const name = `${ontology}_aggregate_ccres_${label}`;\n          onDownload(url, name);\n        }\n\n        const link = document.createElement(\"a\");\n        link.href = url;\n        link.download = filename;\n\n        document.body.appendChild(link);\n        link.click();\n        document.body.removeChild(link);\n      }, index * 500); // 500ms delay between downloads (some browsers prevent against mutliple downloads at once)\n    });\n  }, [all, allFile, availibleDownloads, ncFile, noccl, onDownload, ontology]);\n\n  return (\n    <>\n      <Tooltip\n        title={\n          availibleDownloads.length === 0 ? (\n            \"No Aggregate cCRE Download Options\"\n          ) : (\n            <Box>\n              Download cCREs in {ontology.charAt(0).toUpperCase() + ontology.slice(1)}:\n              <ul style={{ margin: 0, paddingLeft: 16 }}>\n                {availibleDownloads.map((d) => (\n                  <li key={d.filename}>{d.label}</li>\n                ))}\n              </ul>\n              (Opens Download Dialog)\n            </Box>\n          )\n        }\n        placement=\"left\"\n        arrow\n      >\n        <span>\n          <IconButton\n            onClick={(e) => {\n              e.stopPropagation();\n              handleOpenDialog();\n            }}\n            disabled={availibleDownloads.length === 0}\n          >\n            <Download />\n          </IconButton>\n        </span>\n      </Tooltip>\n      <Dialog\n        open={isDialogOpen}\n        onClose={(event) => {\n          (event as React.MouseEvent).stopPropagation();\n          setIsDialogOpen(false);\n        }}\n        aria-labelledby=\"export-dialog-title\"\n        disableScrollLock\n        slotProps={{\n          backdrop: {\n            sx: {\n              backgroundColor: \"rgba(255, 255, 255, 0.1)\",\n              backdropFilter: \"blur(2px)\",\n            },\n          },\n        }}\n        onClick={(e) => e.stopPropagation()}\n      >\n        <DialogTitle id=\"export-dialog-title\">\n          Download cCREs in {ontology.charAt(0).toUpperCase() + ontology.slice(1)}:\n        </DialogTitle>\n        <DialogContent>\n          <Stack>\n            <FormControlLabel\n              control={<Checkbox checked={all} onChange={(e) => setAll(e.target.checked)} disabled={!allFile} />}\n              label={`Aggregate cCREs (all biosamples)${allFileSize ? \" - \" + formatFileSize(allFileSize) : \"\"}`}\n            />\n            <FormControlLabel\n              control={<Checkbox checked={noccl} onChange={(e) => setNoccl(e.target.checked)} disabled={!ncFile} />}\n              label={`Aggregate cCREs (excluding cancer cell lines)${nocclFileSize ? \" - \" + formatFileSize(nocclFileSize) : \"\"}`}\n            />\n            {availibleDownloads.length <= 1 && (\n              <>\n                <Divider sx={{ marginTop: 1 }} />\n                <Typography marginTop={1}>\n                  <strong>No cancerous cell lines available in this tissue</strong>\n                </Typography>\n              </>\n            )}\n          </Stack>\n        </DialogContent>\n        <DialogActions>\n          <Button\n            onClick={() => {\n              setIsDialogOpen(false);\n            }}\n          >\n            Cancel\n          </Button>\n          <Button\n            variant=\"contained\"\n            onClick={() => {\n              handleDownload();\n              setIsDialogOpen(false);\n            }}\n          >\n            Download\n          </Button>\n        </DialogActions>\n      </Dialog>\n    </>\n  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package/dist/ui-components.es55.js

@@ -0,0 +1,215 @@
+function p(t, i) {
+  const e = [];
+  t = t.replace(/,/g, "");
+  let c, o, r;
+  if (t.includes(":") && t.includes("-"))
+    c = t.split(":")[0], o = parseInt(t.split(":")[1].split("-")[0]) || 0, r = parseInt(t.split(":")[1].split("-")[1]) || o + 1e3;
+  else if (t.includes("	")) {
+    const [h, l, d] = t.split("	");
+    c = h, o = parseInt(l), r = parseInt(d);
+  } else
+    return e;
+  const s = c.replace(/chrx$/, "chrX").replace(/chry$/, "chrY"), a = m[i][c];
+  return r > o && a && r <= a && e.push({
+    title: `${s}:${o.toLocaleString()}-${r.toLocaleString()}`,
+    domain: {
+      chromosome: s,
+      start: o,
+      end: r
+    },
+    description: `${s}:${o.toLocaleString()}-${r.toLocaleString()}`,
+    type: "Coordinate"
+  }), e;
+}
+function n(t, i, e) {
+  return t ? t.slice(0, i).map((c) => ({
+    title: e.getTitle(c),
+    description: e.getDescription(c),
+    domain: {
+      chromosome: c.coordinates.chromosome,
+      start: c.coordinates.start,
+      end: c.coordinates.end
+    },
+    type: e.type
+  })) : [];
+}
+function g(t, i) {
+  return n(t, i, {
+    getTitle: (e) => e.id,
+    getDescription: (e) => `${e.coordinates.chromosome}:${e.coordinates.start}-${e.coordinates.end}`,
+    type: "SNP"
+  });
+}
+function $(t, i, e) {
+  return n(t, i, {
+    getTitle: (c) => c.name,
+    getDescription: (c) => {
+      let o = "";
+      return c.versions.forEach((r, s) => o += "V" + r.version + " " + r.id + (s === c.versions.length - 1 ? "" : `
+`)), `${c.description}
+${o}
+${c.coordinates.chromosome}:${c.coordinates.start}-${c.coordinates.end}`;
+    },
+    type: "Gene"
+  });
+}
+function u(t, i) {
+  return t.slice(0, i).map((e) => ({
+    title: e.disease_trait,
+    description: `${e.author.replace("_", " ")} (${e.studyid.split("-")[1]})
+${e.parent_terms.join(",")}
+ ${e.has_enrichment_info ? "Biosample Enrichment" : ""}`,
+    domain: void 0,
+    id: e.studyid,
+    type: "Study"
+  }));
+}
+function y(t) {
+  return t.map((i) => ({
+    title: i.label,
+    description: i.description ?? "",
+    domain: void 0,
+    id: i.value,
+    type: "Ome"
+  }));
+}
+function v(t, i) {
+  return n(t, i, {
+    getTitle: (e) => e.accession,
+    getDescription: (e) => `${e.coordinates.chromosome}:${e.coordinates.start}-${e.coordinates.end}`,
+    type: "iCRE"
+  });
+}
+function f(t, i) {
+  return n(t, i, {
+    getTitle: (e) => e.accession,
+    getDescription: (e) => `${e.coordinates.chromosome}:${e.coordinates.start}-${e.coordinates.end}${e.isiCRE ? ", iCRE" : ""}`,
+    type: "cCRE"
+  });
+}
+function R(t, i) {
+  return t.filter((e) => e.input !== e.v4_match_or_intersecting).slice(0, i).map((e) => {
+    const c = e.input_region, o = e.v4_match_or_intersecting;
+    return {
+      title: e.input,
+      // !!! Do not change this format without also modifying SCREEN's /search page. This specific formatting is relied upon
+      description: `(Registry ${e.input_latest_previous_version})
+${e.input_region}
+${o ? `Intersects v4 cCRE${o.includes(",") ? "s" : ""}: ${o.replace(",", ", ")}` : "No intersecting v4 cCREs"}`,
+      domain: {
+        chromosome: c.split(":")[0],
+        start: parseInt(c.split(":")[1].split("-")[0]),
+        end: parseInt(c.split(":")[1].split("-")[1])
+      },
+      type: "Legacy cCRE"
+    };
+  });
+}
+const b = [{
+  label: "Proteomics",
+  value: "proteomics",
+  keywords: ["protein", "mass spec"]
+}, {
+  label: "WGS",
+  value: "WGS",
+  keywords: ["whole genome sequencing", "genome sequencing", "genomics"],
+  description: "Whole Genome Sequencing"
+}, {
+  label: "WGBS",
+  value: "WGBS",
+  keywords: ["whole genome bisulfite sequencing", "epigenomics", "methylation"],
+  description: "Whole Genome Bisulfite Sequencing"
+}, {
+  label: "ATAC",
+  value: "ATAC",
+  keywords: ["chromatin accessibility", "atac-seq"],
+  description: "ATAC-seq"
+}, {
+  label: "RNA",
+  value: "RNA",
+  keywords: ["rna-seq", "transcriptomics", "gene expression"],
+  description: "RNA-seq"
+}, {
+  label: "Metabolomics",
+  value: "metabolomics"
+}, {
+  label: "Lipidomics",
+  value: "lipidomics"
+}, {
+  label: "Metallomics",
+  value: "metallomics"
+}, {
+  label: "Exposomics",
+  value: "exposomics"
+}], m = {
+  GRCh38: {
+    chr1: 248956422,
+    chr2: 242193529,
+    chr3: 198295559,
+    chr4: 190214555,
+    chr5: 181538259,
+    chr6: 170805979,
+    chr7: 159345973,
+    chr8: 145138636,
+    chr9: 138394717,
+    chr10: 133797422,
+    chr11: 135086622,
+    chr12: 133275309,
+    chr13: 114364328,
+    chr14: 107043718,
+    chr15: 101991189,
+    chr16: 90338345,
+    chr17: 83257441,
+    chr18: 80373285,
+    chr19: 58617616,
+    chr20: 64444167,
+    chr21: 46709983,
+    chr22: 50818468,
+    chrX: 156040895,
+    chrx: 156040895,
+    chrY: 57227415,
+    chry: 57227415
+  },
+  mm10: {
+    chr1: 195471971,
+    chr2: 182113224,
+    chr3: 160039680,
+    chr4: 156508116,
+    chr5: 151834684,
+    chr6: 149736546,
+    chr7: 145441459,
+    chr8: 129401213,
+    chr9: 124595110,
+    chr10: 130694993,
+    chr11: 122082543,
+    chr12: 120129022,
+    chr13: 120421639,
+    chr14: 124902244,
+    chr15: 104043685,
+    chr16: 98207768,
+    chr17: 94987271,
+    chr18: 90702639,
+    chr19: 61431566,
+    chrX: 171031299,
+    chrx: 171031299,
+    chrY: 91744698,
+    chry: 91744698
+  }
+};
+function C(t) {
+  const i = t.includes("	"), e = t.includes("-"), c = t.length >= 4 && /^[0-9xyXY]$/.test(t[3]);
+  return (i || e) && t.startsWith("chr") && c;
+}
+export {
+  b as OmesList,
+  f as ccreResultList,
+  $ as geneResultList,
+  p as getCoordinates,
+  v as icreResultList,
+  C as isDomain,
+  R as legacyCcreResultList,
+  y as omeResultsList,
+  g as snpResultList,
+  u as studyResultList
+};
+//# sourceMappingURL=ui-components.es55.js.map

package/dist/ui-components.es55.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ui-components.es55.js","sources":["../src/components/GenomeSearch/utils.ts"],"sourcesContent":["import { CCREResponse, GeneResponse, ICREResponse, LegacyCcreResponse, Result, ResultType, SnpResponse, StudyResponse } from \"./types\";\n\n/**\n * Get the coordinates from a string input.\n * @param input - The input string to search for coordinates\n * @param assembly - The assembly to search for coordinates\n * @returns An array of results with the coordinates\n */\nexport function getCoordinates(input: string, assembly: string): Result[] {\n  const results: Result[] = [];\n  input = input.replace(/,/g, \"\");\n\n  let chromosome: string, start: number, end: number;\n\n  if (input.includes(\":\") && input.includes(\"-\")) {\n    chromosome = input.split(\":\")[0];\n    start = parseInt(input.split(\":\")[1].split(\"-\")[0]) || 0;\n    end = parseInt(input.split(\":\")[1].split(\"-\")[1]) || start + 1000;\n  } else if (input.includes(\"\\t\")) {\n    const [chr, startStr, endStr] = input.split(\"\\t\");\n    chromosome = chr;\n    start = parseInt(startStr);\n    end = parseInt(endStr);\n  } else {\n    return results;\n  }\n\n  // Normalize chromosome name to use capital X and Y\n  const normalizedChromosome = chromosome.replace(/chrx$/, \"chrX\").replace(/chry$/, \"chrY\");\n\n  const chrLength = chromosomeLengths[assembly][chromosome];\n  if (end > start && chrLength && end <= chrLength) {\n    results.push({\n      title: `${normalizedChromosome}:${start.toLocaleString()}-${end.toLocaleString()}`,\n      domain: {\n        chromosome: normalizedChromosome,\n        start: start,\n        end: end,\n      },\n      description: `${normalizedChromosome}:${start.toLocaleString()}-${end.toLocaleString()}`,\n      type: \"Coordinate\",\n    });\n  }\n\n  return results;\n}\n\n// Common interface for result formatting options\ninterface ResultFormatterOptions<T> {\n  getTitle: (result: T) => string;\n  getDescription: (result: T) => string;\n  type: string;\n}\n\n// Generic formatter function\nfunction formatResults<T extends { coordinates: { chromosome: string; start: number; end: number } }>(\n  results: T[] | null,\n  limit: number,\n  options: ResultFormatterOptions<T>\n): Result[] {\n  if (!results) {\n    return [];\n  }\n  return results.slice(0, limit).map((result) => ({\n    title: options.getTitle(result),\n    description: options.getDescription(result),\n    domain: {\n      chromosome: result.coordinates.chromosome,\n      start: result.coordinates.start,\n      end: result.coordinates.end,\n    },\n    type: options.type as ResultType,\n  }));\n}\n\n// Specific formatters using the generic function\nexport function snpResultList(results: SnpResponse[], limit: number): Result[] {\n  return formatResults(results, limit, {\n    getTitle: (result) => result.id,\n    getDescription: (result) =>\n      `${result.coordinates.chromosome}:${result.coordinates.start}-${result.coordinates.end}`,\n    type: \"SNP\",\n  });\n}\n\nexport function geneResultList(results: GeneResponse[], limit: number, showVersions: boolean): Result[] {\n  return formatResults(results, limit, {\n    getTitle: (result) => result.name,\n    getDescription: (result) => {\n      let idStr = \"\";\n      result.versions.forEach(\n        (x, i) => (idStr += \"V\" + x.version + \" \" + x.id + (i === result.versions.length - 1 ? \"\" : \"\\n\"))\n      );\n      return `${result.description}\\n${idStr}\\n${result.coordinates.chromosome}:${result.coordinates.start}-${result.coordinates.end}`;\n    },\n    type: \"Gene\",\n  });\n}\n\nexport function studyResultList(results: StudyResponse[], limit: number): Result[] {\n  return results.slice(0, limit).map((result) => ({\n    title: result.disease_trait,\n    description: `${result.author.replace(\"_\", \" \")} (${result.studyid.split(\"-\")[1]})\\n${result.parent_terms.join(\",\")}\\n ${result.has_enrichment_info ? \"Biosample Enrichment\" : \"\"}`,\n    domain: undefined,\n    id: result.studyid,\n    type: \"Study\",\n  }));\n}\n\nexport function omeResultsList(results: OmeOption[]): Result[] {\n  return results.map((ome) => ({\n    title: ome.label,\n    description: ome.description ?? \"\",\n    domain: undefined,\n    id: ome.value,\n    type: \"Ome\",\n  }));\n}\n\nexport function icreResultList(results: ICREResponse[], limit: number): Result[] {\n  return formatResults(results, limit, {\n    getTitle: (result) => result.accession,\n    getDescription: (result) =>\n      `${result.coordinates.chromosome}:${result.coordinates.start}-${result.coordinates.end}`,\n    type: \"iCRE\",\n  });\n}\n\nexport function ccreResultList(results: CCREResponse[], limit: number): Result[] {\n  return formatResults(results, limit, {\n    getTitle: (result) => result.accession,\n    getDescription: (result) =>\n      `${result.coordinates.chromosome}:${result.coordinates.start}-${\n        result.coordinates.end\n      }${result.isiCRE ? \", iCRE\" : \"\"}`,\n    type: \"cCRE\",\n  });\n}\n\nexport function legacyCcreResultList(results: LegacyCcreResponse[], limit: number): Result[] {\n  return results\n    .filter((result) => result.input !== result.v4_match_or_intersecting) //filter v4 cCREs\n    .slice(0, limit)\n    .map((result) => {\n      const region = result.input_region;\n      const overlapping = result.v4_match_or_intersecting\n      return {\n        title: result.input,\n        // !!! Do not change this format without also modifying SCREEN's /search page. This specific formatting is relied upon\n        description: `(Registry ${result.input_latest_previous_version})\\n${result.input_region}\\n${overlapping ? `Intersects v4 cCRE${overlapping.includes(\",\") ? \"s\" : \"\"}: ${overlapping.replace(\",\", \", \")}` : \"No intersecting v4 cCREs\"}`,\n        domain: {\n          chromosome: region.split(\":\")[0],\n          start: parseInt(region.split(\":\")[1].split(\"-\")[0]),\n          end: parseInt(region.split(\":\")[1].split(\"-\")[1]),\n        },\n        type: \"Legacy cCRE\",\n      };\n    });\n}\n\nexport interface OmeOption {\n  label: string;\n  value: string;\n  keywords?: string[];\n  description?: string;\n}\n//allows the user to search more freely and get the result they are looking for\n//will look at label as well as keywords\nexport const OmesList: OmeOption[] = [\n  {\n    label: \"Proteomics\",\n    value: \"proteomics\",\n    keywords: [\"protein\", \"mass spec\"],\n  },\n  {\n    label: \"WGS\",\n    value: \"WGS\",\n    keywords: [\"whole genome sequencing\", \"genome sequencing\", \"genomics\"],\n    description: \"Whole Genome Sequencing\"\n  },\n  {\n    label: \"WGBS\",\n    value: \"WGBS\",\n    keywords: [\"whole genome bisulfite sequencing\", \"epigenomics\", \"methylation\"],\n    description: \"Whole Genome Bisulfite Sequencing\"\n  },\n  {\n    label: \"ATAC\",\n    value: \"ATAC\",\n    keywords: [\"chromatin accessibility\", \"atac-seq\"],\n    description: \"ATAC-seq\"\n  },\n  {\n    label: \"RNA\",\n    value: \"RNA\",\n    keywords: [\"rna-seq\", \"transcriptomics\", \"gene expression\"],\n    description: \"RNA-seq\"\n  },\n  {\n    label: \"Metabolomics\",\n    value: \"metabolomics\",\n  },\n  {\n    label: \"Lipidomics\",\n    value: \"lipidomics\",\n  },\n  {\n    label: \"Metallomics\",\n    value: \"metallomics\",\n  },\n  {\n    label: \"Exposomics\",\n    value: \"exposomics\",\n  },\n];\n\n// Object to store chromosome lengths for GRCh38 and mm10\nconst chromosomeLengths: { [key: string]: { [key: string]: number } } = {\n  GRCh38: {\n    chr1: 248956422,\n    chr2: 242193529,\n    chr3: 198295559,\n    chr4: 190214555,\n    chr5: 181538259,\n    chr6: 170805979,\n    chr7: 159345973,\n    chr8: 145138636,\n    chr9: 138394717,\n    chr10: 133797422,\n    chr11: 135086622,\n    chr12: 133275309,\n    chr13: 114364328,\n    chr14: 107043718,\n    chr15: 101991189,\n    chr16: 90338345,\n    chr17: 83257441,\n    chr18: 80373285,\n    chr19: 58617616,\n    chr20: 64444167,\n    chr21: 46709983,\n    chr22: 50818468,\n    chrX: 156040895,\n    chrx: 156040895,\n    chrY: 57227415,\n    chry: 57227415,\n  },\n  mm10: {\n    chr1: 195471971,\n    chr2: 182113224,\n    chr3: 160039680,\n    chr4: 156508116,\n    chr5: 151834684,\n    chr6: 149736546,\n    chr7: 145441459,\n    chr8: 129401213,\n    chr9: 124595110,\n    chr10: 130694993,\n    chr11: 122082543,\n    chr12: 120129022,\n    chr13: 120421639,\n    chr14: 124902244,\n    chr15: 104043685,\n    chr16: 98207768,\n    chr17: 94987271,\n    chr18: 90702639,\n    chr19: 61431566,\n    chrX: 171031299,\n    chrx: 171031299,\n    chrY: 91744698,\n    chry: 91744698,\n  },\n};\n\nexport function isDomain(input: string) {\n  const hasTabs = input.includes(\"\\t\");\n  const hasHyphens = input.includes(\"-\");\n  const hasChromosomeNumber = input.length >= 4 && /^[0-9xyXY]$/.test(input[3]);\n  return (hasTabs || hasHyphens) && input.startsWith(\"chr\") && 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