@weng-lab/ui-components 2.0.3 → 2.1.1

package/dist/ui-components.es54.js

@@ -1,165 +1,245 @@
-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.es108.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 = $;
-  let d;
-  e[17] !== t || e[18] !== o ? (d = t.length === 0 ? "No Aggregate cCRE Download Options" : /* @__PURE__ */ l.jsxs(fe, { children: [
-    "Download cCREs in ",
-    o.charAt(0).toUpperCase() + o.slice(1),
-    ":",
-    /* @__PURE__ */ l.jsx("ul", { style: {
-      margin: 0,
-      paddingLeft: 16
-    }, children: t.map(Fe) }),
-    "(Opens Download Dialog)"
-  ] }), e[17] = t, e[18] = o, e[19] = d) : d = e[19];
-  let f;
-  e[20] !== U ? (f = (s) => {
-    s.stopPropagation(), U();
-  }, e[20] = U, e[21] = f) : f = e[21];
-  const q = t.length === 0;
-  let R;
-  e[22] === Symbol.for("react.memo_cache_sentinel") ? (R = /* @__PURE__ */ l.jsx(_e, {}), e[22] = R) : R = e[22];
-  let m;
-  e[23] !== f || e[24] !== q ? (m = /* @__PURE__ */ l.jsx("span", { children: /* @__PURE__ */ l.jsx(pe, { onClick: f, disabled: q, children: R }) }), e[23] = f, e[24] = q, e[25] = m) : m = e[25];
-  let g;
-  e[26] !== d || e[27] !== m ? (g = /* @__PURE__ */ l.jsx(he, { title: d, placement: "left", arrow: !0, children: m }), e[26] = d, e[27] = m, e[28] = g) : g = e[28];
-  let T;
-  e[29] === Symbol.for("react.memo_cache_sentinel") ? (T = (s) => {
-    s.stopPropagation(), F(!1);
-  }, e[29] = T) : T = e[29];
-  let z;
-  e[30] === Symbol.for("react.memo_cache_sentinel") ? (z = {
-    backdrop: {
-      sx: {
-        backgroundColor: "rgba(255, 255, 255, 0.1)",
-        backdropFilter: "blur(2px)"
+const d = `
+  query suggestions($assembly: String!, $snpid: String!) {
+      snpAutocompleteQuery(assembly: $assembly, snpid: $snpid) {
+          id
+          coordinates {
+              chromosome
+              start
+              end
+          }
+      }
+  }
+`, y = `
+  query Genes(
+      $id: [String]
+      $name: [String]
+      $strand: String
+      $chromosome: String
+      $start: Int
+      $end: Int
+      $gene_type: String
+      $havana_id: String
+      $name_prefix: [String!]
+      $limit: Int
+      $assembly: String!
+      $version: Int
+  ) {
+      gene(
+          id: $id
+          name: $name
+          strand: $strand
+          chromosome: $chromosome
+          start: $start
+          end: $end
+          gene_type: $gene_type
+          havana_id: $havana_id
+          name_prefix: $name_prefix
+          limit: $limit
+          assembly: $assembly
+          orderby: "name"
+          version: $version
+      ) {
+          id
+          name
+          coordinates {
+              chromosome
+              start
+              end
+          }
+      }
+  }
+`, g = `
+  query iCREQuery($accession_prefix: [String!], $limit: Int) {
+      iCREQuery(accession_prefix: $accession_prefix, limit: $limit) {
+          rdhs
+          accession
+          celltypes
+          coordinates {
+              start
+              end
+              chromosome
+          }
+      }
+  }
+`, _ = `
+  query cCREAutocompleteQuery(
+    $accession_prefix: [String!]
+    $assembly: String!
+    $includeiCREs: Boolean
+    $limit: Int
+  ) {
+    cCREAutocompleteQuery(
+      includeiCREs: $includeiCREs
+      assembly: $assembly
+      limit: $limit
+      accession_prefix: $accession_prefix
+    ) {
+      accession
+      isiCRE
+      coordinates {
+        chromosome
+        start
+        end
       }
     }
-  }, e[30] = z) : z = e[30];
-  let B;
-  e[31] !== o ? (B = o.charAt(0).toUpperCase(), e[31] = o, e[32] = B) : B = e[32];
-  const G = B + o.slice(1);
-  let p;
-  e[33] !== G ? (p = /* @__PURE__ */ l.jsxs(ue, { id: "export-dialog-title", children: [
-    "Download cCREs in ",
-    G,
-    ":"
-  ] }), e[33] = G, e[34] = p) : p = e[34];
-  let L;
-  e[35] === Symbol.for("react.memo_cache_sentinel") ? (L = (s) => oe(s.target.checked), e[35] = L) : L = e[35];
-  const H = !a;
-  let h;
-  e[36] !== r || e[37] !== H ? (h = /* @__PURE__ */ l.jsx(X, { checked: r, onChange: L, disabled: H }), e[36] = r, e[37] = H, e[38] = h) : h = e[38];
-  const J = `Aggregate cCREs (all biosamples)${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)${D ? " - " + ee(D) : ""}`;
-  let b;
-  e[46] !== x || e[47] !== Q ? (b = /* @__PURE__ */ l.jsx(Y, { control: x, label: Q }), e[46] = x, e[47] = Q, e[48] = b) : b = e[48];
-  let j;
-  e[49] !== t.length ? (j = t.length <= 1 && /* @__PURE__ */ l.jsxs(l.Fragment, { children: [
-    /* @__PURE__ */ l.jsx(me, { sx: {
-      marginTop: 1
-    } }),
-    /* @__PURE__ */ l.jsx(ge, { marginTop: 1, children: /* @__PURE__ */ l.jsx("strong", { children: "No cancerous cell lines available in this tissue" }) })
-  ] }), e[49] = t.length, e[50] = j) : j = e[50];
-  let C;
-  e[51] !== u || e[52] !== b || e[53] !== j ? (C = /* @__PURE__ */ l.jsx(xe, { children: /* @__PURE__ */ l.jsxs(be, { children: [
-    u,
-    b,
-    j
-  ] }) }), e[51] = u, e[52] = b, e[53] = j, e[54] = C) : C = e[54];
-  let N;
-  e[55] === Symbol.for("react.memo_cache_sentinel") ? (N = /* @__PURE__ */ l.jsx(Z, { onClick: () => {
-    F(!1);
-  }, children: "Cancel" }), e[55] = N) : N = e[55];
-  let _;
-  e[56] !== M ? (_ = /* @__PURE__ */ l.jsxs(je, { children: [
-    N,
-    /* @__PURE__ */ l.jsx(Z, { variant: "contained", onClick: () => {
-      M(), F(!1);
-    }, children: "Download" })
-  ] }), e[56] = M, e[57] = _) : _ = e[57];
-  let w;
-  e[58] !== I || e[59] !== p || e[60] !== C || e[61] !== _ ? (w = /* @__PURE__ */ l.jsxs(Ce, { open: I, onClose: T, "aria-labelledby": "export-dialog-title", disableScrollLock: !0, slotProps: z, onClick: Ae, children: [
-    p,
-    C,
-    _
-  ] }), e[58] = I, e[59] = p, e[60] = C, e[61] = _, e[62] = w) : w = e[62];
-  let P;
-  return e[63] !== w || e[64] !== g ? (P = /* @__PURE__ */ l.jsxs(l.Fragment, { children: [
-    g,
-    w
-  ] }), e[63] = w, e[64] = g, e[65] = P) : P = e[65], P;
-};
-function ye(n) {
-  return n.label === "Excluding Cancer Cell Lines";
-}
-function Se(n) {
-  return n.label === "All Biosamples";
-}
-function Fe(n) {
-  return /* @__PURE__ */ l.jsx("li", { children: n.label }, n.filename);
+  }
+`, h = `
+  query getv2v3CcreMapping($accessions: [String], $assembly: String!) {
+    ccreMappings: getv2cCREMappings(
+      v2_accession: $accessions
+      assembly: $assembly
+    ) {
+      input: v2_accession
+      input_latest_previous_version: ccre_version
+      input_region: v2_region
+      v4_match_or_intersecting: v4_accession
+      v4_region
+    }
+  }
+`, u = `
+query getGWASStudyMetadata($studyid: [String], $limit: Int, $studyname_prefix: [String], $parent_terms: [String]){
+    getGWASStudiesMetadata(studyid: $studyid, limit: $limit, parent_terms: $parent_terms, studyname_prefix: $studyname_prefix )
+    {
+        studyid
+        author
+        disease_trait
+        has_enrichment_info
+        population
+        parent_terms
+        total_ld_blocks
+        ld_blocks_overlapping_ccres
+        overlapping_ccres
+    }
 }
-function Ae(n) {
-  return n.stopPropagation();
+`, f = async (e, s, n) => (await fetch("https://screen.api.wenglab.org/graphql", {
+  method: "POST",
+  body: JSON.stringify({
+    query: g,
+    variables: {
+      accession_prefix: [e],
+      limit: s
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: n
+})).json(), v = async (e, s, n, t, r) => (await fetch("https://screen.api.wenglab.org/graphql", {
+  method: "POST",
+  body: JSON.stringify({
+    query: _,
+    variables: {
+      accession_prefix: [e],
+      assembly: s.toLowerCase(),
+      limit: n,
+      includeiCREs: t
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: r
+})).json(), E = async (e, s, n) => (await fetch("https://screen.api.wenglab.org/graphql", {
+  method: "POST",
+  body: JSON.stringify({
+    query: h,
+    variables: {
+      accessions: [e],
+      assembly: s
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: n
+})).json(), R = async (e, s, n, t, r) => {
+  let o = t ? typeof t == "number" ? [t] : t : [s === "GRCh38" ? 40 : 25];
+  o = o.sort((i, a) => a - i);
+  const m = await Promise.all(o.map((i) => fetch("https://screen.api.wenglab.org/graphql", {
+    method: "POST",
+    body: JSON.stringify({
+      query: y,
+      variables: {
+        assembly: s.toLowerCase(),
+        name_prefix: e,
+        version: i,
+        limit: n
+      }
+    }),
+    headers: {
+      "Content-Type": "application/json"
+    },
+    signal: r
+  }).then((a) => a.json()))), p = /* @__PURE__ */ new Map();
+  return m.forEach((i, a) => {
+    (i.data.gene || []).forEach((c) => {
+      p.has(c.name) ? p.get(c.name).versions.push({
+        id: c.id,
+        version: o[a]
+      }) : p.set(c.name, {
+        gene: c,
+        versions: [{
+          id: c.id,
+          version: o[a]
+        }]
+      });
+    });
+  }), await Promise.all(Array.from(p.values()).map(async ({
+    gene: i,
+    versions: a
+  }) => {
+    const l = await C(i.name);
+    return {
+      ...i,
+      description: `${$(l || i.name)}`,
+      versions: a
+    };
+  }));
+}, $ = (e) => e.split(" ").map((s) => s.charAt(0).toUpperCase() + s.slice(1)).join(" ");
+async function C(e) {
+  const n = await (await fetch("https://clinicaltables.nlm.nih.gov/api/ncbi_genes/v3/search?authenticity_token=&terms=" + e.toUpperCase())).json(), t = n[3] && n[3].filter((r) => r[3] === e.toUpperCase());
+  return t && t.length >= 1 ? t[0][4] : null;
 }
+const T = async (e, s, n, t) => (await fetch("https://screen.api.wenglab.org/graphql", {
+  method: "POST",
+  body: JSON.stringify({
+    query: d,
+    variables: {
+      assembly: s.toLowerCase(),
+      snpid: e,
+      limit: n
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: t
+})).json(), O = async (e, s, n) => (await fetch("https://screen.api.wenglab.org/graphql", {
+  method: "POST",
+  body: JSON.stringify({
+    query: u,
+    variables: {
+      studyname_prefix: [e],
+      limit: s
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: n
+})).json();
 export {
-  Oe as AggregateDownloadButton,
-  ke as getAvailableFiles
+  _ as CCRE_AUTOCOMPLETE_QUERY,
+  y as GENE_AUTOCOMPLETE_QUERY,
+  u as GWAS_AUTOCOMPLETE_QUERY,
+  g as ICRE_AUTOCOMPLETE_QUERY,
+  h as LEGACY_CCRE_QUERY,
+  d as SNP_AUTOCOMPLETE_QUERY,
+  v as getCCREs,
+  R as getGenes,
+  f as getICREs,
+  E as getLegacyCCREs,
+  T as getSNPs,
+  O as getStudys
 };
 //# sourceMappingURL=ui-components.es54.js.map

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

@@ -1 +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)${nocclFileSize ? \" - \" + formatFileSize(nocclFileSize) : \"\"}`}\n            />\n            {availibleDownloads.length <= 1 && (\n              <>\n                <Divider sx={{ marginTop: 1 }} />\n                <Typography marginTop={1}>\n                  <strong>No cancerous cell lines available in this tissue</strong>\n                </Typography>\n              </>\n            )}\n          </Stack>\n        </DialogContent>\n        <DialogActions>\n          <Button\n            onClick={() => {\n              setIsDialogOpen(false);\n            }}\n          >\n            Cancel\n          </Button>\n          <Button\n            variant=\"contained\"\n            onClick={() => {\n              handleDownload();\n              setIsDialogOpen(false);\n            }}\n          >\n            Download\n          </Button>\n        </DialogActions>\n      </Dialog>\n    </>\n  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+{"version":3,"file":"ui-components.es54.js","sources":["../src/components/GenomeSearch/queries.ts"],"sourcesContent":["import { GeneResponse, GenomeSearchProps } from \"./types\";\n\nexport const SNP_AUTOCOMPLETE_QUERY = `\n  query suggestions($assembly: String!, $snpid: String!) {\n      snpAutocompleteQuery(assembly: $assembly, snpid: $snpid) {\n          id\n          coordinates {\n              chromosome\n              start\n              end\n          }\n      }\n  }\n`;\n\nexport const GENE_AUTOCOMPLETE_QUERY = `\n  query Genes(\n      $id: [String]\n      $name: [String]\n      $strand: String\n      $chromosome: String\n      $start: Int\n      $end: Int\n      $gene_type: String\n      $havana_id: String\n      $name_prefix: [String!]\n      $limit: Int\n      $assembly: String!\n      $version: Int\n  ) {\n      gene(\n          id: $id\n          name: $name\n          strand: $strand\n          chromosome: $chromosome\n          start: $start\n          end: $end\n          gene_type: $gene_type\n          havana_id: $havana_id\n          name_prefix: $name_prefix\n          limit: $limit\n          assembly: $assembly\n          orderby: \"name\"\n          version: $version\n      ) {\n          id\n          name\n          coordinates {\n              chromosome\n              start\n              end\n          }\n      }\n  }\n`;\n\nexport const ICRE_AUTOCOMPLETE_QUERY = `\n  query iCREQuery($accession_prefix: [String!], $limit: Int) {\n      iCREQuery(accession_prefix: $accession_prefix, limit: $limit) {\n          rdhs\n          accession\n          celltypes\n          coordinates {\n              start\n              end\n              chromosome\n          }\n      }\n  }\n`;\n\nexport const CCRE_AUTOCOMPLETE_QUERY = `\n  query cCREAutocompleteQuery(\n    $accession_prefix: [String!]\n    $assembly: String!\n    $includeiCREs: Boolean\n    $limit: Int\n  ) {\n    cCREAutocompleteQuery(\n      includeiCREs: $includeiCREs\n      assembly: $assembly\n      limit: $limit\n      accession_prefix: $accession_prefix\n    ) {\n      accession\n      isiCRE\n      coordinates {\n        chromosome\n        start\n        end\n      }\n    }\n  }\n`;\n\nexport const LEGACY_CCRE_QUERY = `\n  query getv2v3CcreMapping($accessions: [String], $assembly: String!) {\n    ccreMappings: getv2cCREMappings(\n      v2_accession: $accessions\n      assembly: $assembly\n    ) {\n      input: v2_accession\n      input_latest_previous_version: ccre_version\n      input_region: v2_region\n      v4_match_or_intersecting: v4_accession\n      v4_region\n    }\n  }\n`\n\nexport const GWAS_AUTOCOMPLETE_QUERY = `\nquery getGWASStudyMetadata($studyid: [String], $limit: Int, $studyname_prefix: [String], $parent_terms: [String]){\n    getGWASStudiesMetadata(studyid: $studyid, limit: $limit, parent_terms: $parent_terms, studyname_prefix: $studyname_prefix )\n    {\n        studyid\n        author\n        disease_trait\n        has_enrichment_info\n        population\n        parent_terms\n        total_ld_blocks\n        ld_blocks_overlapping_ccres\n        overlapping_ccres\n    }\n}\n`;\n\nexport const getICREs = async (value: string, limit: number, signal?: AbortSignal) => {\n  const response = await fetch(\"https://screen.api.wenglab.org/graphql\", {\n    method: \"POST\",\n    body: JSON.stringify({\n      query: ICRE_AUTOCOMPLETE_QUERY,\n      variables: {\n        accession_prefix: [value],\n        limit: limit,\n      },\n    }),\n    headers: { \"Content-Type\": \"application/json\" },\n    signal,\n  });\n  return response.json();\n};\n\nexport const getCCREs = async (value: string, assembly: GenomeSearchProps[\"assembly\"], limit: number, showiCREFlag: boolean, signal?: AbortSignal) => {\n  const response = await fetch(\"https://screen.api.wenglab.org/graphql\", {\n    method: \"POST\",\n    body: JSON.stringify({\n      query: CCRE_AUTOCOMPLETE_QUERY,\n      variables: {\n        accession_prefix: [value],\n        assembly: assembly.toLowerCase(),\n        limit: limit,\n        includeiCREs: showiCREFlag,\n      },\n    }),\n    headers: { \"Content-Type\": \"application/json\" },\n    signal,\n  });\n  return response.json();\n};\n\nexport const getLegacyCCREs = async (value: string, assembly: GenomeSearchProps[\"assembly\"], signal?: AbortSignal) => {\n  const response = await fetch(\"https://screen.api.wenglab.org/graphql\", {\n    method: \"POST\",\n    body: JSON.stringify({\n      query: LEGACY_CCRE_QUERY,\n      variables: {\n        accessions: [value],\n        assembly,\n      },\n    }),\n    headers: { \"Content-Type\": \"application/json\" },\n    signal,\n  });\n  return response.json();\n};\n\nexport const getGenes = async (\n  value: string,\n  assembly: GenomeSearchProps[\"assembly\"],\n  limit: number,\n  geneVersions: GenomeSearchProps[\"geneVersion\"],\n  signal?: AbortSignal\n) => {\n  let versions = geneVersions\n    ? typeof geneVersions === \"number\"\n      ? [geneVersions]\n      : geneVersions\n    : [assembly === \"GRCh38\" ? 40 : 25];\n\n  // sort versions from high to low (prioritize newest versions in map)\n  versions = versions.sort((a, b) => b - a);\n\n  // Fetch genes for all versions\n  const versionResults = await Promise.all(\n    versions.map((version) =>\n      fetch(\"https://screen.api.wenglab.org/graphql\", {\n        method: \"POST\",\n        body: JSON.stringify({\n          query: GENE_AUTOCOMPLETE_QUERY,\n          variables: {\n            assembly: assembly.toLowerCase(),\n            name_prefix: value,\n            version: version,\n            limit: limit,\n          },\n        }),\n        headers: { \"Content-Type\": \"application/json\" },\n        signal,\n      }).then((res) => res.json())\n    )\n  );\n\n  // Combine and deduplicate results\n  const geneMap = new Map<string, { gene: any; versions: { id: string; version: number }[] }>();\n\n  versionResults.forEach((result, idx) => {\n    const genes = result.data.gene || [];\n    genes.forEach((gene: any) => {\n      if (!geneMap.has(gene.name)) {\n        geneMap.set(gene.name, { gene, versions: [{ id: gene.id, version: versions[idx] }] });\n      } else {\n        // if gene already exists, just add legacy versions to list.\n        const existing = geneMap.get(gene.name)!;\n        existing.versions.push({ id: gene.id, version: versions[idx] });\n      }\n    });\n  });\n\n  // Convert map to array and fetch descriptions\n  const out = await Promise.all(\n    Array.from(geneMap.values()).map(async ({ gene, versions }) => {\n      const description = await getDescription(gene.name);\n      return {\n        ...gene,\n        description: `${toTitleCase(description || gene.name)}`,\n        versions,\n      };\n    })\n  );\n\n  return out;\n};\nconst toTitleCase = (str: string) =>\n  str\n    .split(\" \")\n    .map((word) => word.charAt(0).toUpperCase() + word.slice(1))\n    .join(\" \");\n\nasync function getDescription(name: string): Promise<string | null> {\n  const response = await fetch(\n    \"https://clinicaltables.nlm.nih.gov/api/ncbi_genes/v3/search?authenticity_token=&terms=\" + name.toUpperCase()\n  );\n  const data = await response.json();\n  const matches = data[3] && data[3].filter((x: string[]) => x[3] === name.toUpperCase());\n  return matches && matches.length >= 1 ? matches[0][4] : null;\n}\n\nexport const getSNPs = async (value: string, assembly: GenomeSearchProps[\"assembly\"], limit: number, signal?: AbortSignal) => {\n  const response = await fetch(\"https://screen.api.wenglab.org/graphql\", {\n    method: \"POST\",\n    body: JSON.stringify({\n      query: SNP_AUTOCOMPLETE_QUERY,\n      variables: {\n        assembly: assembly.toLowerCase(),\n        snpid: value,\n        limit: limit,\n      },\n    }),\n    headers: { \"Content-Type\": \"application/json\" },\n    signal,\n  });\n  return response.json();\n};\n\nexport const getStudys = async (value: string, limit: number, signal?: 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