@weng-lab/ui-components 2.0.3 → 2.1.1

package/dist/ui-components.es55.js

@@ -1,215 +1,73 @@
-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
-  }
+import { j as t } from "./ui-components.es13.js";
+import { c as S } from "./ui-components.es14.js";
+import { Stack as D, Typography as y, IconButton as C, Divider as v, Box as g, Button as _, Modal as k } from "@mui/material";
+import G from "./ui-components.es27.js";
+const P = (o) => {
+  const e = S.c(24), {
+    open: h,
+    onClose: l,
+    onDownloadSVG: b,
+    onDownloadPNG: u,
+    plotTitle: j
+  } = o;
+  let n;
+  e[0] !== u ? (n = {
+    label: "PNG",
+    action: u
+  }, e[0] = u, e[1] = n) : n = e[1];
+  let r;
+  e[2] !== b ? (r = {
+    label: "SVG",
+    action: b
+  }, e[2] = b, e[3] = r) : r = e[3];
+  let d;
+  e[4] !== n || e[5] !== r ? (d = [n, r].filter(I), e[4] = n, e[5] = r, e[6] = d) : d = e[6];
+  const w = d;
+  let m;
+  e[7] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (m = {
+    position: "absolute",
+    top: "50%",
+    left: "50%",
+    transform: "translate(-50%, -50%)",
+    bgcolor: "background.paper",
+    boxShadow: 24,
+    borderRadius: 2,
+    p: 3,
+    width: 360
+  }, e[7] = m) : m = e[7];
+  let i;
+  e[8] !== j ? (i = /* @__PURE__ */ t.jsxs(y, { variant: "h6", fontWeight: 600, mb: 1, children: [
+    "Download ",
+    j
+  ] }), e[8] = j, e[9] = i) : i = e[9];
+  let f;
+  e[10] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (f = /* @__PURE__ */ t.jsx(y, { variant: "body2", color: "text.secondary", mb: 2, children: "Choose a file format to export your plot." }), e[10] = f) : f = e[10];
+  let p;
+  e[11] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (p = /* @__PURE__ */ t.jsx(v, { flexItem: !0 }), e[11] = p) : p = e[11];
+  let a;
+  e[12] !== w ? (a = /* @__PURE__ */ t.jsx(D, { spacing: 1.5, divider: p, children: w.map(B) }), e[12] = w, e[13] = a) : a = e[13];
+  let s;
+  e[14] !== l ? (s = /* @__PURE__ */ t.jsx(g, { mt: 3, textAlign: "right", children: /* @__PURE__ */ t.jsx(_, { onClick: l, children: "Close" }) }), e[14] = l, e[15] = s) : s = e[15];
+  let c;
+  e[16] !== i || e[17] !== a || e[18] !== s ? (c = /* @__PURE__ */ t.jsxs(g, { sx: m, children: [
+    i,
+    f,
+    a,
+    s
+  ] }), e[16] = i, e[17] = a, e[18] = s, e[19] = c) : c = e[19];
+  let x;
+  return e[20] !== l || e[21] !== h || e[22] !== c ? (x = /* @__PURE__ */ t.jsx(k, { open: h, onClose: l, children: c }), e[20] = l, e[21] = h, e[22] = c, e[23] = x) : x = e[23], x;
 };
-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;
+function I(o) {
+  return o.action;
+}
+function B(o) {
+  return /* @__PURE__ */ t.jsxs(D, { direction: "row", alignItems: "center", justifyContent: "space-between", children: [
+    /* @__PURE__ */ t.jsx(y, { variant: "body1", children: o.label }),
+    /* @__PURE__ */ t.jsx(C, { color: "primary", onClick: o.action, "aria-label": `Download ${o.label}`, children: /* @__PURE__ */ t.jsx(G, {}) })
+  ] }, o.label);
 }
 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
+  P as default
 };
 //# sourceMappingURL=ui-components.es55.js.map

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

@@ -1 +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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package/dist/ui-components.es56.js

@@ -1,245 +1,33 @@
-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: $accession_prefix
-    ) {
-      accession
-      isiCRE
-      coordinates {
-        chromosome
-        start
-        end
-      }
-    }
-  }
-`, h = `
-  query getv2v3CcreMapping($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: $studyname_prefix )
-    {
-        studyid
-        author
-        disease_trait
-        has_enrichment_info
-        population
-        parent_terms
-        total_ld_blocks
-        ld_blocks_overlapping_ccres
-        overlapping_ccres
-    }
+import { j as c } from "./ui-components.es13.js";
+import { c as f } from "./ui-components.es14.js";
+import { useState as x } from "react";
+import b from "./ui-components.es21.js";
+function j(l) {
+  const e = f.c(9), {
+    value: t,
+    figures: n
+  } = l;
+  let r;
+  e[0] !== t ? (r = /* @__PURE__ */ new Set([t]), e[0] = t, e[1] = r) : r = e[1];
+  const [o, d] = x(r);
+  o.has(t) || d(/* @__PURE__ */ new Set([...o, t]));
+  let s;
+  if (e[2] !== n || e[3] !== o || e[4] !== t) {
+    let i;
+    e[6] !== o || e[7] !== t ? (i = (u, a) => {
+      const m = t === a, p = o.has(a);
+      return /* @__PURE__ */ c.jsx(b, { display: m ? "block" : "none", height: "100%", width: "100%", overflow: "auto", padding: 1, sx: {
+        border: "1px solid",
+        borderColor: "divider",
+        borderRadius: 1,
+        position: "relative"
+      }, children: p && u.component }, `figure-${a}`);
+    }, e[6] = o, e[7] = t, e[8] = i) : i = e[8], s = n.map(i), e[2] = n, e[3] = o, e[4] = t, e[5] = s;
+  } else
+    s = e[5];
+  return s;
 }
-`, 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 {
-  _ 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
+  j as default
 };
 //# sourceMappingURL=ui-components.es56.js.map

package/dist/ui-components.es56.js.map

@@ -1 +1 @@
-{"version":3,"file":"ui-components.es56.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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