@weng-lab/ui-components 3.0.1-beta.0 → 3.0.1-beta.2

package/dist/ui-components.es51.js.map

@@ -1 +1 @@
-{"version":3,"file":"ui-components.es51.js","sources":["../../../node_modules/.pnpm/@mui+system@7.3.9_@emotion+react@11.14.0_@types+react@19.2.14_react@19.2.4__@emotion+st_100059df2673d7a323eb0d2da91385ea/node_modules/@mui/system/esm/colorManipulator/colorManipulator.js"],"sourcesContent":["import _formatErrorMessage from \"@mui/utils/formatMuiErrorMessage\";\n/* eslint-disable @typescript-eslint/naming-convention */\nimport clamp from '@mui/utils/clamp';\n\n/**\n * Returns a number whose value is limited to the given range.\n * @param {number} value The value to be clamped\n * @param {number} min The lower boundary of the output range\n * @param {number} max The upper boundary of the output range\n * @returns {number} A number in the range [min, max]\n */\nfunction clampWrapper(value, min = 0, max = 1) {\n  if (process.env.NODE_ENV !== 'production') {\n    if (value < min || value > max) {\n      console.error(`MUI: The value provided ${value} is out of range [${min}, ${max}].`);\n    }\n  }\n  return clamp(value, min, max);\n}\n\n/**\n * Converts a color from CSS hex format to CSS rgb format.\n * @param {string} color - Hex color, i.e. #nnn or #nnnnnn\n * @returns {string} A CSS rgb color string\n */\nexport function hexToRgb(color) {\n  color = color.slice(1);\n  const re = new RegExp(`.{1,${color.length >= 6 ? 2 : 1}}`, 'g');\n  let colors = color.match(re);\n  if (colors && colors[0].length === 1) {\n    colors = colors.map(n => n + n);\n  }\n  if (process.env.NODE_ENV !== 'production') {\n    if (color.length !== color.trim().length) {\n      console.error(`MUI: The color: \"${color}\" is invalid. Make sure the color input doesn't contain leading/trailing space.`);\n    }\n  }\n  return colors ? `rgb${colors.length === 4 ? 'a' : ''}(${colors.map((n, index) => {\n    return index < 3 ? parseInt(n, 16) : Math.round(parseInt(n, 16) / 255 * 1000) / 1000;\n  }).join(', ')})` : '';\n}\nfunction intToHex(int) {\n  const hex = int.toString(16);\n  return hex.length === 1 ? `0${hex}` : hex;\n}\n\n/**\n * Returns an object with the type and values of a color.\n *\n * Note: Does not support rgb % values.\n * @param {string} color - CSS color, i.e. one of: #nnn, #nnnnnn, rgb(), rgba(), hsl(), hsla(), color()\n * @returns {object} - A MUI color object: {type: string, values: number[]}\n */\nexport function decomposeColor(color) {\n  // Idempotent\n  if (color.type) {\n    return color;\n  }\n  if (color.charAt(0) === '#') {\n    return decomposeColor(hexToRgb(color));\n  }\n  const marker = color.indexOf('(');\n  const type = color.substring(0, marker);\n  if (!['rgb', 'rgba', 'hsl', 'hsla', 'color'].includes(type)) {\n    throw new Error(process.env.NODE_ENV !== \"production\" ? `MUI: Unsupported \\`${color}\\` color.\\n` + 'The following formats are supported: #nnn, #nnnnnn, rgb(), rgba(), hsl(), hsla(), color().' : _formatErrorMessage(9, color));\n  }\n  let values = color.substring(marker + 1, color.length - 1);\n  let colorSpace;\n  if (type === 'color') {\n    values = values.split(' ');\n    colorSpace = values.shift();\n    if (values.length === 4 && values[3].charAt(0) === '/') {\n      values[3] = values[3].slice(1);\n    }\n    if (!['srgb', 'display-p3', 'a98-rgb', 'prophoto-rgb', 'rec-2020'].includes(colorSpace)) {\n      throw new Error(process.env.NODE_ENV !== \"production\" ? `MUI: unsupported \\`${colorSpace}\\` color space.\\n` + 'The following color spaces are supported: srgb, display-p3, a98-rgb, prophoto-rgb, rec-2020.' : _formatErrorMessage(10, colorSpace));\n    }\n  } else {\n    values = values.split(',');\n  }\n  values = values.map(value => parseFloat(value));\n  return {\n    type,\n    values,\n    colorSpace\n  };\n}\n\n/**\n * Returns a channel created from the input color.\n *\n * @param {string} color - CSS color, i.e. one of: #nnn, #nnnnnn, rgb(), rgba(), hsl(), hsla(), color()\n * @returns {string} - The channel for the color, that can be used in rgba or hsla colors\n */\nexport const colorChannel = color => {\n  const decomposedColor = decomposeColor(color);\n  return decomposedColor.values.slice(0, 3).map((val, idx) => decomposedColor.type.includes('hsl') && idx !== 0 ? `${val}%` : val).join(' ');\n};\nexport const private_safeColorChannel = (color, warning) => {\n  try {\n    return colorChannel(color);\n  } catch (error) {\n    if (warning && process.env.NODE_ENV !== 'production') {\n      console.warn(warning);\n    }\n    return color;\n  }\n};\n\n/**\n * Converts a color object with type and values to a string.\n * @param {object} color - Decomposed color\n * @param {string} color.type - One of: 'rgb', 'rgba', 'hsl', 'hsla', 'color'\n * @param {array} color.values - [n,n,n] or [n,n,n,n]\n * @returns {string} A CSS color string\n */\nexport function recomposeColor(color) {\n  const {\n    type,\n    colorSpace\n  } = color;\n  let {\n    values\n  } = color;\n  if (type.includes('rgb')) {\n    // Only convert the first 3 values to int (i.e. not alpha)\n    values = values.map((n, i) => i < 3 ? parseInt(n, 10) : n);\n  } else if (type.includes('hsl')) {\n    values[1] = `${values[1]}%`;\n    values[2] = `${values[2]}%`;\n  }\n  if (type.includes('color')) {\n    values = `${colorSpace} ${values.join(' ')}`;\n  } else {\n    values = `${values.join(', ')}`;\n  }\n  return `${type}(${values})`;\n}\n\n/**\n * Converts a color from CSS rgb format to CSS hex format.\n * @param {string} color - RGB color, i.e. rgb(n, n, n)\n * @returns {string} A CSS rgb color string, i.e. #nnnnnn\n */\nexport function rgbToHex(color) {\n  // Idempotent\n  if (color.startsWith('#')) {\n    return color;\n  }\n  const {\n    values\n  } = decomposeColor(color);\n  return `#${values.map((n, i) => intToHex(i === 3 ? Math.round(255 * n) : n)).join('')}`;\n}\n\n/**\n * Converts a color from hsl format to rgb format.\n * @param {string} color - HSL color values\n * @returns {string} rgb color values\n */\nexport function hslToRgb(color) {\n  color = decomposeColor(color);\n  const {\n    values\n  } = color;\n  const h = values[0];\n  const s = values[1] / 100;\n  const l = values[2] / 100;\n  const a = s * Math.min(l, 1 - l);\n  const f = (n, k = (n + h / 30) % 12) => l - a * Math.max(Math.min(k - 3, 9 - k, 1), -1);\n  let type = 'rgb';\n  const rgb = [Math.round(f(0) * 255), Math.round(f(8) * 255), Math.round(f(4) * 255)];\n  if (color.type === 'hsla') {\n    type += 'a';\n    rgb.push(values[3]);\n  }\n  return recomposeColor({\n    type,\n    values: rgb\n  });\n}\n/**\n * The relative brightness of any point in a color space,\n * normalized to 0 for darkest black and 1 for lightest white.\n *\n * Formula: https://www.w3.org/TR/WCAG20-TECHS/G17.html#G17-tests\n * @param {string} color - CSS color, i.e. one of: #nnn, #nnnnnn, rgb(), rgba(), hsl(), hsla(), color()\n * @returns {number} The relative brightness of the color in the range 0 - 1\n */\nexport function getLuminance(color) {\n  color = decomposeColor(color);\n  let rgb = color.type === 'hsl' || color.type === 'hsla' ? decomposeColor(hslToRgb(color)).values : color.values;\n  rgb = rgb.map(val => {\n    if (color.type !== 'color') {\n      val /= 255; // normalized\n    }\n    return val <= 0.03928 ? val / 12.92 : ((val + 0.055) / 1.055) ** 2.4;\n  });\n\n  // Truncate at 3 digits\n  return Number((0.2126 * rgb[0] + 0.7152 * rgb[1] + 0.0722 * rgb[2]).toFixed(3));\n}\n\n/**\n * Calculates the contrast ratio between two colors.\n *\n * Formula: https://www.w3.org/TR/WCAG20-TECHS/G17.html#G17-tests\n * @param {string} foreground - CSS color, i.e. one of: #nnn, #nnnnnn, rgb(), rgba(), hsl(), hsla()\n * @param {string} background - CSS color, i.e. one of: #nnn, #nnnnnn, rgb(), rgba(), hsl(), hsla()\n * @returns {number} A contrast ratio value in the range 0 - 21.\n */\nexport function getContrastRatio(foreground, background) {\n  const lumA = getLuminance(foreground);\n  const lumB = getLuminance(background);\n  return (Math.max(lumA, lumB) + 0.05) / (Math.min(lumA, lumB) + 0.05);\n}\n\n/**\n * Sets the absolute transparency of a color.\n * Any existing alpha values are overwritten.\n * @param {string} color - CSS color, i.e. one of: #nnn, #nnnnnn, rgb(), rgba(), hsl(), hsla(), color()\n * @param {number} value - value to set the alpha channel to in the range 0 - 1\n * @returns {string} A CSS color string. Hex input values are returned as rgb\n */\nexport function alpha(color, value) {\n  color = decomposeColor(color);\n  value = clampWrapper(value);\n  if (color.type === 'rgb' || color.type === 'hsl') {\n    color.type += 'a';\n  }\n  if (color.type === 'color') {\n    color.values[3] = `/${value}`;\n  } else {\n    color.values[3] = value;\n  }\n  return recomposeColor(color);\n}\nexport function private_safeAlpha(color, value, warning) {\n  try {\n    return alpha(color, value);\n  } catch (error) {\n    if (warning && process.env.NODE_ENV !== 'production') {\n      console.warn(warning);\n    }\n    return color;\n  }\n}\n\n/**\n * Darkens a color.\n * @param {string} color - CSS color, i.e. one of: #nnn, #nnnnnn, rgb(), rgba(), hsl(), hsla(), color()\n * @param {number} coefficient - multiplier in the range 0 - 1\n * @returns {string} A CSS color string. Hex input values are returned as rgb\n */\nexport function darken(color, coefficient) {\n  color = decomposeColor(color);\n  coefficient = clampWrapper(coefficient);\n  if (color.type.includes('hsl')) {\n    color.values[2] *= 1 - coefficient;\n  } else if (color.type.includes('rgb') || color.type.includes('color')) {\n    for (let i = 0; i < 3; i += 1) {\n      color.values[i] *= 1 - coefficient;\n    }\n  }\n  return recomposeColor(color);\n}\nexport function private_safeDarken(color, coefficient, warning) {\n  try {\n    return darken(color, coefficient);\n  } catch (error) {\n    if (warning && process.env.NODE_ENV !== 'production') {\n      console.warn(warning);\n    }\n    return color;\n  }\n}\n\n/**\n * Lightens a color.\n * @param {string} color - CSS color, i.e. one of: #nnn, #nnnnnn, rgb(), rgba(), hsl(), hsla(), color()\n * @param {number} coefficient - multiplier in the range 0 - 1\n * @returns {string} A CSS color string. Hex input values are returned as rgb\n */\nexport function lighten(color, coefficient) {\n  color = decomposeColor(color);\n  coefficient = clampWrapper(coefficient);\n  if (color.type.includes('hsl')) {\n    color.values[2] += (100 - color.values[2]) * coefficient;\n  } else if (color.type.includes('rgb')) {\n    for (let i = 0; i < 3; i += 1) {\n      color.values[i] += (255 - color.values[i]) * coefficient;\n    }\n  } else if (color.type.includes('color')) {\n    for (let i = 0; i < 3; i += 1) {\n      color.values[i] += (1 - color.values[i]) * coefficient;\n    }\n  }\n  return recomposeColor(color);\n}\nexport function private_safeLighten(color, coefficient, warning) {\n  try {\n    return lighten(color, coefficient);\n  } catch (error) {\n    if (warning && process.env.NODE_ENV !== 'production') {\n      console.warn(warning);\n    }\n    return color;\n  }\n}\n\n/**\n * Darken or lighten a color, depending on its luminance.\n * Light colors are darkened, dark colors are lightened.\n * @param {string} color - CSS color, i.e. one of: #nnn, #nnnnnn, rgb(), rgba(), hsl(), hsla(), color()\n * @param {number} coefficient=0.15 - multiplier in the range 0 - 1\n * @returns {string} A CSS color string. 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package/dist/ui-components.es52.js

@@ -1,9 +1,212 @@
-import { createContext as o, useContext as t } from "react";
-const n = o({
-  onDownload: void 0
-}), r = () => t(n);
+function p(t, c) {
+  const e = [];
+  t = t.replace(/,/g, "");
+  let i, o, r;
+  if (t.includes(":") && t.includes("-"))
+    i = 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("	");
+    i = h, o = parseInt(l), r = parseInt(d);
+  } else
+    return e;
+  const s = i.replace(/chrx$/, "chrX").replace(/chry$/, "chrY"), a = m[c][s];
+  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, c, e) {
+  return t ? t.slice(0, c).map((i) => ({
+    title: e.getTitle(i),
+    description: e.getDescription(i),
+    domain: {
+      chromosome: i.coordinates.chromosome,
+      start: i.coordinates.start,
+      end: i.coordinates.end
+    },
+    type: e.type
+  })) : [];
+}
+function g(t, c) {
+  return n(t, c, {
+    getTitle: (e) => e.id,
+    getDescription: (e) => `${e.coordinates.chromosome}:${e.coordinates.start}-${e.coordinates.end}`,
+    type: "SNP"
+  });
+}
+function $(t, c, e) {
+  return n(t, c, {
+    getTitle: (i) => i.name,
+    getDescription: (i) => {
+      let o = "";
+      return i.versions.forEach((r, s) => o += "V" + r.version + " " + r.id + (s === i.versions.length - 1 ? "" : `
+`)), `${i.description}
+${o}
+${i.coordinates.chromosome}:${i.coordinates.start}-${i.coordinates.end}`;
+    },
+    type: "Gene"
+  });
+}
+function u(t, c) {
+  return t.slice(0, c).map((e) => ({
+    title: e.disease_trait,
+    description: `${e.author.replace("_", " ")} (${e.studyid.split("-")[1]})
+${e.parent_terms.join(",")}
+ ${e.has_enrichment_info ? "Biosample Enrichment" : ""}`,
+    domain: void 0,
+    id: e.studyid,
+    type: "Study"
+  }));
+}
+function y(t) {
+  return t.map((c) => ({
+    title: c.label,
+    description: c.description ?? "",
+    domain: void 0,
+    id: c.value,
+    type: "Ome"
+  }));
+}
+function v(t, c) {
+  return n(t, c, {
+    getTitle: (e) => e.accession,
+    getDescription: (e) => `${e.coordinates.chromosome}:${e.coordinates.start}-${e.coordinates.end}`,
+    type: "iCRE"
+  });
+}
+function f(t, c) {
+  return n(t, c, {
+    getTitle: (e) => e.accession,
+    getDescription: (e) => `${e.coordinates.chromosome}:${e.coordinates.start}-${e.coordinates.end}${e.isiCRE ? ", iCRE" : ""}`,
+    type: "cCRE"
+  });
+}
+function R(t, c) {
+  return t.filter((e) => e.input !== e.v4_match_or_intersecting).slice(0, c).map((e) => {
+    const i = 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
+      // At most two overlapping v4 cCREs are ever returned, so a single (non-global) comma replace is sufficient for the "a, b" rendering.
+      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: i.split(":")[0],
+        start: parseInt(i.split(":")[1].split("-")[0]),
+        end: parseInt(i.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,
+    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,
+    chrY: 91744698
+  }
+};
+function C(t) {
+  const c = t.includes("	"), e = t.includes("-"), i = t.length >= 4 && /^[0-9xyXY]$/.test(t[3]);
+  return (c || e) && t.startsWith("chr") && i;
+}
 export {
-  n as DownloadContext,
-  r as useDownloadContext
+  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.es52.js.map

package/dist/ui-components.es52.js.map

@@ -1 +1 @@
-{"version":3,"file":"ui-components.es52.js","sources":["../src/components/BiosampleTable/DownloadContext.tsx"],"sourcesContent":["import { createContext, useContext } from \"react\";\n\nexport type DownloadContextType = {\n  onDownload?: (url: string, name: string) => void;\n};\n\nexport const DownloadContext = createContext<DownloadContextType>({\n  onDownload: undefined,\n});\n\nexport const useDownloadContext = () => useContext(DownloadContext);\n"],"names":["DownloadContext","createContext","onDownload","undefined","useDownloadContext","useContext"],"mappings":";AAMO,MAAMA,IAAkBC,EAAmC;AAAA,EAChEC,YAAYC;AACd,CAAC,GAEYC,IAAqBA,MAAMC,EAAWL,CAAe;"}
+{"version":3,"file":"ui-components.es52.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][normalizedChromosome];\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        // At most two overlapping v4 cCREs are ever returned, so a single (non-global) comma replace is sufficient for the \"a, b\" rendering.\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    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    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.es53.js

@@ -1,57 +1,253 @@
-const s = async (e, n) => {
-  try {
-    const a = await fetch(e, {
-      method: "HEAD"
-    });
-    if (!a.ok)
-      throw new Error("Error fetching file size for " + e);
-    const t = a.headers.get("Content-Length");
-    t && n(parseInt(t, 10));
-  } catch (a) {
-    console.error(a), n(-1);
+const y = `
+  query suggestions($assembly: String!, $snpid: String!, $limit: Int) {
+    snpAutocompleteQuery(assembly: $assembly, snpid: $snpid, limit: $limit) {
+      id
+      coordinates {
+        chromosome
+        start
+        end
+      }
+    }
   }
-}, o = (e) => e === -1 ? "Unknown Size" : (e / 1e6).toFixed(1) + " MB", i = (e) => {
-  switch (e) {
-    case "atac":
-      return "ATAC";
-    case "ctcf":
-      return "CTCF";
-    case "dnase":
-      return "DNase";
-    case "h3k27ac":
-      return "H3K27ac";
-    case "h3k4me3":
-      return "H3K4me3";
+`, u = `
+  query Genes(
+      $name_prefix: [String!]
+      $idprefix: [String!]
+      $limit: Int
+      $assembly: String!
+      $version: Int
+      $includealiassearch: Boolean
+  ) {
+      gene(
+          name_prefix: $name_prefix
+          idprefix: $idprefix
+          limit: $limit
+          assembly: $assembly
+          orderby: "name"
+          version: $version
+          includealiassearch: $includealiassearch
+      ) {
+          id
+          name
+          description
+          coordinates {
+              chromosome
+              start
+              end
+          }
+          alias    
+      }
   }
-};
-function f(e) {
-  const {
-    dnase: n,
-    h3k27ac: a,
-    h3k4me3: t,
-    ctcf: c,
-    atac: r
-  } = e;
-  return n && a && t && c && r ? "All assays available" : !n && !a && !t && !c && !r ? "No assays available" : `Available:
-${n ? `DNase
-` : ""}${a ? `H3K27ac
-` : ""}${t ? `H3K4me3
-` : ""}${c ? `CTCF
-` : ""}${r ? `ATAC
-` : ""}`;
+`, _ = `
+  query iCREQuery($accession_prefix: [String!], $limit: Int) {
+      iCREQuery(accession_prefix: $accession_prefix, limit: $limit) {
+          rdhs
+          accession
+          celltypes
+          coordinates {
+              start
+              end
+              chromosome
+          }
+      }
+  }
+`, h = `
+  query cCREAutocompleteQuery(
+    $accession: [String!]
+    $accession_prefix: [String!]
+    $assembly: String!
+    $includeiCREs: Boolean
+    $limit: Int
+  ) {
+    cCREAutocompleteQuery(
+      includeiCREs: $includeiCREs
+      assembly: $assembly
+      limit: $limit
+      accession: $accession
+      accession_prefix: $accession_prefix
+    ) {
+      accession
+      isiCRE
+      coordinates {
+        chromosome
+        start
+        end
+      }
+    }
+  }
+`, C = `
+  query getv2v3CcreMapping($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
+    }
+  }
+`, $ = `
+query getGWASStudyMetadata($limit: Int, $studyname_prefix: [String]){
+    getGWASStudiesMetadata(limit: $limit, studyname_prefix: $studyname_prefix )
+    {
+        studyid
+        author
+        disease_trait
+        has_enrichment_info
+        population
+        parent_terms
+        total_ld_blocks
+        ld_blocks_overlapping_ccres
+        overlapping_ccres
+    }
 }
-const h = {
-  dnase: "#06DA93",
-  h3k27ac: "#FFCD00",
-  h3k4me3: "#FF0000",
-  ctcf: "#00B0F0",
-  atac: "#02c7b9"
-};
+`, b = async (e, s, i, t) => (await fetch(i, {
+  method: "POST",
+  body: JSON.stringify({
+    query: _,
+    variables: {
+      accession_prefix: [e],
+      limit: s
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: t
+})).json(), v = async (e, s, i, t, o, p) => {
+  const r = e.length === 12;
+  return (await fetch(o, {
+    method: "POST",
+    body: JSON.stringify({
+      query: h,
+      variables: {
+        ...r ? {
+          accession: [e.toUpperCase()]
+        } : {
+          accession_prefix: [e]
+        },
+        assembly: s,
+        limit: i,
+        includeiCREs: t
+      }
+    }),
+    headers: {
+      "Content-Type": "application/json"
+    },
+    signal: p
+  })).json();
+}, R = async (e, s, i, t) => (await fetch(i, {
+  method: "POST",
+  body: JSON.stringify({
+    query: C,
+    variables: {
+      accessions: [e],
+      assembly: s
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: t
+})).json(), x = async (e, s, i, t, o, p) => {
+  let r = t ? typeof t == "number" ? [t] : t : [s === "GRCh38" ? 40 : 25];
+  r = r.sort((n, a) => a - n);
+  const m = await Promise.all(r.map((n) => fetch(o, {
+    method: "POST",
+    body: JSON.stringify({
+      query: u,
+      variables: {
+        assembly: s.toLowerCase(),
+        ...s.toLowerCase() === "mm10" && e.toUpperCase().startsWith("ENSMUSG") || s.toLowerCase() === "grch38" && e.toUpperCase().startsWith("ENSG") ? {
+          idprefix: e.split(".")[0]
+        } : {
+          name_prefix: e
+        },
+        version: n,
+        limit: i,
+        includealiassearch: !0
+      }
+    }),
+    headers: {
+      "Content-Type": "application/json"
+    },
+    signal: p
+  }).then((a) => a.json()))), l = /* @__PURE__ */ new Map();
+  return m.forEach((n, a) => {
+    (n.data.gene || []).forEach((c) => {
+      l.has(c.name) ? l.get(c.name).versions.push({
+        id: c.id,
+        version: r[a]
+      }) : l.set(c.name, {
+        gene: c,
+        versions: [{
+          id: c.id,
+          version: r[a]
+        }]
+      });
+    });
+  }), await Promise.all(Array.from(l.values()).map(async ({
+    gene: n,
+    versions: a
+  }) => {
+    const d = await g(n.name);
+    return {
+      ...n,
+      description: `${f(n.description || n.name || d)} ${n.alias ? `(${n.alias})` : ""}`,
+      versions: a
+    };
+  }));
+}, f = (e) => e.split(" ").map((s) => s.charAt(0).toUpperCase() + s.slice(1)).join(" ");
+async function g(e) {
+  try {
+    const i = await (await fetch("https://clinicaltables.nlm.nih.gov/api/ncbi_genes/v3/search?authenticity_token=&terms=" + e.toUpperCase())).json(), t = i[3] && i[3].filter((o) => o[3] === e.toUpperCase());
+    return t && t.length >= 1 ? t[0][4] : null;
+  } catch {
+    return null;
+  }
+}
+const T = async (e, s, i, t, o) => (await fetch(t, {
+  method: "POST",
+  body: JSON.stringify({
+    query: y,
+    variables: {
+      assembly: s.toLowerCase(),
+      snpid: e,
+      limit: i
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: o
+})).json(), O = async (e, s, i, t) => (await fetch(i, {
+  method: "POST",
+  body: JSON.stringify({
+    query: $,
+    variables: {
+      studyname_prefix: [e],
+      limit: s
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: t
+})).json();
 export {
-  h as ASSAY_COLORS,
-  f as assayHoverInfo,
-  s as fetchFileSize,
-  i as formatAssay,
-  o as formatFileSize
+  h as CCRE_AUTOCOMPLETE_QUERY,
+  u as GENE_AUTOCOMPLETE_QUERY,
+  $ as GWAS_AUTOCOMPLETE_QUERY,
+  _ as ICRE_AUTOCOMPLETE_QUERY,
+  C as LEGACY_CCRE_QUERY,
+  y as SNP_AUTOCOMPLETE_QUERY,
+  v as getCCREs,
+  x as getGenes,
+  b as getICREs,
+  R as getLegacyCCREs,
+  T as getSNPs,
+  O as getStudys
 };
 //# sourceMappingURL=ui-components.es53.js.map

package/dist/ui-components.es53.js.map

@@ -1 +1 @@
-{"version":3,"file":"ui-components.es53.js","sources":["../src/components/BiosampleTable/helpers.ts"],"sourcesContent":["/**\n * \n * @param url \n * @param handleSetState \n * \n * Attempts to fetch the file size, and sets state with given fn. -1 if unsucessful\n */\nexport const fetchFileSize = async (url: string, handleSetState: (fileSize: number) => void) => {\n  try {\n    const response = await fetch(url, { method: \"HEAD\" });\n    if (!response.ok) {\n      throw new Error(\"Error fetching file size for \" + url)\n    }\n    const contentLength = response.headers.get(\"Content-Length\");\n    if (contentLength) {\n      handleSetState(parseInt(contentLength, 10));\n    }\n  } catch (error) {\n    console.error(error);\n    handleSetState(-1)\n  }\n};\n\nexport const formatFileSize = (fileSize: number) => fileSize === -1 ? \"Unknown Size\" : (fileSize / 1000000).toFixed(1) + \" MB\"\n/**\n *\n * @param assay\n * @returns Formatted assay name\n */\nexport const formatAssay = (assay: CcreAssay) => {\n  switch (assay) {\n    case \"atac\":\n      return \"ATAC\";\n    case \"ctcf\":\n      return \"CTCF\";\n    case \"dnase\":\n      return \"DNase\";\n    case \"h3k27ac\":\n      return \"H3K27ac\";\n    case \"h3k4me3\":\n      return \"H3K4me3\";\n  }\n};\n\nimport { CcreAssay } from \"./types\";\n\n/**\n *\n * @param assays\n * @returns string to display on hover above available assay wheel\n */\nexport function assayHoverInfo(assays: Record<CcreAssay, string | null>) {\n  const { dnase, h3k27ac, h3k4me3, ctcf, atac } = assays;\n\n  if (dnase && h3k27ac && h3k4me3 && ctcf && atac) {\n    return \"All assays available\";\n  } else if (!dnase && !h3k27ac && !h3k4me3 && !ctcf && !atac) {\n    return \"No assays available\";\n  } else\n    return `Available:\\n${dnase ? \"DNase\\n\" : \"\"}${h3k27ac ? \"H3K27ac\\n\" : \"\"}${h3k4me3 ? \"H3K4me3\\n\" : \"\"}${ctcf ? \"CTCF\\n\" : \"\"}${\n      atac ? \"ATAC\\n\" : \"\"\n    }`;\n}\n\nexport const ASSAY_COLORS: Record<CcreAssay, string> = {\n  dnase: \"#06DA93\",\n  h3k27ac: \"#FFCD00\",\n  h3k4me3: \"#FF0000\",\n  ctcf: \"#00B0F0\",\n  atac: \"#02c7b9\",\n};"],"names":["fetchFileSize","url","handleSetState","response","fetch","method","ok","Error","contentLength","headers","get","parseInt","error","console","formatFileSize","fileSize","toFixed","formatAssay","assay","assayHoverInfo","assays","dnase","h3k27ac","h3k4me3","ctcf","atac","ASSAY_COLORS"],"mappings":"AAOO,MAAMA,IAAgB,OAAOC,GAAaC,MAA+C;AAC9F,MAAI;AACF,UAAMC,IAAW,MAAMC,MAAMH,GAAK;AAAA,MAAEI,QAAQ;AAAA,IAAA,CAAQ;AACpD,QAAI,CAACF,EAASG;AACZ,YAAM,IAAIC,MAAM,kCAAkCN,CAAG;AAEvD,UAAMO,IAAgBL,EAASM,QAAQC,IAAI,gBAAgB;AAC3D,IAAIF,KACFN,EAAeS,SAASH,GAAe,EAAE,CAAC;AAAA,EAE9C,SAASI,GAAO;AACdC,YAAQD,MAAMA,CAAK,GACnBV,EAAe,EAAE;AAAA,EACnB;AACF,GAEaY,IAAiBA,CAACC,MAAqBA,MAAa,KAAK,kBAAkBA,IAAW,KAASC,QAAQ,CAAC,IAAI,OAM5GC,IAAcA,CAACC,MAAqB;AAC/C,UAAQA,GAAAA;AAAAA,IACN,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,EAAA;AAEb;AASO,SAASC,EAAeC,GAA0C;AACvE,QAAM;AAAA,IAAEC,OAAAA;AAAAA,IAAOC,SAAAA;AAAAA,IAASC,SAAAA;AAAAA,IAASC,MAAAA;AAAAA,IAAMC,MAAAA;AAAAA,EAAAA,IAASL;AAEhD,SAAIC,KAASC,KAAWC,KAAWC,KAAQC,IAClC,yBACE,CAACJ,KAAS,CAACC,KAAW,CAACC,KAAW,CAACC,KAAQ,CAACC,IAC9C,wBAEA;AAAA,EAAeJ,IAAQ;AAAA,IAAY,EAAE,GAAGC,IAAU;AAAA,IAAc,EAAE,GAAGC,IAAU;AAAA,IAAc,EAAE,GAAGC,IAAO;AAAA,IAAW,EAAE,GAC3HC,IAAO;AAAA,IAAW,EAAE;AAE1B;AAEO,MAAMC,IAA0C;AAAA,EACrDL,OAAO;AAAA,EACPC,SAAS;AAAA,EACTC,SAAS;AAAA,EACTC,MAAM;AAAA,EACNC,MAAM;AACR;"}
+{"version":3,"file":"ui-components.es53.js","sources":["../src/components/GenomeSearch/queries.ts"],"sourcesContent":["import { GenomeSearchProps } from \"./types\";\n\nexport const SNP_AUTOCOMPLETE_QUERY = `\n  query suggestions($assembly: String!, $snpid: String!, $limit: Int) {\n    snpAutocompleteQuery(assembly: $assembly, snpid: $snpid, limit: $limit) {\n      id\n      coordinates {\n        chromosome\n        start\n        end\n      }\n    }\n  }\n`;\n\nexport const GENE_AUTOCOMPLETE_QUERY = `\n  query Genes(\n      $name_prefix: [String!]\n      $idprefix: [String!]\n      $limit: Int\n      $assembly: String!\n      $version: Int\n      $includealiassearch: Boolean\n  ) {\n      gene(\n          name_prefix: $name_prefix\n          idprefix: $idprefix\n          limit: $limit\n          assembly: $assembly\n          orderby: \"name\"\n          version: $version\n          includealiassearch: $includealiassearch\n      ) {\n          id\n          name\n          description\n          coordinates {\n              chromosome\n              start\n              end\n          }\n          alias    \n      }\n  }\n`;\n\nexport const ICRE_AUTOCOMPLETE_QUERY = `\n  query iCREQuery($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: [String!]\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: $accession\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: $assembly\n    ) {\n      input: v2_accession\n      input_latest_previous_version: ccre_version\n      input_region: v2_region\n      v4_match_or_intersecting: v4_accession\n      v4_region\n    }\n  }\n`\n\nexport const GWAS_AUTOCOMPLETE_QUERY = `\nquery getGWASStudyMetadata($limit: Int, $studyname_prefix: [String]){\n    getGWASStudiesMetadata(limit: $limit, 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, url: string, signal?: AbortSignal) => {\n  const response = await fetch(url, {\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, url: string, signal?: AbortSignal) => {\n  const isExactAccession = value.length === 12;\n  const response = await fetch(url, {\n    method: \"POST\",\n    body: JSON.stringify({\n      query: CCRE_AUTOCOMPLETE_QUERY,\n      variables: {\n        ...(isExactAccession\n          ? { accession: [value.toUpperCase()] }\n          : { accession_prefix: [value] }),\n        assembly,\n        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\"], url: string, signal?: AbortSignal) => {\n  const response = await fetch(url, {\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  url: string,\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(url, {\n      method: \"POST\",\n      body: JSON.stringify({\n        query: GENE_AUTOCOMPLETE_QUERY,\n        variables: {\n          assembly: assembly.toLowerCase(),\n          ...(\n            (\n              (assembly.toLowerCase() === \"mm10\" && value.toUpperCase().startsWith(\"ENSMUSG\")) ||\n              (assembly.toLowerCase() === \"grch38\" && value.toUpperCase().startsWith(\"ENSG\"))\n            )\n              ? { idprefix: value.split(\".\")[0] }\n              : { name_prefix: value }\n          ),\n          version: version,\n          limit: limit,\n          includealiassearch: true\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(gene.description || gene.name || description)} ${gene.alias ? `(${gene.alias})` : ''}`,\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  try {\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  } catch {\n    return null;\n  }\n}\n\nexport const getSNPs = async (value: string, assembly: GenomeSearchProps[\"assembly\"], limit: number, url: string, signal?: AbortSignal) => {\n  const response = await fetch(url, {\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, url: string, signal?: AbortSignal) => {\n  const response = await fetch(url, {\n    method: \"POST\",\n    body: JSON.stringify({\n      query: GWAS_AUTOCOMPLETE_QUERY,\n      variables: {\n        studyname_prefix: [value],\n        limit,\n      },\n    }),\n    headers: { \"Content-Type\": \"application/json\" },\n    signal,\n  });\n\n  return 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