@weng-lab/ui-components 2.1.0 → 2.2.0

package/dist/ui-components.es62.js

@@ -1,36 +1,215 @@
-import { __exports as e } from "./ui-components.es69.js";
-/**
- * @license React
- * react-jsx-runtime.production.js
- *
- * Copyright (c) Meta Platforms, Inc. and affiliates.
- *
- * This source code is licensed under the MIT license found in the
- * LICENSE file in the root directory of this source tree.
- */
-var s;
-function a() {
-  if (s) return e;
-  s = 1;
-  var i = Symbol.for("react.transitional.element"), _ = Symbol.for("react.fragment");
-  function o(l, r, t) {
-    var u = null;
-    if (t !== void 0 && (u = "" + t), r.key !== void 0 && (u = "" + r.key), "key" in r) {
-      t = {};
-      for (var n in r)
-        n !== "key" && (t[n] = r[n]);
-    } else t = r;
-    return r = t.ref, {
-      $$typeof: i,
-      type: l,
-      key: u,
-      ref: r !== void 0 ? r : null,
-      props: t
+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
   }
-  return e.Fragment = _, e.jsx = o, e.jsxs = o, e;
+};
+function C(t) {
+  const i = t.includes("	"), e = t.includes("-"), c = t.length >= 4 && /^[0-9xyXY]$/.test(t[3]);
+  return (i || e) && t.startsWith("chr") && c;
 }
 export {
-  a as __require
+  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.es62.js.map

package/dist/ui-components.es62.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ui-components.es62.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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