@weng-lab/ui-components 2.0.1 → 2.0.2

package/dist/ui-components.es55.js

@@ -1,215 +1,57 @@
-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
+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);
+  }
+}, 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";
   }
 };
-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 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
+` : ""}`;
+}
+const h = {
+  dnase: "#06DA93",
+  h3k27ac: "#FFCD00",
+  h3k4me3: "#FF0000",
+  ctcf: "#00B0F0",
+  atac: "#02c7b9"
+};
 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
+  h as ASSAY_COLORS,
+  f as assayHoverInfo,
+  s as fetchFileSize,
+  i as formatAssay,
+  o as formatFileSize
 };
 //# 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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