@weng-lab/ui-components 2.0.3 → 2.1.0

package/dist/ui-components.es58.js

@@ -1,5 +1,215 @@
-var e = { exports: {} };
+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
+  }
+};
+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 {
-  e as __module
+  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.es58.js.map

package/dist/ui-components.es58.js.map

@@ -1 +1 @@
-{"version":3,"file":"ui-components.es58.js","sources":[],"sourcesContent":[],"names":[],"mappings":";"}
+{"version":3,"file":"ui-components.es58.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\") && hasChromosomeNumber;\n}\n"],"names":["getCoordinates","input","assembly","results","replace","chromosome","start","end","includes","split","parseInt","chr","startStr","endStr","normalizedChromosome","chrLength","chromosomeLengths","push","title","toLocaleString","domain","description","type","formatResults","limit","options","slice","map","result","getTitle","getDescription","coordinates","snpResultList","id","geneResultList","showVersions","name","idStr","versions","forEach","x","i","version","length","studyResultList","disease_trait","author","studyid","parent_terms","join","has_enrichment_info","undefined","omeResultsList","ome","label","value","icreResultList","accession","ccreResultList","isiCRE","legacyCcreResultList","filter","v4_match_or_intersecting","region","input_region","overlapping","input_latest_previous_version","OmesList","keywords","GRCh38","chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX","chrx","chrY","chry","mm10","isDomain","hasTabs","hasHyphens","hasChromosomeNumber","test","startsWith"],"mappings":"AAQO,SAASA,EAAeC,GAAeC,GAA4B;AACxE,QAAMC,IAAoB,CAAA;AAC1BF,EAAAA,IAAQA,EAAMG,QAAQ,MAAM,EAAE;AAE9B,MAAIC,GAAoBC,GAAeC;AAEvC,MAAIN,EAAMO,SAAS,GAAG,KAAKP,EAAMO,SAAS,GAAG;AAC3CH,IAAAA,IAAaJ,EAAMQ,MAAM,GAAG,EAAE,CAAC,GAC/BH,IAAQI,SAAST,EAAMQ,MAAM,GAAG,EAAE,CAAC,EAAEA,MAAM,GAAG,EAAE,CAAC,CAAC,KAAK,GACvDF,IAAMG,SAAST,EAAMQ,MAAM,GAAG,EAAE,CAAC,EAAEA,MAAM,GAAG,EAAE,CAAC,CAAC,KAAKH,IAAQ;AAAA,WACpDL,EAAMO,SAAS,GAAI,GAAG;AAC/B,UAAM,CAACG,GAAKC,GAAUC,CAAM,IAAIZ,EAAMQ,MAAM,GAAI;AAChDJ,IAAAA,IAAaM,GACbL,IAAQI,SAASE,CAAQ,GACzBL,IAAMG,SAASG,CAAM;AAAA,EACvB;AACE,WAAOV;AAIT,QAAMW,IAAuBT,EAAWD,QAAQ,SAAS,MAAM,EAAEA,QAAQ,SAAS,MAAM,GAElFW,IAAYC,EAAkBd,CAAQ,EAAEG,CAAU;AACxD,SAAIE,IAAMD,KAASS,KAAaR,KAAOQ,KACrCZ,EAAQc,KAAK;AAAA,IACXC,OAAO,GAAGJ,CAAoB,IAAIR,EAAMa,gBAAgB,IAAIZ,EAAIY,eAAAA,CAAgB;AAAA,IAChFC,QAAQ;AAAA,MACNf,YAAYS;AAAAA,MACZR,OAAAA;AAAAA,MACAC,KAAAA;AAAAA,IAAAA;AAAAA,IAEFc,aAAa,GAAGP,CAAoB,IAAIR,EAAMa,gBAAgB,IAAIZ,EAAIY,eAAAA,CAAgB;AAAA,IACtFG,MAAM;AAAA,EAAA,CACP,GAGInB;AACT;AAUA,SAASoB,EACPpB,GACAqB,GACAC,GACU;AACV,SAAKtB,IAGEA,EAAQuB,MAAM,GAAGF,CAAK,EAAEG,IAAKC,CAAAA,OAAY;AAAA,IAC9CV,OAAOO,EAAQI,SAASD,CAAM;AAAA,IAC9BP,aAAaI,EAAQK,eAAeF,CAAM;AAAA,IAC1CR,QAAQ;AAAA,MACNf,YAAYuB,EAAOG,YAAY1B;AAAAA,MAC/BC,OAAOsB,EAAOG,YAAYzB;AAAAA,MAC1BC,KAAKqB,EAAOG,YAAYxB;AAAAA,IAAAA;AAAAA,IAE1Be,MAAMG,EAAQH;AAAAA,EAAAA,EACd,IAXO,CAAA;AAYX;AAGO,SAASU,EAAc7B,GAAwBqB,GAAyB;AAC7E,SAAOD,EAAcpB,GAASqB,GAAO;AAAA,IACnCK,UAAWD,OAAWA,EAAOK;AAAAA,IAC7BH,gBAAiBF,CAAAA,MACf,GAAGA,EAAOG,YAAY1B,UAAU,IAAIuB,EAAOG,YAAYzB,KAAK,IAAIsB,EAAOG,YAAYxB,GAAG;AAAA,IACxFe,MAAM;AAAA,EAAA,CACP;AACH;AAEO,SAASY,EAAe/B,GAAyBqB,GAAeW,GAAiC;AACtG,SAAOZ,EAAcpB,GAASqB,GAAO;AAAA,IACnCK,UAAWD,OAAWA,EAAOQ;AAAAA,IAC7BN,gBAAiBF,CAAAA,MAAW;AAC1B,UAAIS,IAAQ;AACZT,aAAAA,EAAOU,SAASC,QACd,CAACC,GAAGC,MAAOJ,KAAS,MAAMG,EAAEE,UAAU,MAAMF,EAAEP,MAAMQ,MAAMb,EAAOU,SAASK,SAAS,IAAI,KAAK;AAAA,EAC9F,GACO,GAAGf,EAAOP,WAAW;AAAA,EAAKgB,CAAK;AAAA,EAAKT,EAAOG,YAAY1B,UAAU,IAAIuB,EAAOG,YAAYzB,KAAK,IAAIsB,EAAOG,YAAYxB,GAAG;AAAA,IAChI;AAAA,IACAe,MAAM;AAAA,EAAA,CACP;AACH;AAEO,SAASsB,EAAgBzC,GAA0BqB,GAAyB;AACjF,SAAOrB,EAAQuB,MAAM,GAAGF,CAAK,EAAEG,IAAKC,CAAAA,OAAY;AAAA,IAC9CV,OAAOU,EAAOiB;AAAAA,IACdxB,aAAa,GAAGO,EAAOkB,OAAO1C,QAAQ,KAAK,GAAG,CAAC,KAAKwB,EAAOmB,QAAQtC,MAAM,GAAG,EAAE,CAAC,CAAC;AAAA,EAAMmB,EAAOoB,aAAaC,KAAK,GAAG,CAAC;AAAA,GAAMrB,EAAOsB,sBAAsB,yBAAyB,EAAE;AAAA,IACjL9B,QAAQ+B;AAAAA,IACRlB,IAAIL,EAAOmB;AAAAA,IACXzB,MAAM;AAAA,EAAA,EACN;AACJ;AAEO,SAAS8B,EAAejD,GAAgC;AAC7D,SAAOA,EAAQwB,IAAK0B,CAAAA,OAAS;AAAA,IAC3BnC,OAAOmC,EAAIC;AAAAA,IACXjC,aAAagC,EAAIhC,eAAe;AAAA,IAChCD,QAAQ+B;AAAAA,IACRlB,IAAIoB,EAAIE;AAAAA,IACRjC,MAAM;AAAA,EAAA,EACN;AACJ;AAEO,SAASkC,EAAerD,GAAyBqB,GAAyB;AAC/E,SAAOD,EAAcpB,GAASqB,GAAO;AAAA,IACnCK,UAAWD,OAAWA,EAAO6B;AAAAA,IAC7B3B,gBAAiBF,CAAAA,MACf,GAAGA,EAAOG,YAAY1B,UAAU,IAAIuB,EAAOG,YAAYzB,KAAK,IAAIsB,EAAOG,YAAYxB,GAAG;AAAA,IACxFe,MAAM;AAAA,EAAA,CACP;AACH;AAEO,SAASoC,EAAevD,GAAyBqB,GAAyB;AAC/E,SAAOD,EAAcpB,GAASqB,GAAO;AAAA,IACnCK,UAAWD,OAAWA,EAAO6B;AAAAA,IAC7B3B,gBAAiBF,CAAAA,MACf,GAAGA,EAAOG,YAAY1B,UAAU,IAAIuB,EAAOG,YAAYzB,KAAK,IAC1DsB,EAAOG,YAAYxB,GAAG,GACrBqB,EAAO+B,SAAS,WAAW,EAAE;AAAA,IAClCrC,MAAM;AAAA,EAAA,CACP;AACH;AAEO,SAASsC,EAAqBzD,GAA+BqB,GAAyB;AAC3F,SAAOrB,EACJ0D,OAAQjC,CAAAA,MAAWA,EAAO3B,UAAU2B,EAAOkC,wBAAwB,EACnEpC,MAAM,GAAGF,CAAK,EACdG,IAAKC,CAAAA,MAAW;AACf,UAAMmC,IAASnC,EAAOoC,cAChBC,IAAcrC,EAAOkC;AAC3B,WAAO;AAAA,MACL5C,OAAOU,EAAO3B;AAAAA;AAAAA,MAEdoB,aAAa,aAAaO,EAAOsC,6BAA6B;AAAA,EAAMtC,EAAOoC,YAAY;AAAA,EAAKC,IAAc,qBAAqBA,EAAYzD,SAAS,GAAG,IAAI,MAAM,EAAE,KAAKyD,EAAY7D,QAAQ,KAAK,IAAI,CAAC,KAAK,0BAA0B;AAAA,MACrOgB,QAAQ;AAAA,QACNf,YAAY0D,EAAOtD,MAAM,GAAG,EAAE,CAAC;AAAA,QAC/BH,OAAOI,SAASqD,EAAOtD,MAAM,GAAG,EAAE,CAAC,EAAEA,MAAM,GAAG,EAAE,CAAC,CAAC;AAAA,QAClDF,KAAKG,SAASqD,EAAOtD,MAAM,GAAG,EAAE,CAAC,EAAEA,MAAM,GAAG,EAAE,CAAC,CAAC;AAAA,MAAA;AAAA,MAElDa,MAAM;AAAA,IAAA;AAAA,EAEV,CAAC;AACL;AAUO,MAAM6C,IAAwB,CACnC;AAAA,EACEb,OAAO;AAAA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package/dist/ui-components.es59.js

@@ -1,36 +1,245 @@
-import { __exports as e } from "./ui-components.es75.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
-    };
+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: $accession_prefix
+    ) {
+      accession
+      isiCRE
+      coordinates {
+        chromosome
+        start
+        end
+      }
+    }
   }
-  return e.Fragment = _, e.jsx = o, e.jsxs = o, e;
+`, h = `
+  query getv2v3CcreMapping($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
+    }
+}
+`, 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 {
-  a as __require
+  _ as CCRE_AUTOCOMPLETE_QUERY,
+  y as GENE_AUTOCOMPLETE_QUERY,
+  u as GWAS_AUTOCOMPLETE_QUERY,
+  g as ICRE_AUTOCOMPLETE_QUERY,
+  h as LEGACY_CCRE_QUERY,
+  d as SNP_AUTOCOMPLETE_QUERY,
+  v as getCCREs,
+  R as getGenes,
+  f as getICREs,
+  E as getLegacyCCREs,
+  T as getSNPs,
+  O as getStudys
 };
 //# sourceMappingURL=ui-components.es59.js.map

package/dist/ui-components.es59.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ui-components.es59.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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