@weng-lab/ui-components 2.1.0 → 2.1.1

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

@@ -1 +1 @@
-{"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\") && 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+{"version":3,"file":"ui-components.es58.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;"}

package/dist/ui-components.es59.js

@@ -1,245 +1,165 @@
-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: $accession_prefix
-    ) {
-      accession
-      isiCRE
-      coordinates {
-        chromosome
-        start
-        end
+import { j as l } from "./ui-components.es13.js";
+import { c as de } from "./ui-components.es14.js";
+import { Box as fe, Divider as me, Typography as ge, IconButton as pe, Tooltip as he, DialogTitle as ue, Checkbox as X, FormControlLabel as Y, DialogContent as xe, Stack as be, Button as Z, DialogActions as je, Dialog as Ce } from "@mui/material";
+import { useState as S } from "react";
+import { Download as _e } from "@mui/icons-material";
+import { ontologyDownloadMap as we } from "./ui-components.es79.js";
+import { formatFileSize as ee, fetchFileSize as le } from "./ui-components.es58.js";
+import { useDownloadContext as De } from "./ui-components.es57.js";
+const ke = (n) => {
+  const e = n.toLowerCase().replace(/\s+/g, "_");
+  return we[e] ?? [];
+}, Oe = (n) => {
+  const e = de.c(66), {
+    ontology: o
+  } = n, [I, F] = S(!1), [c, te] = S(!1), [r, oe] = S(!1), [D, ne] = S(null), [k, ie] = S(null), {
+    onDownload: A
+  } = De();
+  let t, i, E;
+  e[0] !== o ? (t = ke(o), i = t.find(ye)?.filename ?? void 0, E = t.find(Se)?.filename ?? void 0, e[0] = o, e[1] = t, e[2] = i, e[3] = E) : (t = e[1], i = e[2], E = e[3]);
+  const a = E;
+  let v;
+  e[4] !== a || e[5] !== k || e[6] !== i || e[7] !== D ? (v = () => {
+    i && !D && le(`https://downloads.wenglab.org/${i}`, ne), a && !k && le(`https://downloads.wenglab.org/${a}`, ie), F(!0);
+  }, e[4] = a, e[5] = k, e[6] = i, e[7] = D, e[8] = v) : v = e[8];
+  const U = v;
+  let $;
+  e[9] !== r || e[10] !== a || e[11] !== t || e[12] !== i || e[13] !== c || e[14] !== A || e[15] !== o ? ($ = () => {
+    if (!t || t.length === 0)
+      return;
+    const s = [];
+    c && i && s.push({
+      filename: i,
+      label: "excluding_cancer_cell_lines"
+    }), r && a && s.push({
+      filename: a,
+      label: "all_biosamples"
+    }), s.forEach((se, ae) => {
+      const {
+        filename: V,
+        label: ce
+      } = se, W = `https://downloads.wenglab.org/${V}`;
+      setTimeout(() => {
+        if (A) {
+          const re = `${o}_aggregate_ccres_${ce}`;
+          A(W, re);
+        }
+        const y = document.createElement("a");
+        y.href = W, y.download = V, document.body.appendChild(y), y.click(), document.body.removeChild(y);
+      }, ae * 500);
+    });
+  }, e[9] = r, e[10] = a, e[11] = t, e[12] = i, e[13] = c, e[14] = A, e[15] = o, e[16] = $) : $ = e[16];
+  const M = $;
+  let d;
+  e[17] !== t || e[18] !== o ? (d = t.length === 0 ? "No Aggregate cCRE Download Options" : /* @__PURE__ */ l.jsxs(fe, { children: [
+    "Download cCREs in ",
+    o.charAt(0).toUpperCase() + o.slice(1),
+    ":",
+    /* @__PURE__ */ l.jsx("ul", { style: {
+      margin: 0,
+      paddingLeft: 16
+    }, children: t.map(Fe) }),
+    "(Opens Download Dialog)"
+  ] }), e[17] = t, e[18] = o, e[19] = d) : d = e[19];
+  let f;
+  e[20] !== U ? (f = (s) => {
+    s.stopPropagation(), U();
+  }, e[20] = U, e[21] = f) : f = e[21];
+  const q = t.length === 0;
+  let R;
+  e[22] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (R = /* @__PURE__ */ l.jsx(_e, {}), e[22] = R) : R = e[22];
+  let m;
+  e[23] !== f || e[24] !== q ? (m = /* @__PURE__ */ l.jsx("span", { children: /* @__PURE__ */ l.jsx(pe, { onClick: f, disabled: q, children: R }) }), e[23] = f, e[24] = q, e[25] = m) : m = e[25];
+  let g;
+  e[26] !== d || e[27] !== m ? (g = /* @__PURE__ */ l.jsx(he, { title: d, placement: "left", arrow: !0, children: m }), e[26] = d, e[27] = m, e[28] = g) : g = e[28];
+  let T;
+  e[29] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (T = (s) => {
+    s.stopPropagation(), F(!1);
+  }, e[29] = T) : T = e[29];
+  let z;
+  e[30] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (z = {
+    backdrop: {
+      sx: {
+        backgroundColor: "rgba(255, 255, 255, 0.1)",
+        backdropFilter: "blur(2px)"
       }
     }
-  }
-`, h = `
-  query getv2v3CcreMapping($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: $studyname_prefix )
-    {
-        studyid
-        author
-        disease_trait
-        has_enrichment_info
-        population
-        parent_terms
-        total_ld_blocks
-        ld_blocks_overlapping_ccres
-        overlapping_ccres
-    }
+  }, e[30] = z) : z = e[30];
+  let B;
+  e[31] !== o ? (B = o.charAt(0).toUpperCase(), e[31] = o, e[32] = B) : B = e[32];
+  const G = B + o.slice(1);
+  let p;
+  e[33] !== G ? (p = /* @__PURE__ */ l.jsxs(ue, { id: "export-dialog-title", children: [
+    "Download cCREs in ",
+    G,
+    ":"
+  ] }), e[33] = G, e[34] = p) : p = e[34];
+  let L;
+  e[35] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (L = (s) => oe(s.target.checked), e[35] = L) : L = e[35];
+  const H = !a;
+  let h;
+  e[36] !== r || e[37] !== H ? (h = /* @__PURE__ */ l.jsx(X, { checked: r, onChange: L, disabled: H }), e[36] = r, e[37] = H, e[38] = h) : h = e[38];
+  const J = `Aggregate cCREs (all biosamples)${k ? " - " + ee(k) : ""}`;
+  let u;
+  e[39] !== h || e[40] !== J ? (u = /* @__PURE__ */ l.jsx(Y, { control: h, label: J }), e[39] = h, e[40] = J, e[41] = u) : u = e[41];
+  let O;
+  e[42] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (O = (s) => te(s.target.checked), e[42] = O) : O = e[42];
+  const K = !i;
+  let x;
+  e[43] !== c || e[44] !== K ? (x = /* @__PURE__ */ l.jsx(X, { checked: c, onChange: O, disabled: K }), e[43] = c, e[44] = K, e[45] = x) : x = e[45];
+  const Q = `Aggregate cCREs (excluding cancer cell lines)${D ? " - " + ee(D) : ""}`;
+  let b;
+  e[46] !== x || e[47] !== Q ? (b = /* @__PURE__ */ l.jsx(Y, { control: x, label: Q }), e[46] = x, e[47] = Q, e[48] = b) : b = e[48];
+  let j;
+  e[49] !== t.length ? (j = t.length <= 1 && /* @__PURE__ */ l.jsxs(l.Fragment, { children: [
+    /* @__PURE__ */ l.jsx(me, { sx: {
+      marginTop: 1
+    } }),
+    /* @__PURE__ */ l.jsx(ge, { marginTop: 1, children: /* @__PURE__ */ l.jsx("strong", { children: "No cancerous cell lines available in this tissue" }) })
+  ] }), e[49] = t.length, e[50] = j) : j = e[50];
+  let C;
+  e[51] !== u || e[52] !== b || e[53] !== j ? (C = /* @__PURE__ */ l.jsx(xe, { children: /* @__PURE__ */ l.jsxs(be, { children: [
+    u,
+    b,
+    j
+  ] }) }), e[51] = u, e[52] = b, e[53] = j, e[54] = C) : C = e[54];
+  let N;
+  e[55] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (N = /* @__PURE__ */ l.jsx(Z, { onClick: () => {
+    F(!1);
+  }, children: "Cancel" }), e[55] = N) : N = e[55];
+  let _;
+  e[56] !== M ? (_ = /* @__PURE__ */ l.jsxs(je, { children: [
+    N,
+    /* @__PURE__ */ l.jsx(Z, { variant: "contained", onClick: () => {
+      M(), F(!1);
+    }, children: "Download" })
+  ] }), e[56] = M, e[57] = _) : _ = e[57];
+  let w;
+  e[58] !== I || e[59] !== p || e[60] !== C || e[61] !== _ ? (w = /* @__PURE__ */ l.jsxs(Ce, { open: I, onClose: T, "aria-labelledby": "export-dialog-title", disableScrollLock: !0, slotProps: z, onClick: Ae, children: [
+    p,
+    C,
+    _
+  ] }), e[58] = I, e[59] = p, e[60] = C, e[61] = _, e[62] = w) : w = e[62];
+  let P;
+  return e[63] !== w || e[64] !== g ? (P = /* @__PURE__ */ l.jsxs(l.Fragment, { children: [
+    g,
+    w
+  ] }), e[63] = w, e[64] = g, e[65] = P) : P = e[65], P;
+};
+function ye(n) {
+  return n.label === "Excluding Cancer Cell Lines";
 }
-`, 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;
+function Se(n) {
+  return n.label === "All Biosamples";
+}
+function Fe(n) {
+  return /* @__PURE__ */ l.jsx("li", { children: n.label }, n.filename);
+}
+function Ae(n) {
+  return n.stopPropagation();
 }
-const T = async (e, s, n, t) => (await fetch("https://screen.api.wenglab.org/graphql", {
-  method: "POST",
-  body: JSON.stringify({
-    query: d,
-    variables: {
-      assembly: s.toLowerCase(),
-      snpid: e,
-      limit: n
-    }
-  }),
-  headers: {
-    "Content-Type": "application/json"
-  },
-  signal: t
-})).json(), O = async (e, s, n) => (await fetch("https://screen.api.wenglab.org/graphql", {
-  method: "POST",
-  body: JSON.stringify({
-    query: u,
-    variables: {
-      studyname_prefix: [e],
-      limit: s
-    }
-  }),
-  headers: {
-    "Content-Type": "application/json"
-  },
-  signal: n
-})).json();
 export {
-  _ as CCRE_AUTOCOMPLETE_QUERY,
-  y as GENE_AUTOCOMPLETE_QUERY,
-  u as GWAS_AUTOCOMPLETE_QUERY,
-  g as ICRE_AUTOCOMPLETE_QUERY,
-  h as LEGACY_CCRE_QUERY,
-  d as SNP_AUTOCOMPLETE_QUERY,
-  v as getCCREs,
-  R as getGenes,
-  f as getICREs,
-  E as getLegacyCCREs,
-  T as getSNPs,
-  O as getStudys
+  Oe as AggregateDownloadButton,
+  ke as getAvailableFiles
 };
 //# sourceMappingURL=ui-components.es59.js.map

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

@@ -1 +1 @@
-{"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?: AbortSignal) => {\n  const response = await fetch(\"https://screen.api.wenglab.org/graphql\", {\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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+{"version":3,"file":"ui-components.es59.js","sources":["../src/components/BiosampleTable/AggregateDownload.tsx"],"sourcesContent":["import {\n  Button,\n  Tooltip,\n  Box,\n  Checkbox,\n  Dialog,\n  DialogActions,\n  DialogContent,\n  DialogTitle,\n  FormControlLabel,\n  Stack,\n  Typography,\n  Divider,\n  IconButton,\n} from \"@mui/material\";\nimport { useCallback, useMemo, useState } from \"react\";\nimport { Download } from \"@mui/icons-material\";\nimport { ontologyDownloadMap } from \"./ontologyDownloads\";\nimport { fetchFileSize, formatFileSize } from \"./helpers\";\nimport { useDownloadContext } from \"./DownloadContext\";\n\nexport type AggregateDownloadProps = {\n  ontology: string;\n};\n\n/**\n *\n * @param ontology\n * Finds available aggregate file urls for the given ontology in the form `[noccl, ccl]`\n */\n\nexport const getAvailableFiles = (ontology: string) => {\n  const key = ontology.toLowerCase().replace(/\\s+/g, \"_\");\n  return ontologyDownloadMap[key] ?? 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package/dist/ui-components.es6.js

@@ -1,11 +1,11 @@
 import { j as t } from "./ui-components.es13.js";
-import { c as De } from "./ui-components.es15.js";
+import { c as De } from "./ui-components.es14.js";
 import { TableChartRounded as Ge, CloseFullscreenRounded as Re, DragHandle as _e } from "@mui/icons-material";
 import { useTheme as Ie, useMediaQuery as _, IconButton as he, Tooltip as we, Button as Me, Typography as Be, Stack as Te, Box as ee, Divider as Ve, Tab as He, Tabs as Ne } from "@mui/material";
-import je from "./ui-components.es18.js";
+import je from "./ui-components.es27.js";
 import { useState as te, useRef as Oe } from "react";
-import $e from "./ui-components.es19.js";
-import ze from "./ui-components.es20.js";
+import $e from "./ui-components.es55.js";
+import ze from "./ui-components.es56.js";
 function Ee(i) {
   const e = De.c(10), l = Ie();
   let s;
@@ -43,7 +43,7 @@ const tt = (i) => {
     direction: I
   } = i, p = I === void 0 ? "row" : I, [oe, f] = te(0), [o, u] = te(!0), [x, c] = te(!1), [G, R] = te(40), ge = Oe(null), n = Ee(p) === "column", d = Math.min(oe, s.length - 1), a = s[d], M = !!(a?.onDownloadSVG || a?.onDownloadPNG), b = n ? "500px" : "max(60vh, 600px)";
   let B;
-  e[0] === Symbol.for("react.memo_cache_sentinel") ? (B = (r) => {
+  e[0] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (B = (r) => {
     f(r);
   }, e[0] = B) : B = e[0];
   const ye = B;
@@ -64,7 +64,7 @@ const tt = (i) => {
   e[7] !== s ? ($ = s.map(Le), e[7] = s, e[8] = $) : $ = e[8];
   const le = $, ie = `${o ? "Hide" : "Show"} Table`;
   let z, E;
-  e[9] === Symbol.for("react.memo_cache_sentinel") ? (z = {
+  e[9] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (z = {
     mx: -1
   }, E = /* @__PURE__ */ t.jsx(Ge, { color: "primary", fontSize: "small" }), e[9] = z, e[10] = E) : (z = e[9], E = e[10]);
   let g;
@@ -73,7 +73,7 @@ const tt = (i) => {
   e[13] !== g || e[14] !== ie ? (F = /* @__PURE__ */ t.jsx(we, { title: ie, children: g }), e[13] = g, e[14] = ie, e[15] = F) : F = e[15];
   const L = F;
   let U, Q;
-  e[16] === Symbol.for("react.memo_cache_sentinel") ? (U = {
+  e[16] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (U = {
     mx: -1
   }, Q = /* @__PURE__ */ t.jsx(Re, { color: "primary" }), e[16] = U, e[17] = Q) : (U = e[16], Q = e[17]);
   let W;
@@ -85,7 +85,7 @@ const tt = (i) => {
   }, children: "Download" }), e[20] = N, e[21] = n, e[22] = X) : X = e[22];
   const Ce = X, ke = Ue;
   let q;
-  e[23] === Symbol.for("react.memo_cache_sentinel") ? (q = (r) => {
+  e[23] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (q = (r) => {
     if (!r.currentTarget.hasPointerCapture(r.pointerId))
       return;
     const m = ge.current;
@@ -99,7 +99,7 @@ const tt = (i) => {
   e[24] !== n || e[25] !== G || e[26] !== o ? (w = !n && o ? (r) => `${G}% ${r.spacing(2)} minmax(0, 1fr)` : "minmax(0, 1fr)", e[24] = n, e[25] = G, e[26] = o, e[27] = w) : w = e[27];
   const re = n && o ? "auto auto auto auto" : "auto 1fr", ae = !n && o ? 0 : 2, ce = o ? "flex" : "none";
   let A;
-  e[28] === Symbol.for("react.memo_cache_sentinel") ? (A = /* @__PURE__ */ t.jsx(Be, { variant: "h6", sx: {
+  e[28] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (A = /* @__PURE__ */ t.jsx(Be, { variant: "h6", sx: {
     flexGrow: 1
   }, children: "Table View" }), e[28] = A) : A = e[28];
   let T;
@@ -123,9 +123,9 @@ const tt = (i) => {
   } }) }) }), e[33] = n, e[34] = o, e[35] = j) : j = e[35];
   const de = n && o ? 3 : 1, me = !n && o ? 3 : 1, pe = !o && L;
   let J;
-  e[36] === Symbol.for("react.memo_cache_sentinel") ? (J = (r, m) => ye(m), e[36] = J) : J = e[36];
+  e[36] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (J = (r, m) => ye(m), e[36] = J) : J = e[36];
   let K;
-  e[37] === Symbol.for("react.memo_cache_sentinel") ? (K = {
+  e[37] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (K = {
     flexGrow: 1,
     "& .MuiTabs-scrollButtons.Mui-disabled": {
       opacity: 0.3