@weng-lab/ui-components 2.0.3 → 2.1.1

package/dist/ui-components.es10.js.map

@@ -1 +1 @@
-{"version":3,"file":"ui-components.es10.js","sources":["../src/components/BiosampleTable/useEncodeBiosampleData.ts"],"sourcesContent":["import { useEffect, useState } from \"react\"\nimport { EncodeBiosample } from \"./types\"\n\nexport const useEncodeBiosampleData = ({ assembly, skip }: { assembly: \"GRCh38\" | \"mm10\", skip?: boolean }) => {\n  const [loading, setLoading] = useState(false);\n  const [error, setError] = useState(false);\n  const [data, setData] = useState<EncodeBiosample[] | undefined>(undefined);\n\n  const url = assembly === \"GRCh38\" ? \"https://downloads.wenglab.org/human_biosamples_tracks_metadata.json\" : \"https://downloads.wenglab.org/mouse_biosamples_tracks_metadata.json\"\n\n  useEffect(() => {\n    const fetchData = async () => {\n      try {\n        setLoading(true);\n\n        const response = await fetch(url);\n        if (!response.ok) {\n          throw new Error(`Response status: ${response.status}`);\n        }\n        const result = await response.json()\n        const biosamples = result?.data?.ccREBiosampleQuery?.biosamples\n        if (!biosamples) {\n          throw new Error(`No biosamples present in return data`);\n        }\n        setData(biosamples);\n      } catch (err) {\n        setError(true);\n      } finally {\n        setLoading(false);\n      }\n    };\n\n    if (!skip) fetchData();\n  }, [url, skip]);\n\n  return { data, loading, error };\n};"],"names":["useEncodeBiosampleData","assembly","skip","loading","setLoading","useState","error","setError","data","setData","undefined","url","useEffect","response","fetch","ok","Error","status","biosamples","json","ccREBiosampleQuery","fetchData"],"mappings":";AAGO,MAAMA,IAAyBA,CAAC;AAAA,EAAEC,UAAAA;AAAAA,EAAUC,MAAAA;AAAsD,MAAM;AAC7G,QAAM,CAACC,GAASC,CAAU,IAAIC,EAAS,EAAK,GACtC,CAACC,GAAOC,CAAQ,IAAIF,EAAS,EAAK,GAClC,CAACG,GAAMC,CAAO,IAAIJ,EAAwCK,MAAS,GAEnEC,IAAMV,MAAa,WAAW,wEAAwE;AAE5GW,SAAAA,EAAU,MAAM;AAsBd,IAAKV,MArBa,YAAY;AAC5B,UAAI;AACFE,QAAAA,EAAW,EAAI;AAEf,cAAMS,IAAW,MAAMC,MAAMH,CAAG;AAChC,YAAI,CAACE,EAASE;AACZ,gBAAM,IAAIC,MAAM,oBAAoBH,EAASI,MAAM,EAAE;AAGvD,cAAMC,KADS,MAAML,EAASM,KAAAA,IACHX,MAAMY,oBAAoBF;AACrD,YAAI,CAACA;AACH,gBAAM,IAAIF,MAAM,sCAAsC;AAExDP,QAAAA,EAAQS,CAAU;AAAA,MACpB,QAAc;AACZX,QAAAA,EAAS,EAAI;AAAA,MACf,UAAA;AACEH,QAAAA,EAAW,EAAK;AAAA,MAClB;AAAA,IACF,GAEWiB;AAAAA,EACb,GAAG,CAACV,GAAKT,CAAI,CAAC,GAEP;AAAA,IAAEM,MAAAA;AAAAA,IAAML,SAAAA;AAAAA,IAASG,OAAAA;AAAAA,EAAAA;AAC1B;"}
+{"version":3,"file":"ui-components.es10.js","sources":["../src/components/BiosampleTable/columns.tsx"],"sourcesContent":["import {\n  GridColDef,\n  GridComparatorFn,\n  gridRowIdSelector,\n  gridRowNodeSelector,\n  gridRowSelector,\n  isAutogeneratedRow,\n} from \"@mui/x-data-grid-premium\";\nimport { AssayWheel } from \"./AssayWheel\";\nimport { CcreAssay, EncodeBiosample } from \"./types\";\nimport { DownloadButton } from \"./DownloadButton\";\nimport { AggregateDownloadButton, getAvailableFiles } from \"./AggregateDownload\";\nimport { capitalize, Stack, Tooltip } from \"@mui/material\";\nimport { Check, InfoOutline } from \"@mui/icons-material\";\n\n/**\n * @todo at some point, instead of checking for is rowNode.type === \"group\", can use isAutogeneratedRow instead\n */\n\nexport const ontologyCol: GridColDef<EncodeBiosample> = {\n  field: \"ontology\",\n  headerName: \"Organ/Tissue\",\n  type: \"singleSelect\",\n  valueOptions: [\n    \"adipose\",\n    \"adrenal gland\",\n    \"blood\",\n    \"blood vessel\",\n    \"bone\",\n    \"bone marrow\",\n    \"brain\",\n    \"breast\",\n    \"connective tissue\",\n    \"embryo\",\n    \"epithelium\",\n    \"esophagus\",\n    \"eye\",\n    \"fallopian tube\",\n    \"gallbladder\",\n    \"heart\",\n    \"kidney\",\n    \"large intestine\",\n    \"limb\",\n    \"liver\",\n    \"lung\",\n    \"lymphoid tissue\",\n    \"mouth\",\n    \"muscle\",\n    \"nerve\",\n    \"nose\",\n    \"ovary\",\n    \"pancreas\",\n    \"paraythroid gland\",\n    \"penis\",\n    \"placenta\",\n    \"prostate\",\n    \"skin\",\n    \"small intestine\",\n    \"spinal cord\",\n    \"spleen\",\n    \"stomach\",\n    \"testis\",\n    \"thymus\",\n    \"thyroid\",\n    \"urinary bladder\",\n    \"uterus\",\n    \"vagina\",\n  ],\n  valueFormatter: (value) => value && capitalize(value),\n};\n\nexport const displayNameCol: GridColDef<EncodeBiosample> = {\n  field: \"displayname\",\n  headerName: \"Biosample\",\n  valueFormatter: (value) => value && capitalize(value),\n  maxWidth: 300,\n};\n\nexport const sampleTypeCol: GridColDef<EncodeBiosample> = {\n  field: \"sampleType\",\n  headerName: \"Sample Type\",\n  type: \"singleSelect\",\n  valueOptions: [\"tissue\", \"primary cell\", \"cell line\", \"in vitro differentiated cells\", \"organoid\"],\n  valueFormatter: (value) => value && capitalize(value),\n};\n\nexport const lifeStageCol: GridColDef<EncodeBiosample> = {\n  field: \"lifeStage\",\n  headerName: \"Life Stage\",\n  type: \"singleSelect\",\n  valueOptions: [\"adult\", \"embryonic\"],\n  valueFormatter: (value) => value && capitalize(value),\n};\n\nexport const assaysCol: GridColDef<EncodeBiosample> = {\n  field: \"assays\",\n  headerName: \"Assays\",\n  valueGetter: (_, row) => {\n    const availableAssays = [];\n    if (row.dnase_experiment_accession) availableAssays.push(\"DNase\");\n    if (row.atac_experiment_accession) availableAssays.push(\"ATAC\");\n    if (row.h3k4me3_experiment_accession) availableAssays.push(\"H3K4me3\");\n    if (row.h3k27ac_experiment_accession) availableAssays.push(\"H3K27ac\");\n    if (row.ctcf_experiment_accession) availableAssays.push(\"CTCF\");\n    return availableAssays.join(\",\");\n  },\n  sortComparator: (v1, v2) => {\n    const count1 = v1.split(\",\").filter((s: string) => s.length > 0).length;\n    const count2 = v2.split(\",\").filter((s: string) => s.length > 0).length;\n    return count1 - count2;\n  },\n  renderCell: (params) => {\n    if (params.rowNode.type === \"group\") return null;\n    const row = params.row;\n    return (\n      <div onClick={(e) => e.stopPropagation()}>\n        <AssayWheel\n          row={{\n            dnase: row.dnase_experiment_accession,\n            atac: row.atac_experiment_accession,\n            h3k4me3: row.h3k4me3_experiment_accession,\n            h3k27ac: row.h3k27ac_experiment_accession,\n            ctcf: row.ctcf_experiment_accession,\n          }}\n        />\n      </div>\n    );\n  },\n  groupable: false,\n};\n\n// -- Collection Column Helpers --\n\nconst collections = [\"Core\", \"Partial\", \"Ancillary\"] as const;\n\n//Handles the two experiments that have unprocessed H3K4me3 samples which have \"NA\" values in file\n//GM12866_ENCDO000ABQ & neural_crest_cell_ENCDO222AAA\nconst fileExists = (fileID: string | null): Boolean => {\n  return !!fileID && fileID !== \"NA\"\n}\n\nconst getCollectionForSample = (sample: EncodeBiosample): (typeof collections)[number] | null => {\n  const filesAvailable: Record<CcreAssay, Boolean> = {\n    dnase: fileExists(sample.dnase_file_accession),\n    h3k4me3: fileExists(sample.h3k4me3_file_accession),\n    h3k27ac: fileExists(sample.h3k27ac_file_accession),\n    ctcf: fileExists(sample.ctcf_file_accession),\n    atac: fileExists(sample.atac_file_accession),\n  };\n  if (!Object.values(filesAvailable).includes(true)) return null; // True for grouping rows and GM12866_ENCDO000ABQ\n  let collection: (typeof collections)[number] = \"Ancillary\";\n  if (filesAvailable.dnase) {\n    collection = \"Partial\";\n    if (filesAvailable.ctcf && filesAvailable.h3k4me3 && filesAvailable.h3k27ac) {\n      collection = \"Core\";\n    }\n  }\n  return collection;\n};\n\n// define this to properly sort grouping rows and GM12866_ENCDO000ABQ\nconst sortOrder = [...collections, null]\n\nexport const collectionCol: GridColDef<EncodeBiosample> = {\n  field: \"collection\",\n  headerName: \"Collection\",\n  type: \"singleSelect\",\n  valueOptions: [...collections],\n  valueGetter: (_, row) => getCollectionForSample(row),\n  renderCell: (params) => {\n    const row = params.row\n    if (\n      (row.dnase_experiment_accession && !fileExists(row.dnase_file_accession)) ||\n      (row.h3k4me3_experiment_accession && !fileExists(row.h3k4me3_file_accession)) ||\n      (row.h3k27ac_experiment_accession && !fileExists(row.h3k27ac_file_accession)) ||\n      (row.ctcf_experiment_accession && !fileExists(row.ctcf_file_accession))\n    )\n      return (\n        <Tooltip title=\"This sample's H3K4me3 experiment data was not run through the ENCODE pipeline. This assay is ignored when placing this sample in its given collection\">\n          <Stack direction={\"row\"} alignItems={\"center\"}>\n            {row.name === \"GM12866_ENCDO000ABQ\" ? \"NA\" : getCollectionForSample(row)}\n            <InfoOutline fontSize=\"small\" />\n          </Stack>\n        </Tooltip>\n      );\n    else return getCollectionForSample(row);\n  },\n  sortComparator: (v1, v2) => sortOrder.indexOf(v1) - sortOrder.indexOf(v2),\n};\n\n//ENCODE Experiment Accession (plain text)\nexport const dnaseExpCol: GridColDef<EncodeBiosample> = {\n  field: \"dnase_experiment_accession\",\n  headerName: \"DNase Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const h3k4me3ExpCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k4me3_experiment_accession\",\n  headerName: \"H3K4me3 Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const h3k27acExpCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k27ac_experiment_accession\",\n  headerName: \"H3K27ac Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const ctcfExpCol: GridColDef<EncodeBiosample> = {\n  field: \"ctcf_experiment_accession\",\n  headerName: \"CTCF Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const atacExpCol: GridColDef<EncodeBiosample> = {\n  field: \"atac_experiment_accession\",\n  headerName: \"ATAC Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\n\n//ENCODE File ID (plain text)\nexport const dnaseFileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"dnase_file_accession\",\n  headerName: \"DNase File ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const h3k4me3FileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k4me3_file_accession\",\n  headerName: \"H3K4me3 File ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const h3k27acFileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k27ac_file_accession\",\n  headerName: \"H3K27ac File ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const ctcfFileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"ctcf_file_accession\",\n  headerName: \"CTCF File ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const atacFileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"atac_file_accession\",\n  headerName: \"ATAC File ID\",\n  sortable: false,\n  groupable: false,\n};\n\nexport const dnaseZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"dnaseZ\",\n  headerName: \"DNase Z-scores\",\n  valueGetter: (_, row) =>\n    row.dnase_experiment_accession && row.dnase_file_accession\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.dnase_experiment_accession}-${row.dnase_file_accession}.tsv`\n      : null,\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download DNase z-score by cCRE (.tsv) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"DNase\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const h3k4me3ZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k4me3Z\",\n  headerName: \"H3K4me3 Z-scores\",\n  valueGetter: (_, row) =>\n    //check if file exists to handle the two samples with unprocessed h3k4me3 experiments: GM12866_ENCDO000ABQ & neural_crest_cell_ENCDO222AAA\n    row.h3k4me3_experiment_accession && fileExists(row.h3k4me3_file_accession)\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.h3k4me3_experiment_accession}-${row.h3k4me3_file_accession}.tsv`\n      : null,\n  renderCell: (params) => {\n    if ([\"GM12866_ENCDO000ABQ\", \"neural_crest_cell_ENCDO222AAA\"].includes(params.row.name))\n      return (\n        <DownloadButton\n          disabled\n          message={() =>\n            \"This sample's H3K4me3 experiment was not run through the ENCODE Pipeline and thus z-scores are not available\"\n          }\n          url={params.value}\n          displayName={params.row.displayname}\n          assay=\"H3K4me3\"\n          ontology={params.row.ontology}\n        />\n      );\n    else if (!(params.rowNode.type === \"group\") && params.value)\n      return (\n        <DownloadButton\n          message={(fileSize) => `Download H3K4me3 z-score by cCRE (.tsv) - ${fileSize}`}\n          url={params.value}\n          displayName={params.row.displayname}\n          assay=\"H3K4me3\"\n          ontology={params.row.ontology}\n        />\n      );\n  },\n  groupable: false,\n  sortable: false,\n};\n\nexport const h3k27acZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k27acZ\",\n  headerName: \"H3K27ac Z-scores\",\n  valueGetter: (_, row) =>\n    row.h3k27ac_experiment_accession && row.h3k27ac_file_accession\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.h3k27ac_experiment_accession}-${row.h3k27ac_file_accession}.tsv`\n      : null,\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download H3K27ac z-score by cCRE (.tsv) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"H3K27ac\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const ctcfZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"ctcfZ\",\n  headerName: \"CTCF Z-scores\",\n  valueGetter: (_, row) =>\n    row.ctcf_experiment_accession && row.ctcf_file_accession\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.ctcf_experiment_accession}-${row.ctcf_file_accession}.tsv`\n      : null,\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download CTCF z-score by cCRE (.tsv) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"CTCF\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const atacZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"atacZ\",\n  headerName: \"ATAC Z-scores\",\n  valueGetter: (_, row) =>\n    row.atac_experiment_accession && row.atac_file_accession\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.atac_experiment_accession}-${row.atac_file_accession}.tsv`\n      : null,\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download ATAC z-score by cCRE (.tsv) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"ATAC\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const dnaseSignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"dnase_signal_url\",\n  headerName: \"DNase Signal\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download DNase Signal (.bigWig) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"DNase\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const h3k4me3SignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k4me3_signal_url\",\n  headerName: \"H3K4me3 Signal\",\n  valueGetter: (value, row) => (row.h3k4me3_file_accession === \"NA\" ? null : value),\n  renderCell: (params) => {\n    if ([\"GM12866_ENCDO000ABQ\", \"neural_crest_cell_ENCDO222AAA\"].includes(params.row.name))\n      return (\n        <DownloadButton\n          disabled\n          message={() =>\n            \"This sample's H3K4me3 experiment was not run through the ENCODE Pipeline and thus the signal file is not available\"\n          }\n          url={params.value}\n          displayName={params.row.displayname}\n          assay=\"H3K4me3\"\n          ontology={params.row.ontology}\n        />\n      );\n    else if (!(params.rowNode.type === \"group\") && params.value)\n      return (\n        <DownloadButton\n          message={(fileSize) => `Download H3K4me3 Signal (.bigWig) - ${fileSize}`}\n          url={params.value}\n          displayName={params.row.displayname}\n          assay=\"H3K4me3\"\n          ontology={params.row.ontology}\n        />\n      );\n  },\n  groupable: false,\n  sortable: false,\n};\n\nexport const h3k27acSignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k27ac_signal_url\",\n  headerName: \"H3K27ac Signal\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download H3K27ac Signal (.bigWig) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"H3K27ac\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const ctcfSignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"ctcf_signal_url\",\n  headerName: \"CTCF Signal\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download CTCF Signal (.bigWig) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"CTCF\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const atacSignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"atac_signal_url\",\n  headerName: \"ATAC Signal\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download ATAC Signal (.bigWig) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"ATAC\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const chromHmmUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"chromhmm_url\",\n  headerName: \"ChromHMM States\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download ChromHMM States (.bigBed) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"ChromHMM\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const ccreBedUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"bedurl\",\n  headerName: \"cCREs (.bed)\",\n  align: \"center\",\n  valueGetter: (_, row, __, apiRef) => {\n    if (isAutogeneratedRow(row)) {\n      const id = gridRowIdSelector(apiRef, row);\n      const rowNode = gridRowNodeSelector(apiRef, id);\n      const isGroupingByOntology = rowNode.type === \"group\" && rowNode.groupingField === \"ontology\";\n      if (isGroupingByOntology && typeof rowNode.groupingKey === \"string\") {\n        return getAvailableFiles(rowNode.groupingKey)\n          .map((x) => `https://downloads.wenglab.org/${x.filename}`)\n          .join(\",\");\n      } else return null;\n    }\n    const signalIDs = [\n      row.dnase_file_accession,\n      row.h3k4me3_file_accession,\n      row.h3k27ac_file_accession,\n      row.ctcf_file_accession,\n    ].filter((id) => id !== null && id !== undefined && id !== \"NA\");\n    if (!signalIDs.length) return null // aka is ATAC-only\n    return `https://downloads.wenglab.org/Registry-V4/${signalIDs.join(\"_\")}.bed`;\n  },\n  renderCell: (params) => {\n    if (params.rowNode.type === \"group\") {\n      if (params.rowNode.groupingField === \"ontology\") {\n        const ontology = (params.rowNode.groupingKey as string) ?? \"\";\n        return <AggregateDownloadButton ontology={ontology} />;\n      } else return null;\n    }\n    return (\n      <DownloadButton\n        message={(fileSize) =>\n          params.value ? `Download cCREs (.bed) - ${fileSize}` : \"cCREs only available for samples with DNase, H3K4me3, H3H27ac, and/or CTCF data\"\n        }\n        url={params.value}\n        disabled={!params.value} //aka is ATAC-only\n        displayName={params.row.displayname}\n        assay=\"cCREs\"\n        ontology={params.row.ontology}\n      />\n    );\n  },\n  groupable: false,\n  sortable: false,\n};\n\nexport const ccreBigBedUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"bigbedurl\",\n  headerName: \"cCREs (.bigBed)\",\n  align: 'center',\n  valueGetter: (value: string, row) => {\n    if (row.name === \"GM12866_ENCDO000ABQ\") return null //This sample has no cCREs file\n    if (row.name === \"neural_crest_cell_ENCDO222AAA\") return value.replaceAll('_NA_', '_') //The url in file includes \"NA\" H3K4me3 file ID\n    else return value\n  },\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" && (\n      <DownloadButton\n        message={(fileSize) =>\n          params.value ? `Download cCREs (.bigBed) - ${fileSize}` : \"cCREs only available for samples with DNase, H3K4me3, H3H27ac, and/or CTCF data\"\n        }\n        url={params.value}\n        disabled={!params.value} //aka is ATAC-only\n        displayName={params.row.displayname}\n        assay=\"cCREs\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const rnaSeqCheckCol: GridColDef<EncodeBiosample> = {\n  field: \"rnaSeq\",\n  headerName: \"Has RNA Seq\",\n  type: \"boolean\",\n  valueGetter: (_, row) => (isAutogeneratedRow(row) ? null : !!row?.rna_seq_tracks?.length),\n  renderCell: (params) => {\n    if (params.value) {\n      return <Check />;\n    } else return null;\n  },\n};\n\nexport const columns: GridColDef<EncodeBiosample>[] = [\n  displayNameCol,\n  assaysCol,\n  ontologyCol,\n  sampleTypeCol,\n  lifeStageCol,\n  collectionCol,\n  ccreBedUrlCol,\n  ccreBigBedUrlCol,\n  dnaseExpCol,\n  dnaseFileIdCol,\n  dnaseZscoreUrlCol,\n  dnaseSignalUrlCol,\n  atacExpCol,\n  atacFileIdCol,\n  atacZscoreUrlCol,\n  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package/dist/ui-components.es100.js

@@ -1,18 +1,46 @@
-import * as r from "react";
-import { j as c } from "./ui-components.es12.js";
-import n from "./ui-components.es226.js";
-function s(t, e) {
-  function o(i, m) {
-    return /* @__PURE__ */ c.jsx(n, {
-      "data-testid": process.env.NODE_ENV !== "production" ? `${e}Icon` : void 0,
-      ref: m,
-      ...i,
-      children: t
-    });
-  }
-  return process.env.NODE_ENV !== "production" && (o.displayName = `${e}Icon`), o.muiName = n.muiName, /* @__PURE__ */ r.memo(/* @__PURE__ */ r.forwardRef(o));
+import * as i from "react";
+import r from "./ui-components.es85.js";
+import { clsx as t } from "./ui-components.es84.js";
+import n from "./ui-components.es101.js";
+import { j as l } from "./ui-components.es13.js";
+const m = (s) => {
+  const {
+    open: e
+  } = s;
+  return {
+    offset: t(e && n.valueLabelOpen),
+    circle: n.valueLabelCircle,
+    label: n.valueLabelLabel
+  };
+};
+function p(s) {
+  const {
+    children: e,
+    className: c,
+    value: o
+  } = s, a = m(s);
+  return e ? /* @__PURE__ */ i.cloneElement(e, {
+    className: e.props.className
+  }, /* @__PURE__ */ l.jsxs(i.Fragment, {
+    children: [e.props.children, /* @__PURE__ */ l.jsx("span", {
+      className: t(a.offset, c),
+      "aria-hidden": !0,
+      children: /* @__PURE__ */ l.jsx("span", {
+        className: a.circle,
+        children: /* @__PURE__ */ l.jsx("span", {
+          className: a.label,
+          children: o
+        })
+      })
+    })]
+  })) : null;
 }
+process.env.NODE_ENV !== "production" && (p.propTypes = {
+  children: r.element.isRequired,
+  className: r.string,
+  value: r.node
+});
 export {
-  s as default
+  p as default
 };
 //# sourceMappingURL=ui-components.es100.js.map

package/dist/ui-components.es100.js.map

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package/dist/ui-components.es101.js

@@ -1,5 +1,11 @@
-var e = { exports: {} };
+import e from "./ui-components.es91.js";
+import l from "./ui-components.es92.js";
+function t(r) {
+  return e("MuiSlider", r);
+}
+const i = l("MuiSlider", ["root", "active", "colorPrimary", "colorSecondary", "colorError", "colorInfo", "colorSuccess", "colorWarning", "disabled", "dragging", "focusVisible", "mark", "markActive", "marked", "markLabel", "markLabelActive", "rail", "sizeSmall", "thumb", "thumbColorPrimary", "thumbColorSecondary", "thumbColorError", "thumbColorSuccess", "thumbColorInfo", "thumbColorWarning", "track", "trackInverted", "trackFalse", "thumbSizeSmall", "valueLabel", "valueLabelOpen", "valueLabelCircle", "valueLabelLabel", "vertical"]);
 export {
-  e as __module
+  i as default,
+  t as getSliderUtilityClass
 };
 //# sourceMappingURL=ui-components.es101.js.map

package/dist/ui-components.es101.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ui-components.es101.js","sources":["../../../node_modules/.pnpm/@mui+material@7.3.9_@emotion+react@11.14.0_@types+react@19.2.14_react@19.2.4__@emotion+_5efc65b7a21bb615fd4ee8d4bf58b896/node_modules/@mui/material/esm/Slider/sliderClasses.js"],"sourcesContent":["import generateUtilityClasses from '@mui/utils/generateUtilityClasses';\nimport generateUtilityClass from '@mui/utils/generateUtilityClass';\nexport function getSliderUtilityClass(slot) {\n  return generateUtilityClass('MuiSlider', slot);\n}\nconst sliderClasses = generateUtilityClasses('MuiSlider', ['root', 'active', 'colorPrimary', 'colorSecondary', 'colorError', 'colorInfo', 'colorSuccess', 'colorWarning', 'disabled', 'dragging', 'focusVisible', 'mark', 'markActive', 'marked', 'markLabel', 'markLabelActive', 'rail', 'sizeSmall', 'thumb', 'thumbColorPrimary', 'thumbColorSecondary', 'thumbColorError', 'thumbColorSuccess', 'thumbColorInfo', 'thumbColorWarning', 'track', 'trackInverted', 'trackFalse', 'thumbSizeSmall', 'valueLabel', 'valueLabelOpen', 'valueLabelCircle', 'valueLabelLabel', 'vertical']);\nexport default sliderClasses;"],"names":["getSliderUtilityClass","slot","generateUtilityClass","sliderClasses","generateUtilityClasses"],"mappings":";;AAEO,SAASA,EAAsBC,GAAM;AAC1C,SAAOC,EAAqB,aAAaD,CAAI;AAC/C;AACK,MAACE,IAAgBC,EAAuB,aAAa,CAAC,QAAQ,UAAU,gBAAgB,kBAAkB,cAAc,aAAa,gBAAgB,gBAAgB,YAAY,YAAY,gBAAgB,QAAQ,cAAc,UAAU,aAAa,mBAAmB,QAAQ,aAAa,SAAS,qBAAqB,uBAAuB,mBAAmB,qBAAqB,kBAAkB,qBAAqB,SAAS,iBAAiB,cAAc,kBAAkB,cAAc,kBAAkB,oBAAoB,mBAAmB,UAAU,CAAC;","x_google_ignoreList":[0]}

package/dist/ui-components.es102.js

@@ -1,79 +1,27 @@
-import { __exports as r } from "./ui-components.es208.js";
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- * react-is.production.min.js
- *
- * Copyright (c) Facebook, Inc. and its affiliates.
- *
- * This source code is licensed under the MIT license found in the
- * LICENSE file in the root directory of this source tree.
- */
-var _;
-function g() {
-  if (_) return r;
-  _ = 1;
-  var t = typeof Symbol == "function" && Symbol.for, a = t ? Symbol.for("react.element") : 60103, b = t ? Symbol.for("react.portal") : 60106, n = t ? Symbol.for("react.fragment") : 60107, c = t ? Symbol.for("react.strict_mode") : 60108, f = t ? Symbol.for("react.profiler") : 60114, i = t ? Symbol.for("react.provider") : 60109, s = t ? Symbol.for("react.context") : 60110, d = t ? Symbol.for("react.async_mode") : 60111, u = t ? Symbol.for("react.concurrent_mode") : 60111, y = t ? Symbol.for("react.forward_ref") : 60112, l = t ? Symbol.for("react.suspense") : 60113, x = t ? Symbol.for("react.suspense_list") : 60120, m = t ? Symbol.for("react.memo") : 60115, p = t ? Symbol.for("react.lazy") : 60116, C = t ? Symbol.for("react.block") : 60121, M = t ? Symbol.for("react.fundamental") : 60117, v = t ? Symbol.for("react.responder") : 60118, w = t ? Symbol.for("react.scope") : 60119;
-  function o(e) {
-    if (typeof e == "object" && e !== null) {
-      var S = e.$$typeof;
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-            case u:
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-      }
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-  }
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-  }, r.isContextProvider = function(e) {
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-  }, r.typeOf = o, r;
+import i from "./ui-components.es236.js";
+import a from "./ui-components.es237.js";
+import P from "./ui-components.es144.js";
+import S from "./ui-components.es238.js";
+function x(o) {
+  const {
+    elementType: t,
+    externalSlotProps: p,
+    ownerState: e,
+    skipResolvingSlotProps: s = !1,
+    ...n
+  } = o, r = s ? {} : i(p, e), {
+    props: l,
+    internalRef: f
+  } = a({
+    ...n,
+    externalSlotProps: r
+  }), m = P(f, r?.ref, o.additionalProps?.ref);
+  return S(t, {
+    ...l,
+    ref: m
+  }, e);
 }
 export {
-  g as __require
+  x as default
 };
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package/dist/ui-components.es103.js

@@ -1,96 +1,7 @@
-import { __exports as r } from "./ui-components.es209.js";
-/** @license React v16.13.1
- * react-is.development.js
- *
- * Copyright (c) Facebook, Inc. and its affiliates.
- *
- * This source code is licensed under the MIT license found in the
- * LICENSE file in the root directory of this source tree.
- */
-var A;
-function re() {
-  return A ? r : (A = 1, process.env.NODE_ENV !== "production" && function() {
-    var o = typeof Symbol == "function" && Symbol.for, _ = o ? Symbol.for("react.element") : 60103, T = o ? Symbol.for("react.portal") : 60106, t = o ? Symbol.for("react.fragment") : 60107, n = o ? Symbol.for("react.strict_mode") : 60108, s = o ? Symbol.for("react.profiler") : 60114, c = o ? Symbol.for("react.provider") : 60109, i = o ? Symbol.for("react.context") : 60110, v = o ? Symbol.for("react.async_mode") : 60111, f = o ? Symbol.for("react.concurrent_mode") : 60111, u = o ? Symbol.for("react.forward_ref") : 60112, E = o ? Symbol.for("react.suspense") : 60113, y = o ? Symbol.for("react.suspense_list") : 60120, d = o ? Symbol.for("react.memo") : 60115, l = o ? Symbol.for("react.lazy") : 60116, x = o ? Symbol.for("react.block") : 60121, M = o ? Symbol.for("react.fundamental") : 60117, b = o ? Symbol.for("react.responder") : 60118, p = o ? Symbol.for("react.scope") : 60119;
-    function Y(e) {
-      return typeof e == "string" || typeof e == "function" || // Note: its typeof might be other than 'symbol' or 'number' if it's a polyfill.
-      e === t || e === f || e === s || e === n || e === E || e === y || typeof e == "object" && e !== null && (e.$$typeof === l || e.$$typeof === d || e.$$typeof === c || e.$$typeof === i || e.$$typeof === u || e.$$typeof === M || e.$$typeof === b || e.$$typeof === p || e.$$typeof === x);
-    }
-    function a(e) {
-      if (typeof e == "object" && e !== null) {
-        var C = e.$$typeof;
-        switch (C) {
-          case _:
-            var m = e.type;
-            switch (m) {
-              case v:
-              case f:
-              case t:
-              case s:
-              case n:
-              case E:
-                return m;
-              default:
-                var P = m && m.$$typeof;
-                switch (P) {
-                  case i:
-                  case u:
-                  case l:
-                  case d:
-                  case c:
-                    return P;
-                  default:
-                    return C;
-                }
-            }
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-            return C;
-        }
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-    var $ = v, O = f, F = i, N = c, I = _, L = u, h = t, w = l, D = d, g = T, z = s, U = n, V = E, R = !1;
-    function q(e) {
-      return R || (R = !0, console.warn("The ReactIs.isAsyncMode() alias has been deprecated, and will be removed in React 17+. Update your code to use ReactIs.isConcurrentMode() instead. It has the exact same API.")), S(e) || a(e) === v;
-    }
-    function S(e) {
-      return a(e) === f;
-    }
-    function W(e) {
-      return a(e) === i;
-    }
-    function k(e) {
-      return a(e) === c;
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-      return typeof e == "object" && e !== null && e.$$typeof === _;
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-    function G(e) {
-      return a(e) === u;
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-    }
-    function X(e) {
-      return a(e) === l;
-    }
-    function Z(e) {
-      return a(e) === d;
-    }
-    function H(e) {
-      return a(e) === T;
-    }
-    function J(e) {
-      return a(e) === s;
-    }
-    function Q(e) {
-      return a(e) === n;
-    }
-    function j(e) {
-      return a(e) === E;
-    }
-    r.AsyncMode = $, r.ConcurrentMode = O, r.ContextConsumer = F, r.ContextProvider = N, r.Element = I, r.ForwardRef = L, r.Fragment = h, r.Lazy = w, r.Memo = D, r.Portal = g, r.Profiler = z, r.StrictMode = U, r.Suspense = V, r.isAsyncMode = q, r.isConcurrentMode = S, r.isContextConsumer = W, r.isContextProvider = k, r.isElement = B, r.isForwardRef = G, r.isFragment = K, r.isLazy = X, r.isMemo = Z, r.isPortal = H, r.isProfiler = J, r.isStrictMode = Q, r.isSuspense = j, r.isValidElementType = Y, r.typeOf = a;
-  }(), r);
+function n(t) {
+  return typeof t == "string";
 }
 export {
-  re as __require
+  n as default
 };
 //# sourceMappingURL=ui-components.es103.js.map

package/dist/ui-components.es103.js.map

@@ -1 +1 @@
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Symbol.for('react.fragment') : 0xeacb;\nvar REACT_STRICT_MODE_TYPE = hasSymbol ? Symbol.for('react.strict_mode') : 0xeacc;\nvar REACT_PROFILER_TYPE = hasSymbol ? Symbol.for('react.profiler') : 0xead2;\nvar REACT_PROVIDER_TYPE = hasSymbol ? Symbol.for('react.provider') : 0xeacd;\nvar REACT_CONTEXT_TYPE = hasSymbol ? Symbol.for('react.context') : 0xeace; // TODO: We don't use AsyncMode or ConcurrentMode anymore. They were temporary\n// (unstable) APIs that have been removed. Can we remove the symbols?\n\nvar REACT_ASYNC_MODE_TYPE = hasSymbol ? Symbol.for('react.async_mode') : 0xeacf;\nvar REACT_CONCURRENT_MODE_TYPE = hasSymbol ? Symbol.for('react.concurrent_mode') : 0xeacf;\nvar REACT_FORWARD_REF_TYPE = hasSymbol ? Symbol.for('react.forward_ref') : 0xead0;\nvar REACT_SUSPENSE_TYPE = hasSymbol ? Symbol.for('react.suspense') : 0xead1;\nvar REACT_SUSPENSE_LIST_TYPE = hasSymbol ? Symbol.for('react.suspense_list') : 0xead8;\nvar REACT_MEMO_TYPE = hasSymbol ? Symbol.for('react.memo') : 0xead3;\nvar REACT_LAZY_TYPE = hasSymbol ? Symbol.for('react.lazy') : 0xead4;\nvar REACT_BLOCK_TYPE = hasSymbol ? Symbol.for('react.block') : 0xead9;\nvar REACT_FUNDAMENTAL_TYPE = hasSymbol ? Symbol.for('react.fundamental') : 0xead5;\nvar REACT_RESPONDER_TYPE = hasSymbol ? Symbol.for('react.responder') : 0xead6;\nvar REACT_SCOPE_TYPE = hasSymbol ? Symbol.for('react.scope') : 0xead7;\n\nfunction isValidElementType(type) {\n  return typeof type === 'string' || typeof type === 'function' || // Note: its typeof might be other than 'symbol' or 'number' if it's a polyfill.\n  type === REACT_FRAGMENT_TYPE || type === REACT_CONCURRENT_MODE_TYPE || type === REACT_PROFILER_TYPE || type === REACT_STRICT_MODE_TYPE || type === REACT_SUSPENSE_TYPE || type === REACT_SUSPENSE_LIST_TYPE || typeof type === 'object' && type !== null && (type.$$typeof === REACT_LAZY_TYPE || type.$$typeof === REACT_MEMO_TYPE || type.$$typeof === REACT_PROVIDER_TYPE || type.$$typeof === REACT_CONTEXT_TYPE || type.$$typeof === REACT_FORWARD_REF_TYPE || type.$$typeof === REACT_FUNDAMENTAL_TYPE || type.$$typeof === REACT_RESPONDER_TYPE || type.$$typeof === REACT_SCOPE_TYPE || type.$$typeof === REACT_BLOCK_TYPE);\n}\n\nfunction typeOf(object) {\n  if (typeof object === 'object' && object !== null) {\n    var $$typeof = object.$$typeof;\n\n    switch ($$typeof) {\n      case REACT_ELEMENT_TYPE:\n        var type = object.type;\n\n        switch (type) {\n          case REACT_ASYNC_MODE_TYPE:\n          case REACT_CONCURRENT_MODE_TYPE:\n          case REACT_FRAGMENT_TYPE:\n          case REACT_PROFILER_TYPE:\n          case REACT_STRICT_MODE_TYPE:\n          case REACT_SUSPENSE_TYPE:\n            return type;\n\n          default:\n            var $$typeofType = type && type.$$typeof;\n\n            switch ($$typeofType) {\n              case REACT_CONTEXT_TYPE:\n              case REACT_FORWARD_REF_TYPE:\n              case REACT_LAZY_TYPE:\n              case REACT_MEMO_TYPE:\n              case REACT_PROVIDER_TYPE:\n                return $$typeofType;\n\n              default:\n                return $$typeof;\n            }\n\n        }\n\n      case REACT_PORTAL_TYPE:\n        return $$typeof;\n    }\n  }\n\n  return undefined;\n} // AsyncMode is deprecated along with isAsyncMode\n\nvar AsyncMode = REACT_ASYNC_MODE_TYPE;\nvar ConcurrentMode = REACT_CONCURRENT_MODE_TYPE;\nvar ContextConsumer = REACT_CONTEXT_TYPE;\nvar ContextProvider = REACT_PROVIDER_TYPE;\nvar Element = REACT_ELEMENT_TYPE;\nvar ForwardRef = REACT_FORWARD_REF_TYPE;\nvar Fragment = REACT_FRAGMENT_TYPE;\nvar Lazy = REACT_LAZY_TYPE;\nvar Memo = REACT_MEMO_TYPE;\nvar Portal = REACT_PORTAL_TYPE;\nvar Profiler = REACT_PROFILER_TYPE;\nvar StrictMode = REACT_STRICT_MODE_TYPE;\nvar Suspense = REACT_SUSPENSE_TYPE;\nvar hasWarnedAboutDeprecatedIsAsyncMode = false; // AsyncMode should be deprecated\n\nfunction isAsyncMode(object) {\n  {\n    if (!hasWarnedAboutDeprecatedIsAsyncMode) {\n      hasWarnedAboutDeprecatedIsAsyncMode = true; // Using console['warn'] to evade Babel and ESLint\n\n      console['warn']('The ReactIs.isAsyncMode() alias has been deprecated, ' + 'and will be removed in React 17+. Update your code to use ' + 'ReactIs.isConcurrentMode() instead. It has the exact same API.');\n    }\n  }\n\n  return isConcurrentMode(object) || typeOf(object) === REACT_ASYNC_MODE_TYPE;\n}\nfunction isConcurrentMode(object) {\n  return typeOf(object) === REACT_CONCURRENT_MODE_TYPE;\n}\nfunction isContextConsumer(object) {\n  return typeOf(object) === REACT_CONTEXT_TYPE;\n}\nfunction isContextProvider(object) {\n  return typeOf(object) === REACT_PROVIDER_TYPE;\n}\nfunction isElement(object) {\n  return typeof object === 'object' && object !== null && object.$$typeof === REACT_ELEMENT_TYPE;\n}\nfunction isForwardRef(object) {\n  return typeOf(object) === REACT_FORWARD_REF_TYPE;\n}\nfunction isFragment(object) {\n  return typeOf(object) === REACT_FRAGMENT_TYPE;\n}\nfunction isLazy(object) {\n  return typeOf(object) === REACT_LAZY_TYPE;\n}\nfunction isMemo(object) {\n  return typeOf(object) === REACT_MEMO_TYPE;\n}\nfunction isPortal(object) {\n  return typeOf(object) === REACT_PORTAL_TYPE;\n}\nfunction isProfiler(object) {\n  return typeOf(object) 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-object-assign
-(c) Sindre Sorhus
-@license MIT
-*/
-var f, i;
-function p() {
-  if (i) return f;
-  i = 1;
-  var u = Object.getOwnPropertySymbols, b = Object.prototype.hasOwnProperty, l = Object.prototype.propertyIsEnumerable;
-  function O(n) {
-    if (n == null)
-      throw new TypeError("Object.assign cannot be called with null or undefined");
-    return Object(n);
-  }
-  function j() {
-    try {
-      if (!Object.assign)
-        return !1;
-      var n = new String("abc");
-      if (n[5] = "de", Object.getOwnPropertyNames(n)[0] === "5")
-        return !1;
-      for (var s = {}, r = 0; r < 10; r++)
-        s["_" + String.fromCharCode(r)] = r;
-      var a = Object.getOwnPropertyNames(s).map(function(e) {
-        return s[e];
-      });
-      if (a.join("") !== "0123456789")
-        return !1;
-      var t = {};
-      return "abcdefghijklmnopqrst".split("").forEach(function(e) {
-        t[e] = e;
-      }), Object.keys(Object.assign({}, t)).join("") === "abcdefghijklmnopqrst";
-    } catch {
-      return !1;
-    }
-  }
-  return f = j() ? Object.assign : function(n, s) {
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-      r = Object(arguments[e]);
-      for (var c in r)
-        b.call(r, c) && (a[c] = r[c]);
-      if (u) {
-        t = u(r);
-        for (var o = 0; o < t.length; o++)
-          l.call(r, t[o]) && (a[t[o]] = r[t[o]]);
-      }
-    }
-    return a;
-  }, f;
+import e from "./ui-components.es146.js";
+function o(r) {
+  if (typeof r != "string")
+    throw new Error(process.env.NODE_ENV !== "production" ? "MUI: `capitalize(string)` expects a string argument." : e(7));
+  return r.charAt(0).toUpperCase() + r.slice(1);
 }
 export {
-  p as __require
+  o as default
 };
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package/dist/ui-components.es105.js

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-var e, r;
-function _() {
-  if (r) return e;
-  r = 1;
-  var t = "SECRET_DO_NOT_PASS_THIS_OR_YOU_WILL_BE_FIRED";
-  return e = t, e;
+function u(e, r) {
+  return process.env.NODE_ENV === "production" ? () => null : function(...n) {
+    return e(...n) || r(...n);
+  };
 }
 export {
-  _ as __require
+  u as default
 };
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package/dist/ui-components.es106.js

@@ -1,8 +1,12 @@
-var r, e;
-function a() {
-  return e || (e = 1, r = Function.call.bind(Object.prototype.hasOwnProperty)), r;
+import * as o from "react";
+import r from "./ui-components.es191.js";
+import t from "./ui-components.es109.js";
+import m from "./ui-components.es192.js";
+function i() {
+  const e = m(r);
+  return process.env.NODE_ENV !== "production" && o.useDebugValue(e), e[t] || e;
 }
 export {
-  a as __require
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 };
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