@weng-lab/ui-components 1.3.3 → 2.0.1

package/dist/ui-components.es56.js

@@ -0,0 +1,245 @@
+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: $accession_prefix
+    ) {
+      accession
+      isiCRE
+      coordinates {
+        chromosome
+        start
+        end
+      }
+    }
+  }
+`, h = `
+  query getv2v3CcreMapping($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 {
+  _ 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.es56.js.map

package/dist/ui-components.es56.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ui-components.es56.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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package/dist/ui-components.es57.js

@@ -0,0 +1,11 @@
+import { __module as e } from "./ui-components.es58.js";
+import { __require as t } from "./ui-components.es59.js";
+import { __require as i } from "./ui-components.es60.js";
+var r;
+function m() {
+  return r ? e.exports : (r = 1, process.env.NODE_ENV === "production" ? e.exports = t() : e.exports = i(), e.exports);
+}
+export {
+  m as __require
+};
+//# sourceMappingURL=ui-components.es57.js.map

package/dist/ui-components.es57.js.map

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+{"version":3,"file":"ui-components.es57.js","sources":["../../../node_modules/.pnpm/react@19.1.0/node_modules/react/jsx-runtime.js"],"sourcesContent":["'use strict';\n\nif (process.env.NODE_ENV === 'production') {\n  module.exports = require('./cjs/react-jsx-runtime.production.js');\n} else {\n  module.exports = require('./cjs/react-jsx-runtime.development.js');\n}\n"],"names":["jsxRuntimeModule","require$$0","require$$1"],"mappings":";;;;;iCAEI,QAAQ,IAAI,aAAa,eAC3BA,EAAA,UAAiBC,EAAA,IAEjBD,EAAA,UAAiBE,EAAA;;","x_google_ignoreList":[0]}

package/dist/ui-components.es58.js

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+var e = { exports: {} };
+export {
+  e as __module
+};
+//# sourceMappingURL=ui-components.es58.js.map

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

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+{"version":3,"file":"ui-components.es58.js","sources":[],"sourcesContent":[],"names":[],"mappings":";"}

package/dist/ui-components.es59.js

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+import { __exports as e } from "./ui-components.es78.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
+    };
+  }
+  return e.Fragment = _, e.jsx = o, e.jsxs = o, e;
+}
+export {
+  a as __require
+};
+//# sourceMappingURL=ui-components.es59.js.map

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

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+{"version":3,"file":"ui-components.es59.js","sources":["../../../node_modules/.pnpm/react@19.1.0/node_modules/react/cjs/react-jsx-runtime.production.js"],"sourcesContent":["/**\n * @license React\n * react-jsx-runtime.production.js\n *\n * Copyright (c) Meta Platforms, Inc. and affiliates.\n *\n * This source code is licensed under the MIT license found in the\n * LICENSE file in the root directory of this source tree.\n */\n\n\"use strict\";\nvar REACT_ELEMENT_TYPE = Symbol.for(\"react.transitional.element\"),\n  REACT_FRAGMENT_TYPE = Symbol.for(\"react.fragment\");\nfunction jsxProd(type, config, maybeKey) {\n  var key = null;\n  void 0 !== maybeKey && (key = \"\" + maybeKey);\n  void 0 !== config.key && (key = \"\" + config.key);\n  if (\"key\" in config) {\n    maybeKey = {};\n    for (var propName in config)\n      \"key\" !== propName && (maybeKey[propName] = config[propName]);\n  } else maybeKey = config;\n  config = maybeKey.ref;\n  return {\n    $$typeof: REACT_ELEMENT_TYPE,\n    type: type,\n    key: key,\n    ref: void 0 !== config ? config : null,\n    props: maybeKey\n  };\n}\nexports.Fragment = REACT_FRAGMENT_TYPE;\nexports.jsx = jsxProd;\nexports.jsxs = jsxProd;\n"],"names":["REACT_ELEMENT_TYPE","REACT_FRAGMENT_TYPE","jsxProd","type","config","maybeKey","key","propName","reactJsxRuntime_production"],"mappings":";;;;;;;;;;;;;;AAWA,MAAIA,IAAqB,OAAO,IAAI,4BAA4B,GAC9DC,IAAsB,OAAO,IAAI,gBAAgB;AACnD,WAASC,EAAQC,GAAMC,GAAQC,GAAU;AACvC,QAAIC,IAAM;AAGV,QAFWD,MAAX,WAAwBC,IAAM,KAAKD,IACxBD,EAAO,QAAlB,WAA0BE,IAAM,KAAKF,EAAO,MACxC,SAASA,GAAQ;AACnB,MAAAC,IAAW,CAAA;AACX,eAASE,KAAYH;AACnB,QAAUG,MAAV,UAAuBF,EAASE,CAAQ,IAAIH,EAAOG,CAAQ;AAAA,IACjE,MAAS,CAAAF,IAAWD;AAClB,WAAAA,IAASC,EAAS,KACX;AAAA,MACL,UAAUL;AAAA,MACV,MAAMG;AAAA,MACN,KAAKG;AAAA,MACL,KAAgBF,MAAX,SAAoBA,IAAS;AAAA,MAClC,OAAOC;AAAA;EAEX;AACA,SAAAG,EAAA,WAAmBP,GACnBO,EAAA,MAAcN,GACdM,EAAA,OAAeN;;","x_google_ignoreList":[0]}

package/dist/ui-components.es6.js

@@ -0,0 +1,162 @@
+import { j as S } from "./ui-components.es12.js";
+import { capitalize as D } from "@mui/material";
+import I from "./ui-components.es4.js";
+import { columns as G } from "./ui-components.es9.js";
+import { useEncodeBiosampleData as N } from "./ui-components.es10.js";
+import { useRef as O, useState as q, useEffect as H } from "react";
+import { useGridApiRef as P, gridFilteredSortedRowEntriesSelector as z, isAutogeneratedRow as L } from "@mui/x-data-grid-premium";
+import { DownloadContext as V } from "./ui-components.es52.js";
+const W = {
+  rowGrouping: {
+    model: ["ontology"]
+  },
+  sorting: {
+    sortModel: [{
+      field: "collection",
+      sort: "asc"
+    }]
+  },
+  columns: {
+    columnVisibilityModel: {
+      displayname: !1,
+      //only false since it is used as "leafField" in groupingColDef
+      assays: !0,
+      ontology: !0,
+      sampleType: !1,
+      lifeStage: !1,
+      bedurl: !1,
+      bigbedurl: !1,
+      dnase_experiment_accession: !1,
+      dnase_file_accession: !1,
+      dnaseZ: !1,
+      dnase_signal_url: !1,
+      atac_experiment_accession: !1,
+      atac_file_accession: !1,
+      atacZ: !1,
+      atac_signal_url: !1,
+      h3k4me3_experiment_accession: !1,
+      h3k4me3_file_accession: !1,
+      h3k4me3Z: !1,
+      h3k4me3_signal_url: !1,
+      h3k27ac_experiment_accession: !1,
+      h3k27ac_file_accession: !1,
+      h3k27acZ: !1,
+      h3k27ac_signal_url: !1,
+      ctcf_experiment_accession: !1,
+      ctcf_file_accession: !1,
+      ctcfZ: !1,
+      ctcf_signal_url: !1,
+      chromhmm_url: !1,
+      rnaSeq: !1
+    }
+  },
+  filter: {
+    filterModel: {
+      items: [],
+      quickFilterExcludeHiddenColumns: !1
+    }
+  }
+}, $ = {
+  leafField: "displayname",
+  headerName: "Tissue/Biosample",
+  maxWidth: 400,
+  display: "flex",
+  valueFormatter: (o) => D(o)
+}, R = (o, l) => {
+  if (!o.current) return new Set(l);
+  const d = z(o).filter((s) => L(s.model)).filter((s) => o.current?.getRowGroupChildren({
+    groupId: s.id,
+    applyFiltering: !0
+  })?.every((f) => l?.includes(f))).map((s) => s.id);
+  return /* @__PURE__ */ new Set([...l, ...d]);
+}, J = (o, l, i) => {
+  if (!l || !o.current) return;
+  const r = {
+    type: "include",
+    ids: R(o, l)
+  };
+  i(r);
+};
+function se(o) {
+  const {
+    data: l,
+    loading: i,
+    error: r
+  } = N({
+    assembly: o.assembly,
+    skip: o.rows !== void 0
+  }), {
+    loading: d,
+    error: s,
+    assembly: y,
+    //custom added prop
+    rows: u = l ?? [],
+    prefilterBiosamples: f = () => !0,
+    //custom added prop
+    columns: x = G,
+    label: b = "Biosamples",
+    downloadFileName: C = "Biosamples",
+    initialState: M = W,
+    onSelectionChange: k = (e) => null,
+    //custom added prop
+    onRowSelectionModelChange: m,
+    //have to extract here or else overrides to it would break the onSelectionChange functionality
+    onDownload: v,
+    //custom added prop for tracking downloads
+    apiRef: A,
+    selected: t = void 0,
+    onReady: E,
+    getRowId: p = (e) => e.name,
+    ...F
+  } = o, g = O(t);
+  g.current = t;
+  const T = P(), _ = A ?? T, h = u.filter(f), B = (e, a) => {
+    m && m(e, a), k(h.filter((n) => e.ids.has(p(n))));
+  }, Z = x.map((e) => ({
+    ...e,
+    display: "flex"
+  })), [c, w] = q(void 0);
+  H(() => {
+    if (!t) return;
+    const e = {
+      type: "include",
+      ids: R(_, t)
+    };
+    (!c || !(c.ids.isSubsetOf(e.ids) && e.ids.isSubsetOf(c.ids))) && w(e);
+  }, [t]);
+  const j = (e) => {
+    const a = e.current.subscribeEvent("filterModelChange", () => {
+      J(e, g.current, w);
+    }), n = E?.(e);
+    return n ? Array.isArray(n) ? [a, ...n] : [a, n] : a;
+  };
+  return /* @__PURE__ */ S.jsx(V.Provider, { value: {
+    onDownload: v
+  }, children: /* @__PURE__ */ S.jsx(
+    I,
+    {
+      apiRef: _,
+      label: b,
+      downloadFileName: C,
+      rows: h,
+      columns: Z,
+      loading: d || i,
+      error: s || r,
+      initialState: M,
+      rowSelectionModel: c,
+      groupingColDef: $,
+      getRowId: p,
+      getRowHeight: () => "auto",
+      onReady: j,
+      onRowSelectionModelChange: B,
+      disableRowSelectionExcludeModel: !0,
+      keepNonExistentRowsSelected: !0,
+      ...F
+    }
+  ) });
+}
+export {
+  se as BiosampleTable,
+  W as initialTableState
+};
+//# sourceMappingURL=ui-components.es6.js.map

package/dist/ui-components.es6.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ui-components.es6.js","sources":["../src/components/BiosampleTable/BiosampleTable.tsx"],"sourcesContent":["import { capitalize } from \"@mui/material\";\nimport Table from \"../Table/Table\";\nimport { columns as defaultCols } from \"./columns\";\nimport { BiosampleTableProps, EncodeBiosample } from \"./types\";\nimport { useEncodeBiosampleData } from \"./useEncodeBiosampleData\";\nimport { JSX, useEffect, useRef, useState } from \"react\";\nimport {\n  DataGridPremiumProps,\n  GridApiPremium,\n  GridColDef,\n  gridFilteredSortedRowEntriesSelector,\n  GridGroupingColDefOverride,\n  GridRowId,\n  GridRowSelectionModel,\n  isAutogeneratedRow,\n  useGridApiRef,\n} from \"@mui/x-data-grid-premium\";\nimport { DownloadContext } from \"./DownloadContext\";\nimport { GridInitialStatePremium } from \"@mui/x-data-grid-premium/models/gridStatePremium\";\n\n/**\n * This intentionally lists all columns in the visibility model (even visible cols) so that consumers can import and print it out to see all the keys\n * Can also use `allColsHidden` which is an object of all column fields set to false, which you can spread and then override the visible cols in initialState\n */\nexport const initialTableState = {\n  rowGrouping: { model: [\"ontology\"] },\n  sorting: { sortModel: [{ field: \"collection\", sort: \"asc\" } as const] },\n  columns: {\n    columnVisibilityModel: {\n      displayname: false, //only false since it is used as \"leafField\" in groupingColDef\n      assays: true,\n      ontology: true,\n      sampleType: false,\n      lifeStage: false,\n      bedurl: false,\n      bigbedurl: false,\n      dnase_experiment_accession: false,\n      dnase_file_accession: false,\n      dnaseZ: false,\n      dnase_signal_url: false,\n      atac_experiment_accession: false,\n      atac_file_accession: false,\n      atacZ: false,\n      atac_signal_url: false,\n      h3k4me3_experiment_accession: false,\n      h3k4me3_file_accession: false,\n      h3k4me3Z: false,\n      h3k4me3_signal_url: false,\n      h3k27ac_experiment_accession: false,\n      h3k27ac_file_accession: false,\n      h3k27acZ: false,\n      h3k27ac_signal_url: false,\n      ctcf_experiment_accession: false,\n      ctcf_file_accession: false,\n      ctcfZ: false,\n      ctcf_signal_url: false,\n      chromhmm_url: false,\n      rnaSeq: false,\n    },\n  },\n  filter: {\n    filterModel: {\n      items: [],\n      quickFilterExcludeHiddenColumns: false,\n    },\n  },\n} as const satisfies GridInitialStatePremium; \n\nconst groupingColDef: GridGroupingColDefOverride<any> = {\n  leafField: \"displayname\",\n  headerName: \"Tissue/Biosample\",\n  maxWidth: 400,\n  display: \"flex\",\n  valueFormatter: (value) => capitalize(value),\n} as const;\n\n/**\n *\n * @param apiRef\n * @param ids\n * This function is used to add autogenerated row Ids to the list of selected Ids if all children are selected.\n * It is needed so that select/unselect all checkboxes can work properly without passing in the autogenerated row IDs from outside the components.\n * It will add the grouping row ID only if all children are selected\n */\nconst addAutogeneratedRowIdsToChildren = (\n  apiRef: React.RefObject<GridApiPremium | null>,\n  selected: GridRowId[]\n): Set<GridRowId> => {\n  if (!apiRef.current) return new Set(selected)\n\n  const entries = gridFilteredSortedRowEntriesSelector(apiRef)\n  const autogeneratedRows = entries.filter((entry) =>\n    isAutogeneratedRow(entry.model)\n  );\n\n  const autogeneratedIdsToAdd = autogeneratedRows\n    .filter((row) => {\n      const children = apiRef.current?.getRowGroupChildren({ groupId: row.id, applyFiltering: true });\n      const allChildrenSelected = children?.every((id) => selected?.includes(id));\n      return allChildrenSelected;\n    })\n    .map((x) => x.id);\n\n  return new Set([...selected, ...autogeneratedIdsToAdd]);\n};\n\nconst getAndSetRowSelectionModel = (\n  apiRef: React.RefObject<GridApiPremium | null>,\n  selected: GridRowId[] | undefined,\n  setRowSelectionModel: React.Dispatch<React.SetStateAction<GridRowSelectionModel | undefined>>\n) => {\n  if (!selected || !apiRef.current) return undefined;\n  const newModel = { type: \"include\", ids: addAutogeneratedRowIdsToChildren(apiRef, selected) } as const;\n  setRowSelectionModel(newModel);\n};\n\nexport function BiosampleTable(props: BiosampleTableProps): JSX.Element {\n  const {\n    data: encodeSamples,\n    loading: encodeLoading,\n    error: encodeError,\n  } = useEncodeBiosampleData({ assembly: props.assembly, skip: props.rows !== undefined });\n\n  const {\n    loading,\n    error,\n    assembly, //custom added prop\n    rows = encodeSamples ?? [],\n    prefilterBiosamples = () => true, //custom added prop\n    columns = defaultCols,\n    label = \"Biosamples\",\n    downloadFileName = \"Biosamples\",\n    initialState = initialTableState,\n    onSelectionChange = (selected: EncodeBiosample[]) => null, //custom added prop\n    onRowSelectionModelChange, //have to extract here or else overrides to it would break the onSelectionChange functionality\n    onDownload, //custom added prop for tracking downloads\n    apiRef: externalApiRef,\n    selected = undefined,\n    onReady,\n    getRowId = (x: EncodeBiosample) => x.name,\n    ...restProps\n  } = props;\n\n  const selectedRef = useRef(selected);\n  selectedRef.current = selected;\n\n  const internalApiRef = useGridApiRef();\n  // prioritize using the provided apiRef if available, otherwise create a new one\n  const apiRef = externalApiRef ?? internalApiRef;\n\n  const internalRows = rows.filter(prefilterBiosamples);\n\n  const handleRowSelectionModelChange: DataGridPremiumProps[\"onRowSelectionModelChange\"] = (\n    rowSelectionModel,\n    details\n  ) => {\n    if (onRowSelectionModelChange) onRowSelectionModelChange(rowSelectionModel, details);\n    // we are passing disableRowSelectionExcludeModel, so should always be using \"include\"\n    onSelectionChange(internalRows.filter((row) => rowSelectionModel.ids.has(getRowId(row))));\n  };\n\n  const internalFlexColumns: GridColDef[] = columns.map((x) => ({ ...x, display: \"flex\" }));\n\n  const [rowSelectionModel, setRowSelectionModel] = useState<GridRowSelectionModel | undefined>(undefined);\n\n  useEffect(() => {\n    if (!selected) return undefined;\n    const newSelectionModel = { type: \"include\", ids: addAutogeneratedRowIdsToChildren(apiRef, selected) } as const;\n    if (\n      !rowSelectionModel ||\n      !(\n        rowSelectionModel.ids.isSubsetOf(newSelectionModel.ids) &&\n        newSelectionModel.ids.isSubsetOf(rowSelectionModel.ids)\n      )\n    ) {\n      //prevent infinite rerender\n      setRowSelectionModel(newSelectionModel);\n    }\n  }, [selected]);\n\n  const handleOnReady: typeof onReady = (apiRef) => {\n    const internalCleanup = apiRef.current.subscribeEvent(\"filterModelChange\", () => {\n      getAndSetRowSelectionModel(apiRef, selectedRef.current, setRowSelectionModel);\n    });\n    const consumerCleanups = onReady?.(apiRef);\n    if (!consumerCleanups) return internalCleanup;\n    if (Array.isArray(consumerCleanups)) return [internalCleanup, ...consumerCleanups];\n    return [internalCleanup, consumerCleanups];\n  };\n\n  return (\n    <DownloadContext.Provider value={{ onDownload }}>\n      <Table\n        apiRef={apiRef}\n        label={label}\n        downloadFileName={downloadFileName}\n        rows={internalRows}\n        columns={internalFlexColumns}\n        loading={loading || encodeLoading}\n        error={error || encodeError}\n        initialState={initialState}\n        rowSelectionModel={rowSelectionModel}\n        groupingColDef={groupingColDef}\n        getRowId={getRowId}\n        getRowHeight={() => \"auto\"}\n        onReady={handleOnReady}\n        onRowSelectionModelChange={handleRowSelectionModelChange}\n        disableRowSelectionExcludeModel // forces only using \"include\" model for easier mapping\n        keepNonExistentRowsSelected\n        {...restProps}\n      />\n    </DownloadContext.Provider>\n  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