@weng-lab/ui-components 3.0.1 → 3.1.1

package/dist/ui-components.es28.js

@@ -1,78 +1,248 @@
-import * as d from "react";
-import o from "./ui-components.es89.js";
-import { clsx as f } from "./ui-components.es88.js";
-import u from "./ui-components.es210.js";
-import { getTableHeadUtilityClass as b } from "./ui-components.es220.js";
-import { j as n } from "./ui-components.es15.js";
-import { useDefaultProps as T } from "./ui-components.es93.js";
-import y from "./ui-components.es94.js";
-import x from "./ui-components.es34.js";
-const h = (s) => {
-  const {
-    classes: e
-  } = s;
-  return y({
-    root: ["root"]
-  }, b, e);
-}, j = x("thead", {
-  name: "MuiTableHead",
-  slot: "Root"
-})({
-  display: "table-header-group"
-}), v = {
-  variant: "head"
-}, p = "thead", H = /* @__PURE__ */ d.forwardRef(function(e, r) {
-  const a = T({
-    props: e,
-    name: "MuiTableHead"
-  }), {
-    className: c,
-    component: t = p,
-    ...m
-  } = a, l = {
-    ...a,
-    component: t
-  }, i = h(l);
-  return /* @__PURE__ */ n.jsx(u.Provider, {
-    value: v,
-    children: /* @__PURE__ */ n.jsx(j, {
-      as: t,
-      className: f(i.root, c),
-      ref: r,
-      role: t === p ? null : "rowgroup",
-      ownerState: l,
-      ...m
-    })
-  });
-});
-process.env.NODE_ENV !== "production" && (H.propTypes = {
-  // ┌────────────────────────────── Warning ──────────────────────────────┐
-  // │ These PropTypes are generated from the TypeScript type definitions. │
-  // │    To update them, edit the d.ts file and run `pnpm proptypes`.     │
-  // └─────────────────────────────────────────────────────────────────────┘
-  /**
-   * The content of the component, normally `TableRow`.
-   */
-  children: o.node,
-  /**
-   * Override or extend the styles applied to the component.
-   */
-  classes: o.object,
-  /**
-   * @ignore
-   */
-  className: o.string,
-  /**
-   * The component used for the root node.
-   * Either a string to use a HTML element or a component.
-   */
-  component: o.elementType,
-  /**
-   * The system prop that allows defining system overrides as well as additional CSS styles.
-   */
-  sx: o.oneOfType([o.arrayOf(o.oneOfType([o.func, o.object, o.bool])), o.func, o.object])
-});
+const d = `
+  query suggestions($assembly: String!, $snpid: String!, $limit: Int) {
+    snpAutocompleteQuery(assembly: $assembly, snpid: $snpid, limit: $limit) {
+      id
+      coordinates {
+        chromosome
+        start
+        end
+      }
+    }
+  }
+`, u = `
+  query Genes(
+      $name_prefix: [String!]
+      $idprefix: [String!]
+      $limit: Int
+      $assembly: String!
+      $version: Int
+  ) {
+      gene(
+          name_prefix: $name_prefix
+          idprefix: $idprefix
+          limit: $limit
+          assembly: $assembly
+          orderby: "name"
+          version: $version
+      ) {
+          id
+          name
+          coordinates {
+              chromosome
+              start
+              end
+          }
+      }
+  }
+`, _ = `
+  query iCREQuery($accession_prefix: [String!], $limit: Int) {
+      iCREQuery(accession_prefix: $accession_prefix, limit: $limit) {
+          rdhs
+          accession
+          celltypes
+          coordinates {
+              start
+              end
+              chromosome
+          }
+      }
+  }
+`, h = `
+  query cCREAutocompleteQuery(
+    $accession: [String!]
+    $accession_prefix: [String!]
+    $assembly: String!
+    $includeiCREs: Boolean
+    $limit: Int
+  ) {
+    cCREAutocompleteQuery(
+      includeiCREs: $includeiCREs
+      assembly: $assembly
+      limit: $limit
+      accession: $accession
+      accession_prefix: $accession_prefix
+    ) {
+      accession
+      isiCRE
+      coordinates {
+        chromosome
+        start
+        end
+      }
+    }
+  }
+`, C = `
+  query getv2v3CcreMapping($accessions: [String], $assembly: String!) {
+    ccreMappings: getv2cCREMappings(
+      v2_accession: $accessions
+      assembly: $assembly
+    ) {
+      input: v2_accession
+      input_latest_previous_version: ccre_version
+      input_region: v2_region
+      v4_match_or_intersecting: v4_accession
+      v4_region
+    }
+  }
+`, g = `
+query getGWASStudyMetadata($limit: Int, $studyname_prefix: [String]){
+    getGWASStudiesMetadata(limit: $limit, studyname_prefix: $studyname_prefix )
+    {
+        studyid
+        author
+        disease_trait
+        has_enrichment_info
+        population
+        parent_terms
+        total_ld_blocks
+        ld_blocks_overlapping_ccres
+        overlapping_ccres
+    }
+}
+`, b = async (e, s, i, t) => (await fetch(i, {
+  method: "POST",
+  body: JSON.stringify({
+    query: _,
+    variables: {
+      accession_prefix: [e],
+      limit: s
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: t
+})).json(), v = async (e, s, i, t, n, p) => {
+  const a = e.length === 12;
+  return (await fetch(n, {
+    method: "POST",
+    body: JSON.stringify({
+      query: h,
+      variables: {
+        ...a ? {
+          accession: [e.toUpperCase()]
+        } : {
+          accession_prefix: [e]
+        },
+        assembly: s,
+        limit: i,
+        includeiCREs: t
+      }
+    }),
+    headers: {
+      "Content-Type": "application/json"
+    },
+    signal: p
+  })).json();
+}, R = async (e, s, i, t) => (await fetch(i, {
+  method: "POST",
+  body: JSON.stringify({
+    query: C,
+    variables: {
+      accessions: [e],
+      assembly: s
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: t
+})).json(), x = async (e, s, i, t, n, p) => {
+  let a = t ? typeof t == "number" ? [t] : t : [s === "GRCh38" ? 40 : 25];
+  a = a.sort((o, r) => r - o);
+  const m = await Promise.all(a.map((o) => fetch(n, {
+    method: "POST",
+    body: JSON.stringify({
+      query: u,
+      variables: {
+        assembly: s.toLowerCase(),
+        ...s.toLowerCase() === "mm10" && e.toUpperCase().startsWith("ENSMUSG") || s.toLowerCase() === "grch38" && e.toUpperCase().startsWith("ENSG") ? {
+          idprefix: e.split(".")[0]
+        } : {
+          name_prefix: e
+        },
+        version: o,
+        limit: i
+      }
+    }),
+    headers: {
+      "Content-Type": "application/json"
+    },
+    signal: p
+  }).then((r) => r.json()))), l = /* @__PURE__ */ new Map();
+  return m.forEach((o, r) => {
+    (o.data.gene || []).forEach((c) => {
+      l.has(c.name) ? l.get(c.name).versions.push({
+        id: c.id,
+        version: a[r]
+      }) : l.set(c.name, {
+        gene: c,
+        versions: [{
+          id: c.id,
+          version: a[r]
+        }]
+      });
+    });
+  }), await Promise.all(Array.from(l.values()).map(async ({
+    gene: o,
+    versions: r
+  }) => {
+    const y = await E(o.name);
+    return {
+      ...o,
+      description: `${f(y || o.name)}`,
+      versions: r
+    };
+  }));
+}, f = (e) => e.split(" ").map((s) => s.charAt(0).toUpperCase() + s.slice(1)).join(" ");
+async function E(e) {
+  try {
+    const i = await (await fetch("https://clinicaltables.nlm.nih.gov/api/ncbi_genes/v3/search?authenticity_token=&terms=" + e.toUpperCase())).json(), t = i[3] && i[3].filter((n) => n[3] === e.toUpperCase());
+    return t && t.length >= 1 ? t[0][4] : null;
+  } catch {
+    return null;
+  }
+}
+const T = async (e, s, i, t, n) => (await fetch(t, {
+  method: "POST",
+  body: JSON.stringify({
+    query: d,
+    variables: {
+      assembly: s.toLowerCase(),
+      snpid: e,
+      limit: i
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: n
+})).json(), O = async (e, s, i, t) => (await fetch(i, {
+  method: "POST",
+  body: JSON.stringify({
+    query: g,
+    variables: {
+      studyname_prefix: [e],
+      limit: s
+    }
+  }),
+  headers: {
+    "Content-Type": "application/json"
+  },
+  signal: t
+})).json();
 export {
-  H as default
+  h as CCRE_AUTOCOMPLETE_QUERY,
+  u as GENE_AUTOCOMPLETE_QUERY,
+  g as GWAS_AUTOCOMPLETE_QUERY,
+  _ as ICRE_AUTOCOMPLETE_QUERY,
+  C as LEGACY_CCRE_QUERY,
+  d as SNP_AUTOCOMPLETE_QUERY,
+  v as getCCREs,
+  x as getGenes,
+  b as getICREs,
+  R as getLegacyCCREs,
+  T as getSNPs,
+  O as getStudys
 };
 //# sourceMappingURL=ui-components.es28.js.map

package/dist/ui-components.es28.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ui-components.es28.js","sources":["../src/components/GenomeSearch/queries.ts"],"sourcesContent":["import { GenomeSearchProps } from \"./types\";\r\n\r\nexport const SNP_AUTOCOMPLETE_QUERY = `\r\n  query suggestions($assembly: String!, $snpid: String!, $limit: Int) {\r\n    snpAutocompleteQuery(assembly: $assembly, snpid: $snpid, limit: $limit) {\r\n      id\r\n      coordinates {\r\n        chromosome\r\n        start\r\n        end\r\n      }\r\n    }\r\n  }\r\n`;\r\n\r\nexport const GENE_AUTOCOMPLETE_QUERY = `\r\n  query Genes(\r\n      $name_prefix: [String!]\r\n      $idprefix: [String!]\r\n      $limit: Int\r\n      $assembly: String!\r\n      $version: Int\r\n  ) {\r\n      gene(\r\n          name_prefix: $name_prefix\r\n          idprefix: $idprefix\r\n          limit: $limit\r\n          assembly: $assembly\r\n          orderby: \"name\"\r\n          version: $version\r\n      ) {\r\n          id\r\n          name\r\n          coordinates {\r\n              chromosome\r\n              start\r\n              end\r\n          }\r\n      }\r\n  }\r\n`;\r\n\r\nexport const ICRE_AUTOCOMPLETE_QUERY = `\r\n  query iCREQuery($accession_prefix: [String!], $limit: Int) {\r\n      iCREQuery(accession_prefix: $accession_prefix, limit: $limit) {\r\n          rdhs\r\n          accession\r\n          celltypes\r\n          coordinates {\r\n              start\r\n              end\r\n              chromosome\r\n          }\r\n      }\r\n  }\r\n`;\r\n\r\nexport const CCRE_AUTOCOMPLETE_QUERY = `\r\n  query cCREAutocompleteQuery(\r\n    $accession: [String!]\r\n    $accession_prefix: [String!]\r\n    $assembly: String!\r\n    $includeiCREs: Boolean\r\n    $limit: Int\r\n  ) {\r\n    cCREAutocompleteQuery(\r\n      includeiCREs: $includeiCREs\r\n      assembly: $assembly\r\n      limit: $limit\r\n      accession: $accession\r\n      accession_prefix: $accession_prefix\r\n    ) {\r\n      accession\r\n      isiCRE\r\n      coordinates {\r\n        chromosome\r\n        start\r\n        end\r\n      }\r\n    }\r\n  }\r\n`;\r\n\r\nexport const LEGACY_CCRE_QUERY = `\r\n  query getv2v3CcreMapping($accessions: [String], $assembly: String!) {\r\n    ccreMappings: getv2cCREMappings(\r\n      v2_accession: $accessions\r\n      assembly: $assembly\r\n    ) {\r\n      input: v2_accession\r\n      input_latest_previous_version: ccre_version\r\n      input_region: v2_region\r\n      v4_match_or_intersecting: v4_accession\r\n      v4_region\r\n    }\r\n  }\r\n`\r\n\r\nexport const GWAS_AUTOCOMPLETE_QUERY = `\r\nquery getGWASStudyMetadata($limit: Int, $studyname_prefix: [String]){\r\n    getGWASStudiesMetadata(limit: $limit, studyname_prefix: $studyname_prefix )\r\n    {\r\n        studyid\r\n        author\r\n        disease_trait\r\n        has_enrichment_info\r\n        population\r\n        parent_terms\r\n        total_ld_blocks\r\n        ld_blocks_overlapping_ccres\r\n        overlapping_ccres\r\n    }\r\n}\r\n`;\r\n\r\nexport const getICREs = async (value: string, limit: number, url: string, signal?: AbortSignal) => {\r\n  const response = await fetch(url, {\r\n    method: \"POST\",\r\n    body: JSON.stringify({\r\n      query: ICRE_AUTOCOMPLETE_QUERY,\r\n      variables: {\r\n        accession_prefix: [value],\r\n        limit: limit,\r\n      },\r\n    }),\r\n    headers: { \"Content-Type\": \"application/json\" },\r\n    signal,\r\n  });\r\n  return response.json();\r\n};\r\n\r\nexport const getCCREs = async (value: string, assembly: GenomeSearchProps[\"assembly\"], limit: number, showiCREFlag: boolean, url: string, signal?: AbortSignal) => {\r\n  const isExactAccession = value.length === 12;\r\n  const response = await fetch(url, {\r\n    method: \"POST\",\r\n    body: JSON.stringify({\r\n      query: CCRE_AUTOCOMPLETE_QUERY,\r\n      variables: {\r\n        ...(isExactAccession\r\n          ? { accession: [value.toUpperCase()] }\r\n          : { accession_prefix: [value] }),\r\n        assembly,\r\n        limit,\r\n        includeiCREs: showiCREFlag,\r\n      },\r\n    }),\r\n    headers: { \"Content-Type\": \"application/json\" },\r\n    signal,\r\n  });\r\n  return response.json();\r\n};\r\n\r\nexport const getLegacyCCREs = async (value: string, assembly: GenomeSearchProps[\"assembly\"], url: string, signal?: AbortSignal) => {\r\n  const response = await fetch(url, {\r\n    method: \"POST\",\r\n    body: JSON.stringify({\r\n      query: LEGACY_CCRE_QUERY,\r\n      variables: {\r\n        accessions: [value],\r\n        assembly,\r\n      },\r\n    }),\r\n    headers: { \"Content-Type\": \"application/json\" },\r\n    signal,\r\n  });\r\n  return response.json();\r\n};\r\n\r\nexport const getGenes = async (\r\n  value: string,\r\n  assembly: GenomeSearchProps[\"assembly\"],\r\n  limit: number,\r\n  geneVersions: GenomeSearchProps[\"geneVersion\"],\r\n  url: string,\r\n  signal?: AbortSignal\r\n) => {\r\n  let versions = geneVersions\r\n    ? typeof geneVersions === \"number\"\r\n      ? [geneVersions]\r\n      : geneVersions\r\n    : [assembly === \"GRCh38\" ? 40 : 25];\r\n\r\n  // sort versions from high to low (prioritize newest versions in map)\r\n  versions = versions.sort((a, b) => b - a);\r\n\r\n  // Fetch genes for all versions\r\n  const versionResults = await Promise.all(\r\n  versions.map((version) =>\r\n    fetch(url, {\r\n      method: \"POST\",\r\n      body: JSON.stringify({\r\n        query: GENE_AUTOCOMPLETE_QUERY,\r\n        variables: {\r\n          assembly: assembly.toLowerCase(),\r\n          ...(\r\n            (\r\n              (assembly.toLowerCase() === \"mm10\" && value.toUpperCase().startsWith(\"ENSMUSG\")) ||\r\n              (assembly.toLowerCase() === \"grch38\" && value.toUpperCase().startsWith(\"ENSG\"))\r\n            )\r\n              ? { idprefix: value.split(\".\")[0] }\r\n              : { name_prefix: value }\r\n          ),\r\n          version: version,\r\n          limit: limit,\r\n        },\r\n      }),\r\n      headers: { \"Content-Type\": \"application/json\" },\r\n      signal,\r\n    }).then((res) => res.json())\r\n  )\r\n);\r\n\r\n  // Combine and deduplicate results\r\n  const geneMap = new Map<string, { gene: any; versions: { id: string; version: number }[] }>();\r\n\r\n  versionResults.forEach((result, idx) => {\r\n    const genes = result.data.gene || [];\r\n    genes.forEach((gene: any) => {\r\n      if (!geneMap.has(gene.name)) {\r\n        geneMap.set(gene.name, { gene, versions: [{ id: gene.id, version: versions[idx] }] });\r\n      } else {\r\n        // if gene already exists, just add legacy versions to list.\r\n        const existing = geneMap.get(gene.name)!;\r\n        existing.versions.push({ id: gene.id, version: versions[idx] });\r\n      }\r\n    });\r\n  });\r\n\r\n  // Convert map to array and fetch descriptions\r\n  const out = await Promise.all(\r\n    Array.from(geneMap.values()).map(async ({ gene, versions }) => {\r\n      const description = await getDescription(gene.name);\r\n      return {\r\n        ...gene,\r\n        description: `${toTitleCase(description || gene.name)}`,\r\n        versions,\r\n      };\r\n    })\r\n  );\r\n\r\n  return out;\r\n};\r\nconst toTitleCase = (str: string) =>\r\n  str\r\n    .split(\" \")\r\n    .map((word) => word.charAt(0).toUpperCase() + word.slice(1))\r\n    .join(\" \");\r\n\r\nasync function getDescription(name: string): Promise<string | null> {\r\n  try {\r\n    const response = await fetch(\r\n      \"https://clinicaltables.nlm.nih.gov/api/ncbi_genes/v3/search?authenticity_token=&terms=\" + name.toUpperCase()\r\n    );\r\n    const data = await response.json();\r\n    const matches = data[3] && data[3].filter((x: string[]) => x[3] === name.toUpperCase());\r\n    return matches && matches.length >= 1 ? matches[0][4] : null;\r\n  } catch {\r\n    return null;\r\n  }\r\n}\r\n\r\nexport const getSNPs = async (value: string, assembly: GenomeSearchProps[\"assembly\"], limit: number, url: string, signal?: AbortSignal) => {\r\n  const response = await fetch(url, {\r\n    method: \"POST\",\r\n    body: JSON.stringify({\r\n      query: SNP_AUTOCOMPLETE_QUERY,\r\n      variables: {\r\n        assembly: assembly.toLowerCase(),\r\n        snpid: value,\r\n        limit: limit,\r\n      },\r\n    }),\r\n    headers: { \"Content-Type\": \"application/json\" },\r\n    signal,\r\n  });\r\n  return response.json();\r\n};\r\n\r\nexport const getStudys = async (value: string, limit: number, url: string, signal?: AbortSignal) => {\r\n  const response = await fetch(url, {\r\n    method: \"POST\",\r\n    body: JSON.stringify({\r\n      query: GWAS_AUTOCOMPLETE_QUERY,\r\n      variables: {\r\n        studyname_prefix: [value],\r\n        limit,\r\n      },\r\n    }),\r\n    headers: { \"Content-Type\": \"application/json\" },\r\n    signal,\r\n  });\r\n\r\n  return 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package/dist/ui-components.es280.js

@@ -1,42 +1,50 @@
-const d = (o, e, s, c = []) => {
-  let t = o;
-  e.forEach((n, f) => {
-    f === e.length - 1 ? Array.isArray(t) ? t[Number(n)] = s : t && typeof t == "object" && (t[n] = s) : t && typeof t == "object" && (t[n] || (t[n] = c.includes(n) ? [] : {}), t = t[n]);
-  });
-}, j = (o, e, s) => {
-  function c(t, n = [], f = []) {
-    Object.entries(t).forEach(([r, i]) => {
-      (!s || s && !s([...n, r])) && i != null && (typeof i == "object" && Object.keys(i).length > 0 ? c(i, [...n, r], Array.isArray(i) ? [...f, r] : f) : e([...n, r], i, f));
-    });
+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);
   }
-  c(o);
-}, $ = (o, e) => typeof e == "number" ? ["lineHeight", "fontWeight", "opacity", "zIndex"].some((c) => o.includes(c)) || o[o.length - 1].toLowerCase().includes("opacity") ? e : `${e}px` : e;
-function l(o, e) {
-  const {
-    prefix: s,
-    shouldSkipGeneratingVar: c
-  } = e || {}, t = {}, n = {}, f = {};
-  return j(
-    o,
-    (r, i, g) => {
-      if ((typeof i == "string" || typeof i == "number") && (!c || !c(r, i))) {
-        const b = `--${s ? `${s}-` : ""}${r.join("-")}`, p = $(r, i);
-        Object.assign(t, {
-          [b]: p
-        }), d(n, r, `var(${b})`, g), d(f, r, `var(${b}, ${p})`, g);
+  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) {
+    for (var r, a = O(n), t, e = 1; e < arguments.length; e++) {
+      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]]);
       }
-    },
-    (r) => r[0] === "vars"
-    // skip 'vars/*' paths
-  ), {
-    css: t,
-    vars: n,
-    varsWithDefaults: f
-  };
+    }
+    return a;
+  }, f;
 }
 export {
-  d as assignNestedKeys,
-  l as default,
-  j as walkObjectDeep
+  p as __require
 };
 //# sourceMappingURL=ui-components.es280.js.map

package/dist/ui-components.es280.js.map

@@ -1 +1 @@
-{"version":3,"file":"ui-components.es280.js","sources":["../../../node_modules/.pnpm/@mui+system@7.3.9_@emotion+react@11.14.0_@types+react@19.2.14_react@19.2.4__@emotion+st_100059df2673d7a323eb0d2da91385ea/node_modules/@mui/system/esm/cssVars/cssVarsParser.js"],"sourcesContent":["/**\n * This function create an object from keys, value and then assign to target\n *\n * @param {Object} obj : the target object to be assigned\n * @param {string[]} keys\n * @param {string | number} value\n *\n * @example\n * const source = {}\n * assignNestedKeys(source, ['palette', 'primary'], 'var(--palette-primary)')\n * console.log(source) // { palette: { primary: 'var(--palette-primary)' } }\n *\n * @example\n * const source = { palette: { primary: 'var(--palette-primary)' } }\n * assignNestedKeys(source, ['palette', 'secondary'], 'var(--palette-secondary)')\n * console.log(source) // { palette: { primary: 'var(--palette-primary)', secondary: 'var(--palette-secondary)' } }\n */\nexport const assignNestedKeys = (obj, keys, value, arrayKeys = []) => {\n  let temp = obj;\n  keys.forEach((k, index) => {\n    if (index === keys.length - 1) {\n      if (Array.isArray(temp)) {\n        temp[Number(k)] = value;\n      } else if (temp && typeof temp === 'object') {\n        temp[k] = value;\n      }\n    } else if (temp && typeof temp === 'object') {\n      if (!temp[k]) {\n        temp[k] = arrayKeys.includes(k) ? 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