@weng-lab/ui-components 2.1.0 → 2.1.1

package/dist/ui-components.es54.js

@@ -1,39 +1,245 @@
-import { j as r } from "./ui-components.es13.js";
-import { c as d } from "./ui-components.es15.js";
-import { Typography as h, Box as p, Tooltip as j } from "@mui/material";
-import y from "./ui-components.es29.js";
-const S = (x) => {
-  const e = d.c(13), {
-    params: i,
-    tooltipTitle: f,
-    originalRenderHeader: s
-  } = x;
-  let n;
-  e[0] === Symbol.for("react.memo_cache_sentinel") ? (n = {
-    display: "flex",
-    alignItems: "center",
-    gap: 1
-  }, e[0] = n) : n = e[0];
-  let m;
-  e[1] === Symbol.for("react.memo_cache_sentinel") ? (m = {
-    overflow: "hidden",
-    textOverflow: "ellipsis"
-  }, e[1] = m) : m = e[1];
-  let t;
-  e[2] !== s || e[3] !== i ? (t = s ? s(i) : /* @__PURE__ */ r.jsx(h, { variant: "subtitle2", noWrap: !0, children: i.colDef.headerName || i.field }), e[2] = s, e[3] = i, e[4] = t) : t = e[4];
-  let l;
-  e[5] !== t ? (l = /* @__PURE__ */ r.jsx(p, { sx: m, children: t }), e[5] = t, e[6] = l) : l = e[6];
-  let a;
-  e[7] === Symbol.for("react.memo_cache_sentinel") ? (a = /* @__PURE__ */ r.jsx(y, { fontSize: "inherit", color: "primary" }), e[7] = a) : a = e[7];
-  let o;
-  e[8] !== f ? (o = /* @__PURE__ */ r.jsx(j, { title: f, children: a }), e[8] = f, e[9] = o) : o = e[9];
-  let c;
-  return e[10] !== l || e[11] !== o ? (c = /* @__PURE__ */ r.jsxs(p, { sx: n, children: [
-    l,
-    o
-  ] }), e[10] = l, e[11] = o, e[12] = c) : c = e[12], c;
-};
+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 {
-  S as HeaderWithTooltip
+  _ 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.es54.js.map

package/dist/ui-components.es54.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ui-components.es54.js","sources":["../src/components/GenomeSearch/queries.ts"],"sourcesContent":["import { GeneResponse, GenomeSearchProps } from \"./types\";\n\nexport const SNP_AUTOCOMPLETE_QUERY = `\n  query suggestions($assembly: String!, $snpid: String!) {\n      snpAutocompleteQuery(assembly: $assembly, snpid: $snpid) {\n          id\n          coordinates {\n              chromosome\n              start\n              end\n          }\n      }\n  }\n`;\n\nexport const GENE_AUTOCOMPLETE_QUERY = `\n  query Genes(\n      $id: [String]\n      $name: [String]\n      $strand: String\n      $chromosome: String\n      $start: Int\n      $end: Int\n      $gene_type: String\n      $havana_id: String\n      $name_prefix: [String!]\n      $limit: Int\n      $assembly: String!\n      $version: Int\n  ) {\n      gene(\n          id: $id\n          name: $name\n          strand: $strand\n          chromosome: $chromosome\n          start: $start\n          end: $end\n          gene_type: $gene_type\n          havana_id: $havana_id\n          name_prefix: $name_prefix\n          limit: $limit\n          assembly: $assembly\n          orderby: \"name\"\n          version: $version\n      ) {\n          id\n          name\n          coordinates {\n              chromosome\n              start\n              end\n          }\n      }\n  }\n`;\n\nexport const ICRE_AUTOCOMPLETE_QUERY = `\n  query iCREQuery($accession_prefix: [String!], $limit: Int) {\n      iCREQuery(accession_prefix: $accession_prefix, limit: $limit) {\n          rdhs\n          accession\n          celltypes\n          coordinates {\n              start\n              end\n              chromosome\n          }\n      }\n  }\n`;\n\nexport const CCRE_AUTOCOMPLETE_QUERY = `\n  query cCREAutocompleteQuery(\n    $accession_prefix: [String!]\n    $assembly: String!\n    $includeiCREs: Boolean\n    $limit: Int\n  ) {\n    cCREAutocompleteQuery(\n      includeiCREs: $includeiCREs\n      assembly: $assembly\n      limit: $limit\n      accession_prefix: $accession_prefix\n    ) {\n      accession\n      isiCRE\n      coordinates {\n        chromosome\n        start\n        end\n      }\n    }\n  }\n`;\n\nexport const LEGACY_CCRE_QUERY = `\n  query getv2v3CcreMapping($accessions: [String], $assembly: String!) {\n    ccreMappings: getv2cCREMappings(\n      v2_accession: $accessions\n      assembly: $assembly\n    ) {\n      input: v2_accession\n      input_latest_previous_version: ccre_version\n      input_region: v2_region\n      v4_match_or_intersecting: v4_accession\n      v4_region\n    }\n  }\n`\n\nexport const GWAS_AUTOCOMPLETE_QUERY = `\nquery getGWASStudyMetadata($studyid: [String], $limit: Int, $studyname_prefix: [String], $parent_terms: [String]){\n    getGWASStudiesMetadata(studyid: $studyid, limit: $limit, parent_terms: $parent_terms, studyname_prefix: $studyname_prefix )\n    {\n        studyid\n        author\n        disease_trait\n        has_enrichment_info\n        population\n        parent_terms\n        total_ld_blocks\n        ld_blocks_overlapping_ccres\n        overlapping_ccres\n    }\n}\n`;\n\nexport const getICREs = async (value: string, limit: number, signal?: AbortSignal) => {\n  const response = await fetch(\"https://screen.api.wenglab.org/graphql\", {\n    method: \"POST\",\n    body: JSON.stringify({\n      query: ICRE_AUTOCOMPLETE_QUERY,\n      variables: {\n        accession_prefix: [value],\n        limit: limit,\n      },\n    }),\n    headers: { \"Content-Type\": \"application/json\" },\n    signal,\n  });\n  return response.json();\n};\n\nexport const getCCREs = async (value: string, assembly: GenomeSearchProps[\"assembly\"], limit: number, showiCREFlag: boolean, signal?: AbortSignal) => {\n  const response = await fetch(\"https://screen.api.wenglab.org/graphql\", {\n    method: \"POST\",\n    body: JSON.stringify({\n      query: CCRE_AUTOCOMPLETE_QUERY,\n      variables: {\n        accession_prefix: [value],\n        assembly: assembly.toLowerCase(),\n        limit: limit,\n        includeiCREs: showiCREFlag,\n      },\n    }),\n    headers: { \"Content-Type\": \"application/json\" },\n    signal,\n  });\n  return response.json();\n};\n\nexport const getLegacyCCREs = async (value: string, assembly: GenomeSearchProps[\"assembly\"], signal?: AbortSignal) => {\n  const response = await fetch(\"https://screen.api.wenglab.org/graphql\", {\n    method: \"POST\",\n    body: JSON.stringify({\n      query: LEGACY_CCRE_QUERY,\n      variables: {\n        accessions: [value],\n        assembly,\n      },\n    }),\n    headers: { \"Content-Type\": \"application/json\" },\n    signal,\n  });\n  return response.json();\n};\n\nexport const getGenes = async (\n  value: string,\n  assembly: GenomeSearchProps[\"assembly\"],\n  limit: number,\n  geneVersions: GenomeSearchProps[\"geneVersion\"],\n  signal?: AbortSignal\n) => {\n  let versions = geneVersions\n    ? typeof geneVersions === \"number\"\n      ? [geneVersions]\n      : geneVersions\n    : [assembly === \"GRCh38\" ? 40 : 25];\n\n  // sort versions from high to low (prioritize newest versions in map)\n  versions = versions.sort((a, b) => b - a);\n\n  // Fetch genes for all versions\n  const versionResults = await Promise.all(\n    versions.map((version) =>\n      fetch(\"https://screen.api.wenglab.org/graphql\", {\n        method: \"POST\",\n        body: JSON.stringify({\n          query: GENE_AUTOCOMPLETE_QUERY,\n          variables: {\n            assembly: assembly.toLowerCase(),\n            name_prefix: value,\n            version: version,\n            limit: limit,\n          },\n        }),\n        headers: { \"Content-Type\": \"application/json\" },\n        signal,\n      }).then((res) => res.json())\n    )\n  );\n\n  // Combine and deduplicate results\n  const geneMap = new Map<string, { gene: any; versions: { id: string; version: number }[] }>();\n\n  versionResults.forEach((result, idx) => {\n    const genes = result.data.gene || [];\n    genes.forEach((gene: any) => {\n      if (!geneMap.has(gene.name)) {\n        geneMap.set(gene.name, { gene, versions: [{ id: gene.id, version: versions[idx] }] });\n      } else {\n        // if gene already exists, just add legacy versions to list.\n        const existing = geneMap.get(gene.name)!;\n        existing.versions.push({ id: gene.id, version: versions[idx] });\n      }\n    });\n  });\n\n  // Convert map to array and fetch descriptions\n  const out = await Promise.all(\n    Array.from(geneMap.values()).map(async ({ gene, versions }) => {\n      const description = await getDescription(gene.name);\n      return {\n        ...gene,\n        description: `${toTitleCase(description || gene.name)}`,\n        versions,\n      };\n    })\n  );\n\n  return out;\n};\nconst toTitleCase = (str: string) =>\n  str\n    .split(\" \")\n    .map((word) => word.charAt(0).toUpperCase() + word.slice(1))\n    .join(\" \");\n\nasync function getDescription(name: string): Promise<string | null> {\n  const response = await fetch(\n    \"https://clinicaltables.nlm.nih.gov/api/ncbi_genes/v3/search?authenticity_token=&terms=\" + name.toUpperCase()\n  );\n  const data = await response.json();\n  const matches = data[3] && data[3].filter((x: string[]) => x[3] === name.toUpperCase());\n  return matches && matches.length >= 1 ? matches[0][4] : null;\n}\n\nexport const getSNPs = async (value: string, assembly: GenomeSearchProps[\"assembly\"], limit: number, signal?: AbortSignal) => {\n  const response = await fetch(\"https://screen.api.wenglab.org/graphql\", {\n    method: \"POST\",\n    body: JSON.stringify({\n      query: SNP_AUTOCOMPLETE_QUERY,\n      variables: {\n        assembly: assembly.toLowerCase(),\n        snpid: value,\n        limit: limit,\n      },\n    }),\n    headers: { \"Content-Type\": \"application/json\" },\n    signal,\n  });\n  return response.json();\n};\n\nexport const getStudys = async (value: string, limit: number, signal?: AbortSignal) => {\n  const response = await fetch(\"https://screen.api.wenglab.org/graphql\", {\n    method: \"POST\",\n    body: JSON.stringify({\n      query: GWAS_AUTOCOMPLETE_QUERY,\n      variables: {\n        studyname_prefix: [value],\n        limit,\n      },\n    }),\n    headers: { \"Content-Type\": \"application/json\" },\n    signal,\n  });\n\n  return 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package/dist/ui-components.es55.js

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-import { c as p } from "./ui-components.es15.js";
-import { useRef as b, useEffect as v } from "react";
-import z from "./ui-components.es83.js";
-const E = (t, r, h) => {
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-  let s, n;
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-    if (!c)
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-    const f = z(() => {
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-    }, o), d = new ResizeObserver((i) => {
-      for (const m of i)
-        m.borderBoxSize && f();
-    });
-    return d.observe(c), () => {
-      f.clear(), d.disconnect();
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+import { j as t } from "./ui-components.es13.js";
+import { c as S } from "./ui-components.es14.js";
+import { Stack as D, Typography as y, IconButton as C, Divider as v, Box as g, Button as _, Modal as k } from "@mui/material";
+import G from "./ui-components.es27.js";
+const P = (o) => {
+  const e = S.c(24), {
+    open: h,
+    onClose: l,
+    onDownloadSVG: b,
+    onDownloadPNG: u,
+    plotTitle: j
+  } = o;
+  let n;
+  e[0] !== u ? (n = {
+    label: "PNG",
+    action: u
+  }, e[0] = u, e[1] = n) : n = e[1];
+  let r;
+  e[2] !== b ? (r = {
+    label: "SVG",
+    action: b
+  }, e[2] = b, e[3] = r) : r = e[3];
+  let d;
+  e[4] !== n || e[5] !== r ? (d = [n, r].filter(I), e[4] = n, e[5] = r, e[6] = d) : d = e[6];
+  const w = d;
+  let m;
+  e[7] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (m = {
+    position: "absolute",
+    top: "50%",
+    left: "50%",
+    transform: "translate(-50%, -50%)",
+    bgcolor: "background.paper",
+    boxShadow: 24,
+    borderRadius: 2,
+    p: 3,
+    width: 360
+  }, e[7] = m) : m = e[7];
+  let i;
+  e[8] !== j ? (i = /* @__PURE__ */ t.jsxs(y, { variant: "h6", fontWeight: 600, mb: 1, children: [
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+    j
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+  let f;
+  e[10] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (f = /* @__PURE__ */ t.jsx(y, { variant: "body2", color: "text.secondary", mb: 2, children: "Choose a file format to export your plot." }), e[10] = f) : f = e[10];
+  let p;
+  e[11] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (p = /* @__PURE__ */ t.jsx(v, { flexItem: !0 }), e[11] = p) : p = e[11];
+  let a;
+  e[12] !== w ? (a = /* @__PURE__ */ t.jsx(D, { spacing: 1.5, divider: p, children: w.map(B) }), e[12] = w, e[13] = a) : a = e[13];
+  let s;
+  e[14] !== l ? (s = /* @__PURE__ */ t.jsx(g, { mt: 3, textAlign: "right", children: /* @__PURE__ */ t.jsx(_, { onClick: l, children: "Close" }) }), e[14] = l, e[15] = s) : s = e[15];
+  let c;
+  e[16] !== i || e[17] !== a || e[18] !== s ? (c = /* @__PURE__ */ t.jsxs(g, { sx: m, children: [
+    i,
+    f,
+    a,
+    s
+  ] }), e[16] = i, e[17] = a, e[18] = s, e[19] = c) : c = e[19];
+  let x;
+  return e[20] !== l || e[21] !== h || e[22] !== c ? (x = /* @__PURE__ */ t.jsx(k, { open: h, onClose: l, children: c }), e[20] = l, e[21] = h, e[22] = c, e[23] = x) : x = e[23], x;
 };
+function I(o) {
+  return o.action;
+}
+function B(o) {
+  return /* @__PURE__ */ t.jsxs(D, { direction: "row", alignItems: "center", justifyContent: "space-between", children: [
+    /* @__PURE__ */ t.jsx(y, { variant: "body1", children: o.label }),
+    /* @__PURE__ */ t.jsx(C, { color: "primary", onClick: o.action, "aria-label": `Download ${o.label}`, children: /* @__PURE__ */ t.jsx(G, {}) })
+  ] }, o.label);
+}
 export {
-  E as useContainerResize
+  P as default
 };
 //# sourceMappingURL=ui-components.es55.js.map

package/dist/ui-components.es55.js.map

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+{"version":3,"file":"ui-components.es55.js","sources":["../src/components/TwoPaneLayout/DownloadModal.tsx"],"sourcesContent":["import React from \"react\";\nimport { Modal, Box, IconButton, Stack, Typography, Divider, Button } from \"@mui/material\";\nimport DownloadIcon from \"@mui/icons-material/Download\";\n\nexport interface DownloadModalProps {\n  open: boolean;\n  onClose: () => void;\n  onDownloadSVG?: () => void;\n  onDownloadPNG?: () => void;\n  plotTitle: string;\n}\n\nconst DownloadModal: React.FC<DownloadModalProps> = ({ open, onClose, onDownloadSVG, onDownloadPNG, plotTitle }) => {\n  const downloadOptions = [\n    { label: \"PNG\", action: onDownloadPNG },\n    { label: \"SVG\", action: onDownloadSVG },\n  ].filter((option) => option.action);\n\n  return (\n    <Modal open={open} onClose={onClose}>\n      <Box\n        sx={{\n          position: \"absolute\",\n          top: \"50%\",\n          left: \"50%\",\n          transform: \"translate(-50%, -50%)\",\n          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