gramene-search 1.2.69 → 1.2.71

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Files changed (66) hide show
  1. package/.parcel-cache/17e9e143fcf5b59f +0 -0
  2. package/.parcel-cache/182d3536a86f8a99 +0 -0
  3. package/.parcel-cache/1a995a2728ab7c7c +0 -0
  4. package/.parcel-cache/2126881b633272fa.txt +2 -2
  5. package/.parcel-cache/2e66a6362611aea3 +0 -0
  6. package/.parcel-cache/37c075a090d2565c +0 -0
  7. package/.parcel-cache/4014ba3cfd6d6af5 +0 -0
  8. package/.parcel-cache/40cb8a4fff87878d +0 -0
  9. package/.parcel-cache/425346ba6a54d932 +0 -0
  10. package/.parcel-cache/582ac168061284ec +0 -0
  11. package/.parcel-cache/58e6cdaa648addaa +0 -0
  12. package/.parcel-cache/5b011f2f17a4ef9a +0 -0
  13. package/.parcel-cache/5f791e46dc5128e7 +0 -0
  14. package/.parcel-cache/65680aa75a27f755 +0 -0
  15. package/.parcel-cache/75bd0e526cad8639.txt +2 -0
  16. package/.parcel-cache/878e3ffbad677982 +0 -0
  17. package/.parcel-cache/888719e07a5dc53d +0 -0
  18. package/.parcel-cache/99f79b8f67c3938c +0 -0
  19. package/.parcel-cache/9eddc51e1d199de2 +0 -0
  20. package/.parcel-cache/a1c9060289b9a9e3 +0 -0
  21. package/.parcel-cache/a6c49560dea3583b +0 -0
  22. package/.parcel-cache/af6e8df7da4e4cdf +0 -0
  23. package/.parcel-cache/afe9f26fc0492b9a +0 -0
  24. package/.parcel-cache/b5671e06624f773b +0 -0
  25. package/.parcel-cache/b7855bf955616e1f +0 -0
  26. package/.parcel-cache/bdcd06dcc8b23b11 +0 -0
  27. package/.parcel-cache/cdecf11601322051 +0 -0
  28. package/.parcel-cache/d60e419ac6d05e40 +0 -0
  29. package/.parcel-cache/d8d36c1ea9c8d411 +0 -0
  30. package/.parcel-cache/data.mdb +0 -0
  31. package/.parcel-cache/e6d16635757cf0cb +0 -0
  32. package/.parcel-cache/f09b529f4e2ea91e +0 -0
  33. package/.parcel-cache/f8f45c1655f48536 +0 -0
  34. package/.parcel-cache/lock.mdb +0 -0
  35. package/dist/android-chrome-192x192.4d149c27.png +0 -0
  36. package/dist/apple-touch-icon-114x114.27e956ae.png +0 -0
  37. package/dist/apple-touch-icon-120x120.b209ed9f.png +0 -0
  38. package/dist/apple-touch-icon-144x144.9f8e2136.png +0 -0
  39. package/dist/apple-touch-icon-152x152.b6107a9b.png +0 -0
  40. package/dist/apple-touch-icon-180x180.58fbcc65.png +0 -0
  41. package/dist/apple-touch-icon-57x57.f670c755.png +0 -0
  42. package/dist/apple-touch-icon-60x60.3fbc15ae.png +0 -0
  43. package/dist/apple-touch-icon-72x72.a0fd991d.png +0 -0
  44. package/dist/apple-touch-icon-76x76.437b43b5.png +0 -0
  45. package/dist/favicon-16x16.4dd6b101.png +0 -0
  46. package/dist/favicon-32x32.a0d53b79.png +0 -0
  47. package/dist/favicon-96x96.6cd9b68e.png +0 -0
  48. package/dist/genetree.d75946eb.png +0 -0
  49. package/dist/index.css +10 -0
  50. package/dist/index.css.map +1 -1
  51. package/dist/index.js +29 -6
  52. package/dist/index.js.map +1 -1
  53. package/dist/results.a8da7555.png +0 -0
  54. package/dist/sorghum.250fb7b9.js +15812 -0
  55. package/dist/sorghum.250fb7b9.js.map +1 -0
  56. package/dist/sorghum.2c55063b.css +26794 -0
  57. package/dist/sorghum.2c55063b.css.map +1 -0
  58. package/dist/sorghum.b34cb912.js +293195 -0
  59. package/dist/sorghum.b34cb912.js.map +1 -0
  60. package/dist/sorghum.html +39 -0
  61. package/dist/suggestions.099b7c0e.png +0 -0
  62. package/package.json +1 -1
  63. package/src/components/results/GeneList.js +3 -2
  64. package/src/components/results/details/Location.js +1 -1
  65. package/src/components/results/details/Publications.js +12 -5
  66. package/src/components/results/genes.css +9 -0
package/dist/sorghum.html ADDED
@@ -0,0 +1,39 @@
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+ <!DOCTYPE html>
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+ <html lang="en">
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+ <head>
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+ <meta charset="UTF-8">
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+ <title>Gramene Search</title>
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+ <link rel="stylesheet" href="/sorghum.2c55063b.css"><script>window.gramene = {};
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+ gramene.defaultServer = "https://data.sorghumbase.org/sorghum_v6/swagger";
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+
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+ </script>
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+ <script async="" src="/sorghum.250fb7b9.js"></script>
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+ <script async="" src="https://plantreactome.gramene.org/DiagramJs/diagram/diagram.nocache.js"></script>
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+ <link rel="apple-touch-icon" sizes="57x57" href="/apple-touch-icon-57x57.f670c755.png">
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+ <link rel="apple-touch-icon" sizes="60x60" href="/apple-touch-icon-60x60.3fbc15ae.png">
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+ <link rel="apple-touch-icon" sizes="72x72" href="/apple-touch-icon-72x72.a0fd991d.png">
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+ <link rel="apple-touch-icon" sizes="76x76" href="/apple-touch-icon-76x76.437b43b5.png">
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+ <link rel="apple-touch-icon" sizes="114x114" href="/apple-touch-icon-114x114.27e956ae.png">
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+ <link rel="apple-touch-icon" sizes="120x120" href="/apple-touch-icon-120x120.b209ed9f.png">
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+ <link rel="apple-touch-icon" sizes="144x144" href="/apple-touch-icon-144x144.9f8e2136.png">
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+ <link rel="apple-touch-icon" sizes="152x152" href="/apple-touch-icon-152x152.b6107a9b.png">
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+ <link rel="apple-touch-icon" sizes="180x180" href="/apple-touch-icon-180x180.58fbcc65.png">
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+ <link rel="icon" type="image/png" href="/favicon-32x32.a0d53b79.png" sizes="32x32">
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+ <link rel="icon" type="image/png" href="/android-chrome-192x192.4d149c27.png" sizes="192x192">
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+ <link rel="icon" type="image/png" href="/favicon-96x96.6cd9b68e.png" sizes="96x96">
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+ <link rel="icon" type="image/png" href="/favicon-16x16.4dd6b101.png" sizes="16x16">
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+ </head>
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+ <body>
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+ <div id="demo"></div>
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+ <script src="/sorghum.b34cb912.js" defer=""></script>
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+ <script>document.addEventListener("keyup", possiblyFocus);
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+ function possiblyFocus(e) {
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+ if (e.key === "/") {
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+ var el = document.getElementById("search-input");
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+ if (el) el.focus();
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+ }
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+ }
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+
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+ </script>
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+ </body>
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+ </html>
package/dist/suggestions.099b7c0e.png ADDED
Binary file
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "gramene-search",
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- "version": "1.2.69",
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+ "version": "1.2.71",
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  "description": "search wrapper for gramene",
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  "source": "src/index.js",
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  "main": "dist/index.js",
package/src/components/results/GeneList.js CHANGED
@@ -165,10 +165,11 @@ class Gene extends React.Component {
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  }
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  getDetailStatus(d) {
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  if (this.state.expandedDetail === d.id) return 'expanded';
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- return d.available ? 'closed' : 'disabled';
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+ if (d.available) return 'closed'
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+ return d.id === "pubs" ? 'empty' : 'disabled';
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  }
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  setExpanded(d) {
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- if (d.available) {
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+ if (d.available || d.id === "pubs") {
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  if (this.state.expandedDetail === d.id) {
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  this.setState({expandedDetail: null})
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  }
package/src/components/results/details/Location.js CHANGED
@@ -159,7 +159,7 @@ class Location extends React.Component {
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  {name: 'Ensembl Browser', url: `${this.props.ensemblURL}/${gene.system_name}/Gene/Summary?g=${gene._id}`}
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  ];
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  if (gene.annotations.taxonomy.ancestors.includes(4557))
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- links.push({name: 'Phytozome', url: `https://phytozome.jgi.doe.gov/phytomine/keywordSearchResults.do?searchTerm=${jgiify(gene._id)}&searchSubmit=Search`})
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+ links.push({name: 'Phytozome', url: `https://phytozome-next.jgi.doe.gov/report/gene/Sbicolor_v5_1/${jgiify(gene._id)}`})
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  if (gene.taxon_id === 3702)
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  links.push(
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  {name: 'tair', url: `https://www.arabidopsis.org/servlets/TairObject?name=${gene._id}&type=locus`},
package/src/components/results/details/Publications.js CHANGED
@@ -90,9 +90,11 @@ function formatPubsForGene(gene) {
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  if(!gene || !_.isArray(gene.xrefs)) {
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  throw new Error("No xrefs for " + _.get(gene._id));
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  }
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- return gene.xrefs
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- .filter(xr => xr.db === "PUBMED") //dbxrefs.isKnown(xr.db))
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- .sort((a,b) => {
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+ let pubs = gene.xrefs.filter(xr => xr.db === "PUBMED");
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+ if (pubs.length === 0) {
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+ return <tr><td colSpan={3}>No publications found.</td></tr>
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+ }
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+ return pubs.sort((a,b) => {
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  if (a.source) {
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  if (b.source) {
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  if (a.source < b.source) {
@@ -124,11 +126,11 @@ function formatPubsForGene(gene) {
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  )
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  })
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  }
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-
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+ const formURL = 'https://docs.google.com/forms/d/e/1FAIpQLSey-xPyTysdd9c2phXT6kcbjEDeCppG4dLG7LjZCeLpx_KGog/viewform?usp=pp_url&entry.1266455249=';
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  const Publications = ({searchResult, geneDocs}) => (
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  <Detail>
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  <Title key="title">Curated publications</Title>
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- <Description key="description">This gene has been described in the literature:</Description>
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+ <Description key="description">Functions described in the literature:</Description>
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  <Content key="content">
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  <table className="xrefs table">
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  <thead>
@@ -141,6 +143,11 @@ const Publications = ({searchResult, geneDocs}) => (
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  <tbody>
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  {formatPubsForGene(geneDocs[searchResult.id])}
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  </tbody>
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+ <tfoot>
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+ <tr>
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+ <th colSpan={3}>Submit a gene function <a target="_blank" href={formURL + searchResult.id}>here</a></th>
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+ </tr>
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+ </tfoot>
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  </table>
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  </Content>
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  </Detail>
package/src/components/results/genes.css CHANGED
@@ -88,6 +88,15 @@
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  color: lightgray;
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  cursor: not-allowed;
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  }
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+ .gene-detail-tab-empty {
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+ color: darkgreen;
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+ cursor: pointer;
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+ font-style: oblique;
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+ /*background-color: lightgray;*/
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+ }
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+ .gene-detail-tab-empty::before {
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+ content: "Add ";
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+ }
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  .gene-detail-tab-expanded {
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  color: white;
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  background-color: #557B74;