gramene-search 1.2.70 → 1.2.72

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gramene-search",
-  "version": "1.2.70",
+  "version": "1.2.72",
   "description": "search wrapper for gramene",
   "source": "src/index.js",
   "main": "dist/index.js",

package/src/bundles/BAR.js

@@ -0,0 +1,27 @@
+import {createSelector} from "redux-bundler";
+const BARs = {
+  name: 'BARs',
+  getReducer: () => {
+    const initialState = {
+
+    };
+    return (state = initialState, {type, payload}) => {
+      let newState;
+      switch (type) {
+        // case 'GRAMENE_GENOMES_TOGGLED':
+        //   newState = Object.assign({},state);
+        //   newState.show = !newState.show;
+        //   return newState;
+        // case 'GRAMENE_GENOMES_UPDATED':
+        //   newState = Object.assign({}, state);
+        //   newState.active = payload;
+        //   return newState;
+        default:
+          return state;
+      }
+    }
+  },
+  selectBARs: state => state.BARs,
+};
+
+export default BARs;

package/src/components/results/GeneList.js

@@ -165,10 +165,11 @@ class Gene extends React.Component {
   }
   getDetailStatus(d) {
     if (this.state.expandedDetail === d.id) return 'expanded';
-    return d.available ? 'closed' : 'disabled';
+    if (d.available) return 'closed'
+    return d.id === "pubs" ? 'empty' : 'disabled';
   }
   setExpanded(d) {
-    if (d.available) {
+    if (d.available || d.id === "pubs") {
       if (this.state.expandedDetail === d.id) {
         this.setState({expandedDetail: null})
       }

package/src/components/results/details/Expression.js

@@ -5,7 +5,13 @@ import {Tabs, Tab} from 'react-bootstrap';
 const Detail = props => {
   const gene = props.geneDocs[props.searchResult.id];
   let paralogs_url;
-  let gene_url = `/static/atlasWidget.html?reference=0&genes=${gene._id}`;
+  let efp_browser;
+  let gene_url = `/static/atlasWidget.html?reference=0&genes=${gene.atlas_id || gene._id}`;
+  if (gene.taxon_id === 4558) {
+    // efp_browser = `https://bar.utoronto.ca/api/efp_image/efp_sorghum/Stress_Atlas/Absolute/${gene._id.replace('SORBI_3','Sobic.')}`
+    // efp_browser = `https://bar.utoronto.ca/api/efp_image/efp_sorghum/`
+    // efp_browser = `https://bar.utoronto.ca/~asher/efp_sorghum/cgi-bin/efpWeb.cgi?dataSource=Developmental_Atlas&mode=Absolute&primaryGene=${gene._id.replace('SORBI_3','Sobic.')}`
+  }
   if (props.paralogExpression && props.paralogExpression[gene._id]) {
     let paralogs = props.paralogExpression[gene._id].map(p => p.id);
     if (paralogs.length > 1) {
@@ -22,6 +28,8 @@ const Detail = props => {
     {paralogs_url && <Tab eventKey="paralogs" title="Reference Study (all paralogs)">
       <iframe src={paralogs_url} frameBorder="0" width="100%" height="500px"></iframe>
     </Tab>}
+    {efp_browser && <Tab eventKey="eFP" title="eFP browser (BAR)">
+    </Tab>}
   </Tabs>
 };
 

package/src/components/results/details/Publications.js

@@ -90,9 +90,11 @@ function formatPubsForGene(gene) {
   if(!gene || !_.isArray(gene.xrefs)) {
     throw new Error("No xrefs for " + _.get(gene._id));
   }
-  return gene.xrefs
-    .filter(xr => xr.db === "PUBMED") //dbxrefs.isKnown(xr.db))
-    .sort((a,b) => {
+  let pubs = gene.xrefs.filter(xr => xr.db === "PUBMED");
+  if (pubs.length === 0) {
+    return <tr><td colSpan={3}>No publications found.</td></tr>
+  }
+  return pubs.sort((a,b) => {
       if (a.source) {
         if (b.source) {
           if (a.source < b.source) {
@@ -124,11 +126,11 @@ function formatPubsForGene(gene) {
       )
     })
 }
-
+const formURL = 'https://docs.google.com/forms/d/e/1FAIpQLSey-xPyTysdd9c2phXT6kcbjEDeCppG4dLG7LjZCeLpx_KGog/viewform?usp=pp_url&entry.1266455249=';
 const Publications = ({searchResult, geneDocs}) => (
   <Detail>
     <Title key="title">Curated publications</Title>
-    <Description key="description">This gene has been described in the literature:</Description>
+    <Description key="description">Functions described in the literature:</Description>
     <Content key="content">
       <table className="xrefs table">
         <thead>
@@ -141,6 +143,11 @@ const Publications = ({searchResult, geneDocs}) => (
         <tbody>
         {formatPubsForGene(geneDocs[searchResult.id])}
         </tbody>
+        <tfoot>
+          <tr>
+            <th colSpan={3}>Submit a gene function <a target="_blank" href={formURL + searchResult.id}>here</a></th>
+          </tr>
+        </tfoot>
       </table>
     </Content>
   </Detail>

package/src/components/results/genes.css

@@ -88,6 +88,15 @@
     color: lightgray;
     cursor: not-allowed;
 }
+.gene-detail-tab-empty {
+    color: darkgreen;
+    cursor: pointer;
+    font-style: oblique;
+    /*background-color: lightgray;*/
+}
+.gene-detail-tab-empty::before {
+    content: "Add ";
+}
 .gene-detail-tab-expanded {
     color: white;
     background-color: #557B74;

package/src/demo.js

@@ -45,7 +45,8 @@ const panSites = [
     ensemblURL: 'https://ensembl.gramene.org',
     ensemblSite: 'https://ensembl.gramene.org',
     ensemblRest: 'https://data.gramene.org/ensembl66',
-    grameneData: 'https://data.gramene.org/v66',
+    grameneData: 'https://data.gramene.org/v68',
+    ga: 'G-ZTEQBFCRXZ',
     targetTaxonId: 3702,
     alertText: 'Main site'
   },
@@ -77,7 +78,7 @@ const panSites = [
     ensemblRest: 'https://data.gramene.org/pansite-ensembl',
     grameneData: 'https://data.sorghumbase.org/sorghum_v6',
     ga: 'G-L5KXDCCZ16',
-    targetTaxonId: 4588,
+    targetTaxonId: 4558,
     alertText: 'Click the search icon in the menu bar or type / to search'
   },
   {

package/src/index.html

@@ -5,19 +5,10 @@
     <title>Gramene Search</title>
     <script>
       window.gramene = {};
-      gramene.defaultServer = 'https://data.gramene.org/v66/swagger';
+      gramene.defaultServer = 'https://data.gramene.org/v68/swagger';
     </script>
     <script async src="./static/gramene-dalliance/dalliance-all.js"></script>
     <script async src="https://plantreactome.gramene.org/DiagramJs/diagram/diagram.nocache.js"></script>
-    <!-- Global site tag (gtag.js) - Google Analytics -->
-    <script async src="https://www.googletagmanager.com/gtag/js?id=UA-1624628-5"></script>
-    <script>
-        window.dataLayer = window.dataLayer || [];
-        function gtag(){dataLayer.push(arguments);}
-        gtag('js', new Date());
-
-        gtag('config', 'UA-1624628-5');
-    </script>
     <link rel="apple-touch-icon" sizes="57x57" href="./static/icons/apple-touch-icon-57x57.png">
     <link rel="apple-touch-icon" sizes="60x60" href="./static/icons/apple-touch-icon-60x60.png">
     <link rel="apple-touch-icon" sizes="72x72" href="./static/icons/apple-touch-icon-72x72.png">

package/.parcel-cache/75bd0e526cad8639.txt

@@ -1,2 +0,0 @@
-160610964
-1688621248646815000