gramene-search 1.6.47 → 1.7.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gramene-search",
-  "version": "1.6.47",
+  "version": "1.7.0",
   "description": "search wrapper for gramene",
   "source": "src/index.js",
   "main": "dist/index.js",

package/src/components/results/TaxDist.js

@@ -8,7 +8,8 @@ class TaxDist extends React.Component {
   constructor(props) {
     super(props);
     this.state = {
-      collapseEmpties: true
+      collapseEmpties: true,
+      comparaOnly: true
     };
   }
   handleSelection(selections) {
@@ -23,6 +24,9 @@ class TaxDist extends React.Component {
   toggleEmpties() {
     this.setState({collapseEmpties: !this.state.collapseEmpties})
   }
+  toggleCompara() {
+    this.setState({comparaOnly: !this.state.comparaOnly})
+  }
   render() {
     let selectedTaxa = {};
     if (this.props.grameneSearch && this.state.collapseEmpties) {
@@ -31,15 +35,34 @@ class TaxDist extends React.Component {
       })
     }
     else {
-      selectedTaxa = this.props.grameneGenomes.active
+      if (Object.keys(this.props.grameneGenomes.active).length === 0 && this.props.grameneMaps) {
+        Object.keys(this.props.grameneMaps).forEach(tid => selectedTaxa[tid] = true);
+      }
+      else {
+        selectedTaxa = this.props.grameneGenomes.active
+      }
+    }
+    if (this.state.comparaOnly && this.props.grameneMaps) {
+      Object.keys(selectedTaxa).forEach(tid => {
+        if (!this.props.grameneMaps[tid].in_compara) {
+          delete selectedTaxa[tid];
+        }
+      })
     }
     return (
       <div className="results-vis big-vis">
-        {this.props.grameneTaxDist && <button type="button"
-                                              className="btn btn-primary btn-sm"
-                                              onClick={this.toggleEmpties.bind(this)}>
+        {this.props.grameneTaxDist && <span>
+          <button type="button"
+                  className="btn btn-outline-primary btn-sm"
+                  onClick={this.toggleEmpties.bind(this)}>
           {this.state.collapseEmpties ? 'Expand' : 'Collapse'} empty branches
-        </button>}
+          </button>
+          <button type="button"
+                  className="btn btn-outline-success btn-sm"
+                  onClick={this.toggleCompara.bind(this)}>
+            Show {this.state.comparaOnly ? 'all genomes' : 'compara only'}
+          </button>
+        </span>}
         {this.props.grameneTaxDist && <Vis taxonomy={this.props.grameneTaxDist}
                                            selectedTaxa={selectedTaxa}
                                            onSelection={this.handleSelection.bind(this)}
@@ -63,5 +86,6 @@ export default connect(
   'selectGrameneTaxDist',
   'selectGrameneGenomes',
   'selectGrameneSearch',
+  'selectGrameneMaps',
   TaxDist
 );

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

@@ -34,6 +34,7 @@ const Detail = props => {
   const gene = props.geneDocs[props.searchResult.id];
   const [atlasExperiment, setAtlasExperiment] = useState(null);
   const [atlasExperimentList, setAtlasExperimentList] = useState([]);
+  const [atlasFacets, setAtlasFacets] = useState(null);
   const [isLocal, setIsLocal] = useState(false);
   const [activeTab, setActiveTab] = useState('gene');
 
@@ -43,6 +44,7 @@ const Detail = props => {
   useEffect(() => {
     const tid = Math.floor(gene.taxon_id / 1000);
     if (props.expressionStudies[tid]) {
+      let facets={Differential: {}, Baseline: {}};
       let eList = props.expressionStudies[tid].sort((a,b) => {
         const a_name = `${a.type}:${a.description || a._id}`;
         const b_name = `${b.type}:${b.description || b._id}`;
@@ -52,8 +54,9 @@ const Detail = props => {
         const in_gxa = new Set(props.searchResult.expressed_in_gxa_attr_ss);
         eList = eList.filter(e => in_gxa.has(e._id))
       }
+      eList.forEach(e => {e.factors.forEach(factor => facets[e.type][factor] = 1);});
       setAtlasExperimentList(eList);
-
+      setAtlasFacets(facets);
       let refExp = eList.filter(e => e.isRef);
       if (refExp.length === 1) {
         setAtlasExperiment(refExp[0]._id);

package/src/demo.js

@@ -138,9 +138,9 @@ const panSites = [
     ensemblURL: 'https://ensembl-dev.sorghumbase.org',
     ensemblSite: 'https://ensembl-dev.sorghumbase.org',
     ensemblRest: 'https://data.gramene.org/pansite-ensembl-108',
-    grameneData: 'https://data.sorghumbase.org/auth_testing',
+    grameneData: 'https://data.sorghumbase.org/sorghum_v10',
     ga: 'G-L5KXDCCZ16',
-    targetTaxonId: 4558003,
+    targetTaxonId: 4558001,
     alertText: 'Click the search icon in the menu bar or type /',
     showViews: true,
     details: {

package/src/index.html

@@ -5,7 +5,7 @@
     <title>Gramene Search</title>
     <script>
       window.gramene = {};
-      gramene.defaultServer = 'https://data.gramene.org/v68/swagger';
+      gramene.defaultServer = 'https://data.gramene.org/v69/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>
@@ -38,4 +38,4 @@
     }
 </script>
 </body>
-</html>
+</html>

package/src/sorghum.html

@@ -5,7 +5,7 @@
     <title>Gramene Search</title>
     <script>
       window.gramene = {};
-      gramene.defaultServer = 'https://data.sorghumbase.org/sorghum_v9/swagger';
+      gramene.defaultServer = 'https://data.sorghumbase.org/sorghum_v10/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>