gramene-search 1.6.46 → 1.7.0

package/src/components/results/Study.js

@@ -12,12 +12,27 @@ const metaRenderer = params => {
 }
 const sampleRenderer = params => {
   const sampleMeta = params.value;
-  return JSON.stringify(sampleMeta,null,2);
+  return (
+    <label>
+      <input
+        type="checkbox"
+        checked={params.desiredSamples.hasOwnProperty(sampleMeta._id)}
+        onChange={() => params.doToggleExpressionSample(sampleMeta._id)}
+      />
+      &nbsp;{sampleMeta.experiment}-{sampleMeta.group}
+    </label>
+  );
+  // return JSON.stringify(sampleMeta,null,2);
 }
+const connectedSampleRenderer = connect(
+  'selectDesiredSamples', // current set of samples to fetch expression data for
+  'doToggleExpressionSample',
+  sampleRenderer
+);
 const Study = props => {
   let samples = props.expressionSamples[props.id];
   let sampleMetadata = [];
-  let metadataFields = [{ field: "sampleId", cellRenderer: sampleRenderer }];
+  let metadataFields = [{ field: "sampleId", cellRenderer: connectedSampleRenderer }];
   let isFactor={};
   samples.forEach((sample, idx) => {
     if (idx === 0) {
@@ -76,5 +91,4 @@ const Study = props => {
 };
 export default connect(
   'selectExpressionSamples',
-  'doToggleExpressionSample',
   Study);

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/UserGeneLists.js

@@ -55,6 +55,32 @@ const GeneListDisplayComponent = props => {
     }
   };
 
+  // Example functions for viewing and deleting lists
+  const viewGeneList = (list) => {
+    alert(`Viewing gene list: ${list.label}`);
+    props.addFilter({
+      category: 'Gene List',
+      fq_field: 'saved_search',
+      fq_value: list.hash,
+      name: list.label
+    })
+  };
+
+  const deleteGeneList = async (api,listId) => {
+    if (window.confirm('Are you sure you want to delete this gene list?')) {
+      // Replace with the actual delete request
+      try {
+        await fetch(`${api}/gene_lists/${listId}`, {
+          method: 'DELETE',
+        });
+        alert('Gene list deleted!');
+        // Optionally refetch the updated list
+      } catch (err) {
+        alert('Failed to delete gene list.');
+      }
+    }
+  };
+
   // Fetch data when the component is mounted
   useEffect(() => {
     fetchPublicGeneLists();
@@ -76,6 +102,7 @@ const GeneListDisplayComponent = props => {
       {privateGeneLists.length > 0 && (
         <Table striped bordered hover className="mt-4">
           <thead>
+          <tr><th colspan={3}>My gene lists</th></tr>
           <tr>
             <th>List Name</th>
             <th>Number of Genes</th>
@@ -86,7 +113,7 @@ const GeneListDisplayComponent = props => {
           {privateGeneLists.map((list, index) => (
             <tr key={index}>
               <td>{list.label}</td>
-              <td>{list.hash}</td>
+              <td>{list.n_genes || 0}</td>
               <td>
                 <Button variant="info" onClick={() => viewGeneList(list)}>
                   View
@@ -104,6 +131,9 @@ const GeneListDisplayComponent = props => {
       {publicGeneLists.length > 0 ? (
         <Table striped bordered hover className="mt-4">
           <thead>
+          <tr>
+            <th colSpan={3}>Public gene lists</th>
+          </tr>
           <tr>
             <th>List Name</th>
             <th>Number of Genes</th>
@@ -114,7 +144,7 @@ const GeneListDisplayComponent = props => {
           {publicGeneLists.map((list, index) => (
             <tr key={index}>
               <td>{list.label}</td>
-              <td>{list.hash}</td>
+              <td>{list.n_genes || 0}</td>
               <td>
                 <Button variant="info" onClick={() => viewGeneList(list)}>
                   View
@@ -136,27 +166,6 @@ const GeneListDisplayComponent = props => {
   );
 };
 
-// Example functions for viewing and deleting lists
-const viewGeneList = (list) => {
-  alert(`Viewing gene list: ${list.name}\nGenes: ${list.genes.join(', ')}`);
-};
-
-const deleteGeneList = async (api,listId) => {
-  if (window.confirm('Are you sure you want to delete this gene list?')) {
-    // Replace with the actual delete request
-    try {
-      await fetch(`${api}/gene_lists/${listId}`, {
-        method: 'DELETE',
-      });
-      alert('Gene list deleted!');
-      // Optionally refetch the updated list
-    } catch (err) {
-      alert('Failed to delete gene list.');
-    }
-  }
-};
-
-
 const GeneListComponent = props => {
   const [geneList, setGeneList] = useState('');
   const [listHash, setListHash] = useState(null);
@@ -230,6 +239,7 @@ const GeneListComponent = props => {
       label: listName,
       hash: listHash,
       site: props.site,
+      n_genes: validatedList.length,
       isPublic: listIsPublic
     };
     const queryString = new URLSearchParams(queryParams).toString();
@@ -348,7 +358,7 @@ const UserGeneListsComponent = props => {
     <Container fluid>
       <Row>
         <Col><GeneListComponent api={props.configuration.grameneData} site={props.configuration.id}/></Col>
-        <Col><GeneListDisplayComponent api={props.configuration.grameneData} site={props.configuration.id}/></Col>
+        <Col><GeneListDisplayComponent api={props.configuration.grameneData} site={props.configuration.id} addFilter={props.doAcceptGrameneSuggestion}/></Col>
       </Row>
     </Container>
   )
@@ -356,5 +366,6 @@ const UserGeneListsComponent = props => {
 
 export default connect(
   'selectConfiguration',
+  'doAcceptGrameneSuggestion',
   UserGeneListsComponent
 );

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);
@@ -69,13 +72,13 @@ const Detail = props => {
   let paralogs = [];
   if (props.grameneParalogs && props.grameneParalogs[gene._id]) {
     paralogs = props.grameneParalogs[gene._id];
-  } else if(gene.homology) {
+  } else if (gene.homology) {
     props.doRequestParalogs(gene._id, gene.homology.supertree, gene.taxon_id);
   }
   // if (gene.homology && gene.homology.homologous_genes && gene.homology.homologous_genes.within_species_paralog) {
   //   paralogs = gene.homology.homologous_genes.within_species_paralog;
   // }
-  if (paralogs.length > 1 && atlasExperiment) {
+  if (paralogs.length > 0 && atlasExperiment) {
     paralogs_url= `https://dev.gramene.org/static/atlasWidget.html?genes=${paralogs.join(' ')}&experiment=${atlasExperiment}&localAPI=${isLocal}`;
   }
   return <Tabs activeKey={activeTab} onSelect={(k) => setActiveTab(k)}>

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/rice.html

@@ -5,7 +5,7 @@
     <title>Gramene Search</title>
     <script>
       window.gramene = {};
-      gramene.defaultServer = 'https://data.gramene.org/oryza_v8/swagger';
+      gramene.defaultServer = 'https://data.gramene.org/oryza_v9/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>

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>

package/dist/Study.826d318c.js

@@ -1,137 +0,0 @@
-var $eTR7Q$reactjsxruntime = require("react/jsx-runtime");
-var $eTR7Q$react = require("react");
-var $eTR7Q$reduxbundlerreact = require("redux-bundler-react");
-var $eTR7Q$aggridreact = require("ag-grid-react");
-require("ag-grid-community/styles/ag-grid.css");
-require("ag-grid-community/styles/ag-theme-quartz.css");
-
-
-function $parcel$defineInteropFlag(a) {
-  Object.defineProperty(a, '__esModule', {value: true, configurable: true});
-}
-
-function $parcel$export(e, n, v, s) {
-  Object.defineProperty(e, n, {get: v, set: s, enumerable: true, configurable: true});
-}
-
-      var $parcel$global = globalThis;
-    var parcelRequire = $parcel$global["parcelRequire94c2"];
-var parcelRegister = parcelRequire.register;
-parcelRegister("7zuJ6", function(module, exports) {
-
-$parcel$defineInteropFlag(module.exports);
-
-$parcel$export(module.exports, "default", () => $5833a2eeefc77457$export$2e2bcd8739ae039);
-
-
-
-
-
-
-const $5833a2eeefc77457$var$metaRenderer = (params)=>{
-    if (params.value.ontology) return /*#__PURE__*/ (0, $eTR7Q$reactjsxruntime.jsx)("a", {
-        href: `http://purl.obolibrary.org/obo/${params.value.id.replace(":", "_")}`,
-        target: "_blank",
-        children: params.value.label
-    });
-    return params.value.label;
-};
-const $5833a2eeefc77457$var$sampleRenderer = (params)=>{
-    const sampleMeta = params.value;
-    return JSON.stringify(sampleMeta, null, 2);
-};
-const $5833a2eeefc77457$var$Study = (props)=>{
-    let samples = props.expressionSamples[props.id];
-    let sampleMetadata = [];
-    let metadataFields = [
-        {
-            field: "sampleId",
-            cellRenderer: $5833a2eeefc77457$var$sampleRenderer
-        }
-    ];
-    let isFactor = {};
-    samples.forEach((sample, idx)=>{
-        if (idx === 0) {
-            let factors = {
-                headerName: 'Experimental Variables',
-                children: []
-            };
-            sample.factor.forEach((factor)=>{
-                factors.children.push({
-                    field: factor.type,
-                    cellRenderer: $5833a2eeefc77457$var$metaRenderer
-                });
-                isFactor[factor.type] = true;
-            });
-            metadataFields.push(factors);
-            let characteristics = {
-                headerName: 'Sample Characteristics',
-                children: []
-            };
-            sample.characteristic.forEach((ch)=>{
-                if (!isFactor[ch.type]) characteristics.children.push({
-                    field: ch.type,
-                    cellRenderer: $5833a2eeefc77457$var$metaRenderer
-                });
-            });
-            metadataFields.push(characteristics);
-        }
-        let s_info = {
-            sampleId: sample
-        };
-        sample.factor.forEach((factor)=>{
-            s_info[factor.type] = {
-                label: factor.label
-            };
-            if (factor.ontology) {
-                s_info[factor.type]['ontology'] = factor.ontology;
-                s_info[factor.type]['id'] = factor.id;
-            }
-        });
-        sample.characteristic.forEach((ch)=>{
-            s_info[ch.type] = {
-                label: ch.label
-            };
-            if (ch.ontology) {
-                s_info[ch.type]['ontology'] = ch.ontology;
-                s_info[ch.type]['id'] = ch.id;
-            }
-        });
-        sampleMetadata.push(s_info);
-    });
-    const [rowData, setRowData] = (0, $eTR7Q$react.useState)(sampleMetadata);
-    const [colDefs, setColDefs] = (0, $eTR7Q$react.useState)(metadataFields);
-    const defaultColDef = (0, $eTR7Q$react.useMemo)(()=>{
-        return {
-            filter: true
-        };
-    }, []);
-    return /*#__PURE__*/ (0, $eTR7Q$reactjsxruntime.jsxs)("div", {
-        children: [
-            /*#__PURE__*/ (0, $eTR7Q$reactjsxruntime.jsx)("div", {
-                className: "ag-theme-quartz",
-                style: {
-                    height: `${44 * (samples.length + 2)}px`
-                },
-                children: /*#__PURE__*/ (0, $eTR7Q$reactjsxruntime.jsx)((0, $eTR7Q$aggridreact.AgGridReact), {
-                    rowData: rowData,
-                    columnDefs: colDefs,
-                    defaultColDef: defaultColDef
-                })
-            }),
-            /*#__PURE__*/ (0, $eTR7Q$reactjsxruntime.jsxs)("a", {
-                href: `https://www.ebi.ac.uk/gxa/experiments/${props.id}`,
-                children: [
-                    "EBI Atlas Experiment: ",
-                    props.id
-                ]
-            })
-        ]
-    });
-};
-var $5833a2eeefc77457$export$2e2bcd8739ae039 = (0, $eTR7Q$reduxbundlerreact.connect)('selectExpressionSamples', 'doToggleExpressionSample', $5833a2eeefc77457$var$Study);
-
-});
-
-
-//# sourceMappingURL=Study.826d318c.js.map

package/dist/Study.826d318c.js.map

@@ -1 +0,0 @@
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