gramene-search 1.6.45 → 1.6.47

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/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

@@ -69,13 +69,13 @@ 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/components/results/details/VEP.js

@@ -9,7 +9,8 @@ import '@fortawesome/fontawesome-free/css/all.min.css';
 import "./VEP.css";
 
 const ggURL = {
-  IRRI: 'https://gringlobal.irri.org/gringlobal/accessiondetail?id=',
+  xIRRI: 'https://gringlobal.irri.org/gringlobal/accessiondetail?id=',
+  IRRI: 'https://www.irri.org/genesys-rice#/a/',
   ARS: 'https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=',
   ICRISAT: 'https://genebank.icrisat.org/IND/PassportSummary?ID=',
   sorbmutdb: 'https://www.depts.ttu.edu/igcast/sorbmutdb.php',

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/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

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