gramene-search 1.6.22 → 1.6.25

package/.parcel-cache/snapshot-dc1da35000e13623.txt

@@ -1,2 +1,2 @@
-88241069
-1741125262813958000
+64260376
+1746630965227134000

package/dist/index.js

@@ -142,7 +142,8 @@ $9d9aeaf9299e61a1$var$grameneSuggestions.selectGrameneSuggestionsStatus = (0, $g
     if (!queryString) return '';
     if (shouldUpdate) return 'update needed';
     if (isLoading) return 'loading';
-    if (suggestionsRaw) return suggestionsRaw.data.grouped.category.matches + ' terms';
+    if (suggestionsRaw.data) return suggestionsRaw.data.grouped.category.matches + ' terms';
+    console.error(suggestionsRaw);
     return 'error';
 });
 $9d9aeaf9299e61a1$var$grameneSuggestions.selectGrameneSuggestionsReady = (0, $gXNCa$reduxbundler.createSelector)('selectGrameneSuggestionsStatus', (status)=>{
@@ -2261,30 +2262,93 @@ function $9e29a4f60318db7a$var$DynamicIframe(props) {
 }
 const $9e29a4f60318db7a$var$Detail = (props)=>{
     const gene = props.geneDocs[props.searchResult.id];
+    const [atlasExperiment, setAtlasExperiment] = (0, $gXNCa$react.useState)(null);
+    const [atlasExperimentList, setAtlasExperimentList] = (0, $gXNCa$react.useState)([]);
+    const [isLocal, setIsLocal] = (0, $gXNCa$react.useState)(false);
+    const handleLocalAPIChange = (event)=>{
+        setIsLocal(event.target.checked);
+    };
+    (0, $gXNCa$react.useEffect)(()=>{
+        const tid = Math.floor(gene.taxon_id / 1000);
+        if (props.expressionStudies[tid]) {
+            let eList = props.expressionStudies[tid].filter((e)=>e.type === "Baseline");
+            setAtlasExperimentList(eList);
+            let refExp = eList.filter((e)=>e.isRef);
+            if (refExp.length === 1) setAtlasExperiment(refExp[0]._id);
+            else // no reference experiment - choose first
+            setAtlasExperiment(eList[0]._id);
+        }
+    }, [
+        props.expressionStudies
+    ]);
     let paralogs_url;
-    let gene_url = `/static/atlasWidget.html?reference=0&genes=${gene.atlas_id || gene._id}`;
-    if (props.paralogExpression && props.paralogExpression[gene._id]) {
-        let paralogs = props.paralogExpression[gene._id].map((p)=>p.atlas_id || p.id);
-        if (paralogs.length > 1) paralogs_url = `/static/atlasWidget.html?reference=1&genes=${paralogs.join(' ')}`;
-    } else props.doRequestParalogExpression(gene._id);
+    let gene_url = `/static/atlasWidget.html?genes=${gene.atlas_id || gene._id}&localAPI=${isLocal}`;
+    let paralogs = [];
+    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) paralogs_url = `/static/atlasWidget.html?genes=${paralogs.join(' ')}&experiment=${atlasExperiment}&localAPI=${isLocal}`;
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Tabs), {
         children: [
-            paralogs_url && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tab), {
+            paralogs_url && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Tab), {
                 tabClassName: "gxa",
                 eventKey: "paralogs",
-                title: "Reference Study (all paralogs)",
-                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($9e29a4f60318db7a$var$DynamicIframe, {
-                    url: paralogs_url
-                })
-            }),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tab), {
+                title: `Paralogs`,
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Form), {
+                        children: [
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Check, {
+                                type: "switch",
+                                id: "localAPI",
+                                label: "Local API",
+                                checked: isLocal,
+                                onChange: handleLocalAPIChange
+                            }),
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Form).Group, {
+                                as: (0, $gXNCa$reactbootstrap.Row),
+                                className: "mb-3",
+                                controlId: "formGroupExperiment",
+                                children: [
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Label, {
+                                        column: true,
+                                        sm: 1,
+                                        children: "Experiment"
+                                    }),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Col), {
+                                        sm: 5,
+                                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Select, {
+                                            defaultValue: atlasExperiment,
+                                            onChange: (e)=>setAtlasExperiment(e.target.value),
+                                            children: atlasExperimentList.map((experiment, index)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("option", {
+                                                    value: experiment._id,
+                                                    children: experiment.description || experiment._id
+                                                }, index))
+                                        })
+                                    })
+                                ]
+                            })
+                        ]
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($9e29a4f60318db7a$var$DynamicIframe, {
+                        url: paralogs_url
+                    })
+                ]
+            }, "gxaparalogs"),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Tab), {
                 tabClassName: "gxa",
                 eventKey: "gene",
                 title: "All Studies",
-                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($9e29a4f60318db7a$var$DynamicIframe, {
-                    url: gene_url
-                })
-            }),
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Check, {
+                        type: "switch",
+                        id: "localAPI",
+                        label: "Local API",
+                        checked: isLocal,
+                        onChange: handleLocalAPIChange
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($9e29a4f60318db7a$var$DynamicIframe, {
+                        url: gene_url
+                    })
+                ]
+            }, "gxa"),
             (0, $gXNCa$grameneefpbrowser.haveBAR)(gene) && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tab), {
                 tabClassName: "eFP",
                 eventKey: "eFP",
@@ -2292,11 +2356,12 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
                 children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, ($parcel$interopDefault($gXNCa$grameneefpbrowser))), {
                     gene: gene
                 })
-            })
+            }, "bar")
         ]
     });
 };
-var $9e29a4f60318db7a$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectParalogExpression', 'doRequestParalogExpression', $9e29a4f60318db7a$var$Detail);
+var $9e29a4f60318db7a$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)(// 'selectParalogExpression',
+'selectExpressionStudies', 'doRequestParalogExpression', $9e29a4f60318db7a$var$Detail);
 
 
 
@@ -5517,17 +5582,38 @@ var $261baeb81c4d4d8a$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 const $0f50f369018a42ef$var$auth = (0, $gXNCa$firebaseauth.getAuth)((0, $047461923b1badda$export$a4e2c8f07e884e));
 const $0f50f369018a42ef$var$MAX_GENE_IDS = 1000; // Define the maximum number of gene IDs allowed
 const $0f50f369018a42ef$var$GeneListDisplayComponent = (props)=>{
-    const [savedGeneLists, setSavedGeneLists] = (0, $gXNCa$react.useState)([]);
+    const [publicGeneLists, setPublicGeneLists] = (0, $gXNCa$react.useState)([]);
+    const [privateGeneLists, setPrivateGeneLists] = (0, $gXNCa$react.useState)([]);
     const [error, setError] = (0, $gXNCa$react.useState)(null);
     const [user, setUser] = (0, $gXNCa$react.useState)({});
     (0, $gXNCa$firebaseauth.onAuthStateChanged)($0f50f369018a42ef$var$auth, (user)=>setUser(user));
+    const fetchPrivateGeneLists = async ()=>{
+        try {
+            const token = await user.getIdToken();
+            // Replace this with actual fetch from your backend or storage
+            const response = await fetch(`${props.api}/gene_lists?site=${props.site}&isPublic=false`, {
+                method: 'GET',
+                headers: {
+                    "Content-Type": "application/json",
+                    "Authorization": `Bearer ${token}`
+                }
+            });
+            const result = await response.json();
+            if (response.ok) {
+                setError(null);
+                setPrivateGeneLists(result); // array of saved gene lists
+            } else setError('Error fetching gene lists.');
+        } catch (err) {
+            setError('Failed to fetch private gene lists. Please try again later.');
+        }
+    };
     // Fetch saved gene lists from a backend or local storage
-    const fetchSavedGeneLists = async ()=>{
+    const fetchPublicGeneLists = async ()=>{
         try {
             // Replace this with actual fetch from your backend or storage
-            const response = await fetch(`${props.api}/gene-lists`);
+            const response = await fetch(`${props.api}/gene_lists?site=${props.site}&isPublic=true`);
             const result = await response.json();
-            if (response.ok) setSavedGeneLists(result.savedLists); // Assuming savedLists is an array of saved gene lists
+            if (response.ok) setPublicGeneLists(result); // array of saved gene lists
             else setError('Error fetching gene lists.');
         } catch (err) {
             setError('Failed to fetch gene lists. Please try again later.');
@@ -5535,8 +5621,13 @@ const $0f50f369018a42ef$var$GeneListDisplayComponent = (props)=>{
     };
     // Fetch data when the component is mounted
     (0, $gXNCa$react.useEffect)(()=>{
-        fetchSavedGeneLists();
+        fetchPublicGeneLists();
     }, []);
+    (0, $gXNCa$react.useEffect)(()=>{
+        fetchPrivateGeneLists();
+    }, [
+        user
+    ]);
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
         className: "gene-list-display-component",
         children: [
@@ -5547,7 +5638,7 @@ const $0f50f369018a42ef$var$GeneListDisplayComponent = (props)=>{
                 variant: "danger",
                 children: error
             }),
-            savedGeneLists.length > 0 ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Table), {
+            privateGeneLists.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Table), {
                 striped: true,
                 bordered: true,
                 hover: true,
@@ -5569,13 +5660,13 @@ const $0f50f369018a42ef$var$GeneListDisplayComponent = (props)=>{
                         })
                     }),
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("tbody", {
-                        children: savedGeneLists.map((list, index)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
+                        children: privateGeneLists.map((list, index)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
                                 children: [
                                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
-                                        children: list.name
+                                        children: list.label
                                     }),
                                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
-                                        children: list.genes.length
+                                        children: list.hash
                                     }),
                                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("td", {
                                         children: [
@@ -5586,7 +5677,57 @@ const $0f50f369018a42ef$var$GeneListDisplayComponent = (props)=>{
                                             }),
                                             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
                                                 variant: "danger",
-                                                onClick: ()=>$0f50f369018a42ef$var$deleteGeneList(props.api, list.id),
+                                                onClick: ()=>$0f50f369018a42ef$var$deleteGeneList(props.api, list._id),
+                                                className: "ml-2",
+                                                children: "Delete"
+                                            })
+                                        ]
+                                    })
+                                ]
+                            }, index))
+                    })
+                ]
+            }),
+            publicGeneLists.length > 0 ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Table), {
+                striped: true,
+                bordered: true,
+                hover: true,
+                className: "mt-4",
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("thead", {
+                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
+                            children: [
+                                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
+                                    children: "List Name"
+                                }),
+                                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
+                                    children: "Number of Genes"
+                                }),
+                                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
+                                    children: "Actions"
+                                })
+                            ]
+                        })
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("tbody", {
+                        children: publicGeneLists.map((list, index)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
+                                children: [
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
+                                        children: list.label
+                                    }),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
+                                        children: list.hash
+                                    }),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("td", {
+                                        children: [
+                                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+                                                variant: "info",
+                                                onClick: ()=>$0f50f369018a42ef$var$viewGeneList(list),
+                                                children: "View"
+                                            }),
+                                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+                                                variant: "danger",
+                                                onClick: ()=>$0f50f369018a42ef$var$deleteGeneList(props.api, list._id),
                                                 className: "ml-2",
                                                 children: "Delete"
                                             })
@@ -5611,7 +5752,7 @@ const $0f50f369018a42ef$var$viewGeneList = (list)=>{
 const $0f50f369018a42ef$var$deleteGeneList = async (api, listId)=>{
     if (window.confirm('Are you sure you want to delete this gene list?')) // Replace with the actual delete request
     try {
-        await fetch(`${api}/gene-lists/${listId}`, {
+        await fetch(`${api}/gene_lists/${listId}`, {
             method: 'DELETE'
         });
         alert('Gene list deleted!');
@@ -5660,9 +5801,7 @@ const $0f50f369018a42ef$var$GeneListComponent = (props)=>{
                 headers: {
                     'Content-Type': 'application/json'
                 },
-                body: JSON.stringify({
-                    ids: geneArray
-                })
+                body: JSON.stringify(geneArray)
             });
             const result = await response.json();
             if (result.hash) {
@@ -5688,7 +5827,7 @@ const $0f50f369018a42ef$var$GeneListComponent = (props)=>{
         const queryString = new URLSearchParams(queryParams).toString();
         const token = await user.getIdToken();
         try {
-            const response = await fetch(`${props.api}/gene_list?${queryString}`, {
+            const response = await fetch(`${props.api}/gene_lists?${queryString}`, {
                 method: 'POST',
                 headers: {
                     "Content-Type": "application/json",