gramene-search 2.38.2 → 2.39.1

package/dist/index.js

@@ -6351,6 +6351,9 @@ var $d365d8c287ab0c94$export$2e2bcd8739ae039 = $d365d8c287ab0c94$var$ontologyEnr
 //   - expandedDetail: which detail tab is open in the gene-list card
 //   - fullscreen: whether the expanded detail is full-screened
 //   - homology.viewer: 'treevis' | 'tbrowse'
+//   - homology.tree: which of the gene's trees is shown — the homology field
+//     holding it ('gene_tree', or a tree set such as 'wheat'); unset = the
+//     first (gene_tree when the gene has one)
 //   - homology.height: drag-resize height of the homology detail pane
 //   - homology.tbrowse: the tbrowse ViewState (collapsedNodeIds, prunedNodeIds,
 //     swappedNodeIds, compressedNodeIds, nodeOfInterestId, zones, zoneStates,
@@ -6480,6 +6483,14 @@ const $7f865ea0feda21af$var$uiViewState = {
                     return $7f865ea0feda21af$var$setHomology(state, payload.geneId, {
                         viewer: payload.viewer
                     });
+                case 'UI_HOMOLOGY_TREE_SET':
+                    // payload: { geneId, tree }. The tbrowse ViewState belongs to one tree
+                    // (its node ids), so a switch drops it and Homology re-seeds the new
+                    // tree pivoted on the gene.
+                    return $7f865ea0feda21af$var$setHomology(state, payload.geneId, {
+                        tree: payload.tree,
+                        tbrowse: undefined
+                    });
                 case 'UI_HOMOLOGY_HEIGHT_SET':
                     // payload: { geneId, height }
                     return $7f865ea0feda21af$var$setHomology(state, payload.geneId, {
@@ -6542,6 +6553,15 @@ const $7f865ea0feda21af$var$uiViewState = {
                 }
             });
         },
+    doSetHomologyTree: ({ geneId: geneId, tree: tree })=>({ dispatch: dispatch })=>{
+            dispatch({
+                type: 'UI_HOMOLOGY_TREE_SET',
+                payload: {
+                    geneId: geneId,
+                    tree: tree
+                }
+            });
+        },
     doSetHomologyHeight: ({ geneId: geneId, height: height })=>({ dispatch: dispatch })=>{
             dispatch({
                 type: 'UI_HOMOLOGY_HEIGHT_SET',
@@ -6676,7 +6696,7 @@ var $6048209b532f201d$export$2e2bcd8739ae039 = $6048209b532f201d$var$taxTreeView
 //     { geneId,
 //       expandedDetail: string|null,
 //       fullscreen: boolean,
-//       homology: { viewer, height, tbrowse: <ViewState> } | undefined,
+//       homology: { viewer, tree, height, tbrowse: <ViewState> } | undefined,
 //       sequences: { tab, tid, upstream, downstream } | undefined,
 //       expression: { activeTab, atlasExperiment, jgiExperiment,
 //                     jgiAxes: { [jgiExperiment]: { rowFactor, columnFactor } },
@@ -6734,7 +6754,7 @@ const $472fe3745b238881$var$isMeaningfulGene = (entry)=>{
     if (!entry) return false;
     if (entry.expandedDetail) return true;
     if (entry.fullscreen) return true;
-    if (entry.homology && (entry.homology.viewer !== undefined || entry.homology.height !== undefined || entry.homology.tbrowse !== undefined)) return true;
+    if (entry.homology && (entry.homology.viewer !== undefined || entry.homology.tree !== undefined || entry.homology.height !== undefined || entry.homology.tbrowse !== undefined)) return true;
     if (entry.sequences && Object.keys(entry.sequences).length) return true;
     if (entry.expression && Object.keys(entry.expression).length) return true;
     if (entry.primers && Object.keys(entry.primers).length) return true;
@@ -8336,6 +8356,18 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
         studies,
         geneStudyIds
     ]);
+    // Without a baseline study the EBI Studies heatmap has nothing to draw (its
+    // request fails rather than coming back empty), so the tab says so and
+    // points at the differential EBI studies the gene does appear in -- e.g.
+    // Medicago truncatula, whose studies are all differential.
+    const ebiDifferential = (0, $gXNCa$react.useMemo)(()=>{
+        if (!geneStudyIds || !studies) return [];
+        const mine = new Set(geneStudyIds);
+        return studies.filter((e)=>mine.has(e._id) && $9e29a4f60318db7a$var$isDifferential(e) && !$9e29a4f60318db7a$var$isJgiStudy(e)).sort((a, b)=>$9e29a4f60318db7a$var$studyLabel(a) < $9e29a4f60318db7a$var$studyLabel(b) ? -1 : 1);
+    }, [
+        studies,
+        geneStudyIds
+    ]);
     const allJgiKey = JSON.stringify(allJgiStudies.map((e)=>[
             e._id,
             e.name
@@ -8434,7 +8466,43 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
                         role: "status",
                         children: "Loading expression studies\u2026"
                     }),
-                    activeTab === "gene" && studiesSettled && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$grameneatlasheatmap.ExpressionAtlasHeatmap), {
+                    activeTab === "gene" && studiesSettled && !hasEbiBaseline && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                        className: "text-muted small",
+                        role: "status",
+                        children: [
+                            gene.name || gene._id,
+                            " is not in any baseline expression study, so there is no heatmap here.",
+                            ebiDifferential.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+                                children: [
+                                    ' ',
+                                    "It has results in ",
+                                    ebiDifferential.length === 1 ? 'a differential study' : `${ebiDifferential.length} differential studies`,
+                                    " at Expression Atlas:",
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("ul", {
+                                        className: "mt-1 mb-0",
+                                        children: ebiDifferential.map((e)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("li", {
+                                                children: [
+                                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("a", {
+                                                        href: `${$9e29a4f60318db7a$var$EBI_GXA}experiments/${encodeURIComponent(e._id)}/Results?geneQuery=${encodeURIComponent(JSON.stringify([
+                                                            {
+                                                                value: geneQuery
+                                                            }
+                                                        ]))}`,
+                                                        target: "_blank",
+                                                        rel: "noopener noreferrer",
+                                                        children: e.description || e._id
+                                                    }),
+                                                    " (",
+                                                    e._id,
+                                                    ")"
+                                                ]
+                                            }, e._id))
+                                    })
+                                ]
+                            })
+                        ]
+                    }),
+                    activeTab === "gene" && studiesSettled && hasEbiBaseline && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$grameneatlasheatmap.ExpressionAtlasHeatmap), {
                         ...$9e29a4f60318db7a$var$HEATMAP_OPTIONS,
                         resolveUrl: resolveUrl,
                         atlasUrl: atlasUrl,
@@ -9074,28 +9142,38 @@ const $64fad37f770d2bfe$var$TBROWSE_BASE_ZONES = [
     (0, $gXNCa$tbrowse.msaZone),
     (0, $gXNCa$tbrowse.neighborhoodZone)
 ];
-// A gene's tree is either the main Compara tree (homology.gene_tree) or, for
-// genomes in a clade-specific tree set, homology.<tree_set> — e.g. wheat genes
-// carry homology.wheat = {id: 'EplWheatGT_…'}. Solr indexes the tree id under
-// the same name (gene_tree, wheat, oat, …), so `field` is also the fq field.
-// Null when the gene has homologues but no tree at all.
+// A gene's trees: the main Compara tree (homology.gene_tree) and/or trees in
+// clade-specific tree sets, homology.<tree_set> — e.g. a wheat gene may carry
+// gene_tree, homology.wheat = {id: 'EplWheatGT_…'} and homology.barley. Solr
+// indexes each tree id under the same name (gene_tree, wheat, barley, …), so
+// `field` is also the fq field. gene_tree comes first; empty when the gene
+// has homologues but no tree at all.
 const $64fad37f770d2bfe$var$NOT_TREE_KEYS = [
     'homologous_genes',
     'supertree'
 ];
-function $64fad37f770d2bfe$var$geneTreeRef(gene) {
+function $64fad37f770d2bfe$var$geneTreeRefs(gene) {
     const h = gene && gene.homology;
-    if (!h) return null;
-    if (h.gene_tree && h.gene_tree.id) return {
-        field: 'gene_tree',
-        id: h.gene_tree.id
-    };
-    const key = Object.keys(h).find((k)=>!$64fad37f770d2bfe$var$NOT_TREE_KEYS.includes(k) && h[k] && typeof h[k] === 'object' && typeof h[k].id === 'string');
-    return key ? {
-        field: key,
-        id: h[key].id
-    } : null;
+    if (!h) return [];
+    const isTree = (k)=>!$64fad37f770d2bfe$var$NOT_TREE_KEYS.includes(k) && h[k] && typeof h[k] === 'object' && typeof h[k].id === 'string';
+    const keys = Object.keys(h).filter(isTree);
+    keys.sort((a, b)=>a === 'gene_tree' ? -1 : b === 'gene_tree' ? 1 : 0);
+    return keys.map((field)=>({
+            field: field,
+            id: h[field].id,
+            rootTaxonName: h[field].root_taxon_name
+        }));
+}
+// The tree to show: the one picked in the switcher (`field`), else the first.
+function $64fad37f770d2bfe$var$geneTreeRef(gene, field) {
+    const refs = $64fad37f770d2bfe$var$geneTreeRefs(gene);
+    return refs.find((r)=>r.field === field) || refs[0] || null;
 }
+// Switcher label: the tree set and the clade the tree is rooted at.
+const $64fad37f770d2bfe$var$treeLabel = (ref)=>{
+    const set = ref.field === 'gene_tree' ? 'Compara' : ref.field.charAt(0).toUpperCase() + ref.field.slice(1);
+    return ref.rootTaxonName ? `${set} \xb7 ${ref.rootTaxonName}` : set;
+};
 class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$react))).Component {
     constructor(props){
         super(props);
@@ -9132,6 +9210,10 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
     getViewer() {
         return this.getHomologySlice().viewer || 'tbrowse';
     }
+    // The gene's selected tree (see the tree switcher in renderViewerToggle).
+    selectedTreeRef(gene) {
+        return $64fad37f770d2bfe$var$geneTreeRef(gene, this.getHomologySlice().tree);
+    }
     // The genome (gene-structure) zone is opt-in per site via
     // `enable_tbrowse_genome_zone` (defaults to false).
     isGenomeZoneEnabled() {
@@ -9155,6 +9237,12 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         const h = this.getHomologySlice().height;
         return typeof h === 'number' ? h : 600;
     }
+    setTree(field) {
+        this.props.doSetHomologyTree({
+            geneId: this.getGeneId(),
+            tree: field
+        });
+    }
     setViewer(viewer) {
         this.props.doSetHomologyViewer({
             geneId: this.getGeneId(),
@@ -9218,7 +9306,7 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         const id = this.getGeneId();
         if (!this.props.geneDocs.hasOwnProperty(id)) return;
         const gene = this.props.geneDocs[id];
-        const ref = $64fad37f770d2bfe$var$geneTreeRef(gene);
+        const ref = this.selectedTreeRef(gene);
         if (!ref) return;
         const treeId = ref.id;
         const raw = this.props.grameneTrees[treeId];
@@ -9270,7 +9358,7 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         const id = this.getGeneId();
         if (!this.props.geneDocs.hasOwnProperty(id)) return;
         const gene = this.props.geneDocs[id];
-        const ref = $64fad37f770d2bfe$var$geneTreeRef(gene);
+        const ref = this.selectedTreeRef(gene);
         if (!ref) return;
         const treeId = ref.id;
         const raw = this.props.grameneTrees[treeId];
@@ -9566,13 +9654,52 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
                 },
                 children: label
             }, id);
+        // A second row when the gene sits in more than one tree (e.g. a wheat
+        // gene in the Compara, wheat and barley trees).
+        const refs = $64fad37f770d2bfe$var$geneTreeRefs(this.gene);
+        const treeBtn = (ref)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
+                type: "button",
+                title: ref.id,
+                onClick: ()=>this.setTree(ref.field),
+                style: {
+                    padding: '4px 10px',
+                    marginRight: 4,
+                    fontSize: 12,
+                    border: '1px solid #ccc',
+                    background: this.treeRef.field === ref.field ? '#2878dc' : '#fff',
+                    color: this.treeRef.field === ref.field ? '#fff' : '#222',
+                    cursor: 'pointer',
+                    borderRadius: 3
+                },
+                children: $64fad37f770d2bfe$var$treeLabel(ref)
+            }, ref.field);
         return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
             style: {
                 margin: '8px 0'
             },
             children: [
-                btn('tbrowse', 'TBrowse'),
-                btn('treevis', 'TreeVis')
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                    children: [
+                        btn('tbrowse', 'TBrowse'),
+                        btn('treevis', 'TreeVis')
+                    ]
+                }),
+                refs.length > 1 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                    className: "homology-tree-switcher",
+                    style: {
+                        marginTop: 6
+                    },
+                    children: [
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                            style: {
+                                fontSize: 12,
+                                marginRight: 6
+                            },
+                            children: "Gene tree:"
+                        }),
+                        refs.map(treeBtn)
+                    ]
+                })
             ]
         });
     }
@@ -9677,7 +9804,10 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         const id = this.props.searchResult.id;
         if (!this.props.geneDocs.hasOwnProperty(id)) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Spinner), {});
         this.gene = this.props.geneDocs[id];
-        this.treeRef = $64fad37f770d2bfe$var$geneTreeRef(this.gene);
+        this.treeRef = this.selectedTreeRef(this.gene);
+        // Recomputed below only once the selected tree has loaded, so a switch to
+        // a tree still in flight never draws the previous one.
+        this.tree = undefined;
         if (!this.treeRef) {
             // Homologues but no tree (some pan-genome assemblies): offer the
             // ortholog/paralog searches instead of a phylogram.
@@ -9716,10 +9846,10 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
                 /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $5c2c79352d3d7b81$export$393edc798c47379d), {
                     children: "This phylogram shows the relationships between this gene and others similar to it, as determined by Ensembl Compara."
                 }, "description"),
-                this.tree && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $5c2c79352d3d7b81$export$7c6e2c02157bb7d2), {
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $5c2c79352d3d7b81$export$7c6e2c02157bb7d2), {
                     children: [
                         this.renderViewerToggle(),
-                        this.getViewer() === 'tbrowse' ? this.renderTBrowse() : this.renderTreeVis()
+                        !this.tree ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Spinner), {}) : this.getViewer() === 'tbrowse' ? this.renderTBrowse() : this.renderTreeVis()
                     ]
                 }, "content"),
                 this.tree && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $5c2c79352d3d7b81$export$900f1bfcd1cb6476), {
@@ -9732,7 +9862,7 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         });
     }
 }
-var $64fad37f770d2bfe$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneTaxonomy', 'selectGrameneTrees', 'selectGrameneGenomes', 'selectGrameneAPI', 'selectConfiguration', 'selectCuration', 'selectUiViewState', 'doRequestGrameneTree', 'doSetHomologyViewer', 'doSetHomologyHeight', 'doSetHomologyTbrowseViewState', 'doAcceptGrameneSuggestion', 'doReplaceGrameneFilters', $64fad37f770d2bfe$var$Homology);
+var $64fad37f770d2bfe$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneTaxonomy', 'selectGrameneTrees', 'selectGrameneGenomes', 'selectGrameneAPI', 'selectConfiguration', 'selectCuration', 'selectUiViewState', 'doRequestGrameneTree', 'doSetHomologyViewer', 'doSetHomologyTree', 'doSetHomologyHeight', 'doSetHomologyTbrowseViewState', 'doAcceptGrameneSuggestion', 'doReplaceGrameneFilters', $64fad37f770d2bfe$var$Homology);