gramene-search 2.38.1 → 2.39.0

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;
@@ -9074,6 +9094,38 @@ const $64fad37f770d2bfe$var$TBROWSE_BASE_ZONES = [
     (0, $gXNCa$tbrowse.msaZone),
     (0, $gXNCa$tbrowse.neighborhoodZone)
 ];
+// 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$geneTreeRefs(gene) {
+    const h = gene && gene.homology;
+    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);
@@ -9110,6 +9162,10 @@ 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() {
@@ -9133,6 +9189,12 @@ 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(),
@@ -9196,8 +9258,9 @@ 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];
-        if (!gene.homology) return;
-        const treeId = gene.homology.gene_tree.id;
+        const ref = this.selectedTreeRef(gene);
+        if (!ref) return;
+        const treeId = ref.id;
         const raw = this.props.grameneTrees[treeId];
         if (!raw || !raw.taxon_id) return;
         const adapted = (0, $gXNCa$tbrowse.fromGrameneGenetree)([
@@ -9247,8 +9310,9 @@ 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];
-        if (!gene.homology) return;
-        const treeId = gene.homology.gene_tree.id;
+        const ref = this.selectedTreeRef(gene);
+        if (!ref) return;
+        const treeId = ref.id;
         const raw = this.props.grameneTrees[treeId];
         if (!raw || !raw.taxon_id) return;
         // Lazily compute the adapted tbrowse data the same way renderTBrowse
@@ -9260,13 +9324,13 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
                 raw
             ]);
         }
-        this.fetchNeighborhood(treeId);
+        this.fetchNeighborhood(treeId, ref.field);
         // Only pay for gene-structure data when the genome zone is actually enabled.
         if (this.isGenomeZoneEnabled()) this.fetchGeneStructures(treeId, this._tbrowseData.tree);
         // Same for the per-gene expression attributes zone.
-        if (this.isExpressionZoneEnabled()) this.fetchExprAttrs(treeId, this._tbrowseData.tree);
+        if (this.isExpressionZoneEnabled()) this.fetchExprAttrs(treeId, this._tbrowseData.tree, ref.field);
     }
-    fetchNeighborhood(treeId) {
+    fetchNeighborhood(treeId, field = 'gene_tree') {
         if (this._neighborhoodFetchedFor === treeId) return;
         this._neighborhoodFetchedFor = treeId;
         this.setState({
@@ -9274,8 +9338,13 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         });
         const api = this.props.grameneAPI;
         const url = new URL(`${api}/search`);
-        url.searchParams.set('fl', 'id,name,gene_tree,gene_idx,region,start,end,strand,biotype,system_name,description');
-        url.searchParams.set('fq', `{!graph from=compara_neighbors_10 to=compara_idx_multi maxDepth=1}gene_tree:${treeId}`);
+        const fl = 'id,name,gene_tree,gene_idx,region,start,end,strand,biotype,system_name,description';
+        url.searchParams.set('fl', field === 'gene_tree' ? fl : `${fl},${field}`);
+        // cache=false: as a cached fq the graph query caches its seed inside its own
+        // filterCache computeIfAbsent, and Solr's FastLRUCache throws "Recursive
+        // update" (HTTP 500) whenever the two keys collide — for some trees, until
+        // the seed happens to be cached by another request.
+        url.searchParams.set('fq', `{!graph from=compara_neighbors_10 to=compara_idx_multi maxDepth=1 cache=false}${field}:${treeId}`);
         url.searchParams.set('rows', '100000');
         url.searchParams.set('start', '0');
         fetch(url.toString(), {
@@ -9287,6 +9356,11 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
             return res.json();
         }).then((json)=>{
             if (this._neighborhoodFetchedFor !== treeId) return;
+            // The neighborhood zone colours genes by family from doc.gene_tree; in
+            // a clade tree set the family id lives under the set's own field.
+            if (field !== 'gene_tree' && json && json.response && Array.isArray(json.response.docs)) json.response.docs.forEach((d)=>{
+                if (d[field] && !d.gene_tree) d.gene_tree = d[field];
+            });
             this.setState({
                 neighborhood: (0, $gXNCa$tbrowse.fromGrameneNeighborhood)(json),
                 neighborhoodTreeId: treeId,
@@ -9344,13 +9418,13 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         });
     }
     // Fetch the expression attributes (expr_*__attr_*) for this tree's genes in a
-    // single query: scope by gene_tree and the `expression_attributes` capability
+    // single query: scope by the tree's field and the `expression_attributes` capability
     // so only genes that actually have the data come back (rows high enough to
     // cover the whole tree). Uses /search (not /genes, whose trimmed docs omit the
     // attr fields) with an fl glob so the columns are discovered from the data
     // rather than hard-coded. `tree` is still needed to map gene ids to leaf node
     // ids (see buildExprByNode).
-    fetchExprAttrs(treeId, tree) {
+    fetchExprAttrs(treeId, tree, field = 'gene_tree') {
         if (this._exprAttrsFetchedFor === treeId) return;
         this._exprAttrsFetchedFor = treeId;
         this.setState({
@@ -9359,7 +9433,7 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         const api = this.props.grameneAPI;
         const url = new URL(`${api}/search`);
         url.searchParams.set('q', '*:*');
-        url.searchParams.append('fq', `gene_tree:${treeId}`);
+        url.searchParams.append('fq', `${field}:${treeId}`);
         url.searchParams.append('fq', 'capabilities:expression_attributes');
         url.searchParams.set('fl', 'id,expr_*__attr_*');
         url.searchParams.set('rows', '10000');
@@ -9436,7 +9510,7 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         });
     }
     renderTBrowse() {
-        const treeId = this.gene.homology.gene_tree.id;
+        const treeId = this.treeRef.id;
         // Adapted tbrowse data is computed lazily in maybeFetchTbrowseData
         // (called from lifecycle). If the user just flipped to tbrowse and
         // the lifecycle hasn't fired yet, compute it once here without
@@ -9532,20 +9606,59 @@ 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)
+                    ]
+                })
             ]
         });
     }
     filterAllHomologs() {
         this.props.doReplaceGrameneFilters((0, $047461923b1badda$export$964d88edb00bbcaa)({
             category: 'Gene Tree',
-            fq_field: 'gene_tree',
+            fq_field: this.treeRef.field,
             fq_value: this.tree._id,
             name: `Homologs of ${this.gene.name}`
         }));
@@ -9598,14 +9711,14 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         }
     }
     explorations() {
-        let x = [
+        let x = this.tree ? [
             {
                 name: 'Homologs',
                 category: 'Gene Tree',
                 count: this.tree.geneCount,
                 handleClick: this.filterAllHomologs.bind(this)
             }
-        ];
+        ] : [];
         if (this.orthologs) x.push({
             name: 'Orthologs',
             category: 'Gene Tree',
@@ -9643,7 +9756,32 @@ 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];
-        const treeId = this.gene.homology.gene_tree.id;
+        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.
+            this.tree = undefined;
+            this.orthologs = this.orthologList();
+            this.paralogs = this.paralogList();
+            const explorations = this.explorations();
+            return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $5c2c79352d3d7b81$export$47eb42ff093406d4), {
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $5c2c79352d3d7b81$export$393edc798c47379d), {
+                        children: "No gene tree is available for this gene."
+                    }, "description"),
+                    explorations.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $5c2c79352d3d7b81$export$900f1bfcd1cb6476), {
+                        explorations: explorations
+                    }, "explore"),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $5c2c79352d3d7b81$export$b2e089eb3692b073), {
+                        links: this.links()
+                    }, "links")
+                ]
+            });
+        }
+        const treeId = this.treeRef.id;
         if (!this.props.grameneTrees.hasOwnProperty(treeId)) this.props.doRequestGrameneTree(treeId);
         else {
             const tree = this.props.grameneTrees[treeId];
@@ -9660,10 +9798,10 @@ 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), {
@@ -9676,7 +9814,7 @@ 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);