gramene-search 2.38.1 → 2.38.2

package/dist/index.js

@@ -9074,6 +9074,28 @@ 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.
+const $64fad37f770d2bfe$var$NOT_TREE_KEYS = [
+    'homologous_genes',
+    'supertree'
+];
+function $64fad37f770d2bfe$var$geneTreeRef(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;
+}
 class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$react))).Component {
     constructor(props){
         super(props);
@@ -9196,8 +9218,9 @@ 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 = $64fad37f770d2bfe$var$geneTreeRef(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 +9270,9 @@ 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 = $64fad37f770d2bfe$var$geneTreeRef(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 +9284,13 @@ 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 +9298,13 @@ 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 +9316,11 @@ 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 +9378,13 @@ 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 +9393,7 @@ 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 +9470,7 @@ 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
@@ -9545,7 +9579,7 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
     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 +9632,14 @@ 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 +9677,29 @@ 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 = $64fad37f770d2bfe$var$geneTreeRef(this.gene);
+        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];