gramene-search 2.16.0 → 2.18.0

package/dist/index.js

@@ -864,6 +864,17 @@ const $af4441dd29af05df$export$da3188ffd2da2525 = {
         // expansion than orthologs (11 vs 70 for msd2).
         from: 'homology__within_species_paralog',
         to: 'id'
+    },
+    neighborhood: {
+        label: "neighborhood (\xb110)",
+        // Same edge pair TBrowse walks for its neighborhood zone (see
+        // components/results/details/Homology.js). Unlike the homology fields these are
+        // numeric: a gene's compara_neighbors_10 lists the compara_idx values of the 10
+        // genes either side, matched against compara_idx_multi on the target. TBrowse
+        // omits returnRoot, which Solr defaults to true — the same as every expansion
+        // here — so a seed gene expands to 21: itself plus 20 neighbours.
+        from: 'compara_neighbors_10',
+        to: 'compara_idx_multi'
     }
 };
 function $af4441dd29af05df$export$a6dc3fef1cecdf28(node) {
@@ -7411,18 +7422,33 @@ function $541b8b0d8c5501d2$var$logAction(sugg) {
         label: sugg.name
     });
 }
+// The species label under a suggestion. Returns '' rather than throwing when the
+// taxonomy can't explain a taxon: this runs during render, so anything thrown here
+// takes down the whole suggestions panel and the search box looks broken.
+//
+// That is not hypothetical. `grameneTaxonomy` is persisted with a 24h staleAfter, so
+// after a data release adds genomes — v11 added 4558118/4558119/4558120 — every
+// browser still holding the previous release's taxonomy has suggestions referencing
+// taxa it has never heard of. Broad queries ("kinase", "sb") hit all three.
 function $541b8b0d8c5501d2$var$getLowestCommonAncestorName(tids, taxonomy) {
+    if (!Array.isArray(tids) || !taxonomy) return '';
     let lca;
     tids.forEach((tid)=>{
+        const node = taxonomy[tid];
+        if (!node || !Array.isArray(node.ancestors)) return; // unknown taxon: ignore it
         if (!lca) lca = [
-            ...taxonomy[tid].ancestors
+            ...node.ancestors
         ];
         else {
-            let ancestors = new Set(taxonomy[tid].ancestors);
-            while(!ancestors.has(lca[0]))lca.shift();
+            let ancestors = new Set(node.ancestors);
+            // `lca.length &&` matters: with no ancestor in common this shifted an empty
+            // array forever, since ancestors.has(undefined) is never true.
+            while(lca.length && !ancestors.has(lca[0]))lca.shift();
         }
     });
-    return taxonomy[lca[0]].short_name;
+    if (!lca || !lca.length) return '';
+    const root = taxonomy[lca[0]];
+    return root ? root.short_name : '';
 }
 const $541b8b0d8c5501d2$var$TryPan = (props)=>{
     const query = props.query;
@@ -8988,6 +9014,7 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
                         nodeOfInterest: this.gene._id,
                         viewState: effectiveVS,
                         onViewStateChange: onViewStateChange,
+                        densityControls: true,
                         defaultOpenSections: {
                             zones: true,
                             search: true
@@ -20019,6 +20046,7 @@ const $15504f5eba8e73bd$var$TaxDistTbrowse = (props)=>{
                 showHeader: true,
                 rowHeight: 14,
                 fontSize: 10,
+                densityControls: true,
                 autoHeight: true,
                 defaultOpenSections: {
                     search: true,
@@ -20661,7 +20689,7 @@ const $693dd8c7a5607c3a$var$Filter = ({ node: node, moveCopyMode: moveCopyMode,
         // group means "expand whatever this group matches".
         menuItems.push(/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("li", {
             className: "gramene-filter-menu-label",
-            children: "expand filter(s)"
+            children: "expand search"
         }, key++));
         Object.keys((0, $af4441dd29af05df$export$da3188ffd2da2525)).forEach((type)=>{
             const checked = expType === type;