gramene-search 2.19.0 → 2.20.1

package/dist/index.js

@@ -370,6 +370,50 @@ $9d9aeaf9299e61a1$var$grameneMaps.reactGrameneMaps = (0, $gXNCa$reduxbundler.cre
         actionCreator: 'doFetchGrameneMaps'
     };
 });
+/**
+ * The site's reference genome, derived from /maps rather than configured per site.
+ *
+ * `is_anchor` marks the reference genome of a species group and `anchor_taxon_id`
+ * is that group's bare species id. Note the two are deliberately different scales:
+ * an anchor's own taxon_id is genome-level (4558006) and never equals its
+ * anchor_taxon_id (4558), so the anchor is found by group, not by matching ids.
+ *
+ * A deployment is whichever group it carries the most genomes for — sorghum_v11
+ * has 120 of 128 genomes under 4558, whose anchor is 4558006 (Sb bicolor BTx623
+ * v3). Deriving it this way keeps every site correct across releases; the value
+ * that used to be configured had drifted to 4558001, a non-anchor wild relative
+ * (Sb verticilliflorum 353).
+ *
+ * Returns null in two cases callers must tolerate: before /maps has loaded, and
+ * on a release whose /maps carries no anchor fields at all — gramene main is like
+ * that today (114 genomes, not one with is_anchor), so that deployment simply has
+ * no reference genome rather than a wrong one.
+ *
+ * Verified across deployments: sorghum 4558006 (Sb bicolor BTx623 v3),
+ * oryza 39947013 and maize 4577003 (both Nipponbare / B73 v5). The genome-level
+ * id differs per release, which is the reason to resolve it rather than pin it.
+ */ $9d9aeaf9299e61a1$var$grameneMaps.selectTargetTaxonId = (0, $gXNCa$reduxbundler.createSelector)('selectGrameneMaps', (grameneMaps)=>{
+    if (!grameneMaps) return null;
+    const genomes = Object.values(grameneMaps);
+    if (!genomes.length) return null;
+    const perGroup = {};
+    genomes.forEach((g)=>{
+        if (!g || g.anchor_taxon_id === undefined || g.anchor_taxon_id === null) return;
+        const k = String(g.anchor_taxon_id);
+        perGroup[k] = (perGroup[k] || 0) + 1;
+    });
+    let group = null;
+    let best = -1;
+    Object.keys(perGroup).forEach((k)=>{
+        if (perGroup[k] > best) {
+            best = perGroup[k];
+            group = k;
+        }
+    });
+    if (group === null) return null;
+    const anchor = genomes.find((g)=>g && g.is_anchor && String(g.anchor_taxon_id) === group);
+    return anchor ? anchor.taxon_id : null;
+});
 const $9d9aeaf9299e61a1$var$expressionStudies = (0, $gXNCa$reduxbundler.createAsyncResourceBundle)({
     name: 'expressionStudies',
     actionBaseType: 'EXPRESSION_STUDIES',
@@ -672,50 +716,6 @@ const $9d9aeaf9299e61a1$var$grameneTaxDist = {
         return null;
     })
 };
-// this query will give the sorghum orthologs of AT1G01260
-// want to provide these on non-sorghum genes if available
-// http://data.gramene.org/search?q=homology__all_orthologs:AT1G01260&fq=taxon_id:4558&fl=id
-const $9d9aeaf9299e61a1$var$grameneOrthologs = {
-    name: 'grameneOrthologs',
-    getReducer: ()=>{
-        const initialState = {};
-        return (state = initialState, { type: type, payload: payload })=>{
-            let newState;
-            switch(type){
-                case 'GRAMENE_ORTHOLOGS_REQUESTED':
-                    if (!state.hasOwnProperty(payload)) {
-                        newState = Object.assign({}, state);
-                        newState[payload] = [];
-                        return newState;
-                    }
-                    break;
-                case 'GRAMENE_ORTHOLOGS_RECEIVED':
-                    return Object.assign({}, state, payload);
-            }
-            return state;
-        };
-    },
-    doRequestOrthologs: (geneId)=>({ dispatch: dispatch, store: store })=>{
-            const orthologs = store.selectGrameneOrthologs();
-            if (!orthologs.hasOwnProperty(geneId)) {
-                dispatch({
-                    type: 'GRAMENE_ORTHOLOGS_REQUESTED',
-                    payload: geneId
-                });
-                const API = store.selectGrameneAPI();
-                const taxonId = store.selectTargetTaxonId();
-                fetch(`${API}/search?q=homology__all_orthologs:${geneId}&fq=taxon_id:${taxonId}&fl=id`).then((res)=>res.json()).then((res)=>{
-                    let newOrthologs = {};
-                    newOrthologs[geneId] = res.response.docs.map((d)=>d.id);
-                    dispatch({
-                        type: 'GRAMENE_ORTHOLOGS_RECEIVED',
-                        payload: newOrthologs
-                    });
-                });
-            }
-        },
-    selectGrameneOrthologs: (state)=>state.grameneOrthologs
-};
 const $9d9aeaf9299e61a1$var$grameneParalogs = {
     name: 'grameneParalogs',
     getReducer: ()=>{
@@ -819,7 +819,6 @@ $9d9aeaf9299e61a1$export$2e2bcd8739ae039 = [
     $9d9aeaf9299e61a1$var$grameneMaps,
     $9d9aeaf9299e61a1$var$grameneTaxonomy,
     $9d9aeaf9299e61a1$var$grameneTaxDist,
-    $9d9aeaf9299e61a1$var$grameneOrthologs,
     $9d9aeaf9299e61a1$var$grameneParalogs,
     $9d9aeaf9299e61a1$var$grameneGermplasm,
     $9d9aeaf9299e61a1$var$expressionSamples,
@@ -4912,7 +4911,6 @@ const $4b8473139e48e77e$export$c6dbe9be8c8b382e = {
         fg: '#c0392b'
     }
 };
-const $4b8473139e48e77e$export$39a35029fe99c21 = '#d35400'; // specific-to dot / enhanced-in outline
 function $4b8473139e48e77e$export$8ca7625ba2054603(tokens) {
     const out = {};
     (tokens || []).forEach((t)=>{
@@ -8196,7 +8194,7 @@ const $5c2c79352d3d7b81$export$b2e089eb3692b073 = (props)=>/*#__PURE__*/ (0, $gX
 // Host-defined tbrowse zone for the Homology gene tree, redesigned to compare
 // expression across a gene family. Three parts, aligned to the tree leaves:
 //   1. a gene × organ heatmap of ordinal expression levels (expr_organ_level),
-//      with markers on each gene's tissue-specific / -enhanced organs;
+//      tissue-specific / -enhanced organs are noted in cell tooltips;
 //   2. a Max TPM column (expr_max_tpm), log-scaled magnitude;
 //   3. a Stress column of ↑activated / ↓repressed condition chips
 //      (expr_activated_by / expr_repressed_by).
@@ -8388,29 +8386,17 @@ const $cd8bc494277e92a4$var$OrganCell = ({ organ: organ, gene: gene })=>{
     const enhanced = !!(gene && gene.enhancedIn.has(organ));
     const title = level ? `${(0, $4b8473139e48e77e$export$50c1f966fd3af83e)(organ)}: ${(0, $4b8473139e48e77e$export$433053e2c141d410)[level] || level}${specific ? " \xb7 specific" : enhanced ? " \xb7 enhanced" : ''}` : `${(0, $4b8473139e48e77e$export$50c1f966fd3af83e)(organ)}: not assayed`;
     const style = {
-        position: 'relative',
         width: $cd8bc494277e92a4$var$ORGAN_CELL_W,
         height: '100%',
         boxSizing: 'border-box',
         background: level ? (0, $4b8473139e48e77e$export$b352e11f7a2ac9c5)[level] || 'transparent' : 'transparent',
         borderRight: $cd8bc494277e92a4$var$gridBorder
     };
-    // enhanced-in: thin outline; specific-to (stronger): corner dot.
-    if (enhanced && !specific) style.boxShadow = `inset 0 0 0 1px ${0, $4b8473139e48e77e$export$39a35029fe99c21}`;
+    // Tissue-specific / -enhanced organs are reported in the cell's tooltip rather
+    // than with a marker, so the grid reads purely as expression level.
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
         title: title,
-        style: style,
-        children: specific && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
-            style: {
-                position: 'absolute',
-                top: 1,
-                right: 1,
-                width: 4,
-                height: 4,
-                borderRadius: '50%',
-                background: (0, $4b8473139e48e77e$export$39a35029fe99c21)
-            }
-        })
+        style: style
     });
 };
 const $cd8bc494277e92a4$var$StressCell = ({ gene: gene, width: width })=>{
@@ -11484,10 +11470,6 @@ class $6c5c4f90059875bf$var$Gene extends (0, ($parcel$interopDefault($gXNCa$reac
         const panSite = this.props.config.panSite;
         const searchResult = this.props.searchResult;
         const taxName = this.props.taxName;
-        // let orthologs='';
-        // if (this.props.orthologs && this.props.orthologs.hasOwnProperty(searchResult.id)) {
-        //   orthologs = this.props.orthologs[searchResult.id].join(', ');
-        // }
         const numWordsInDescription = searchResult.description.split(' ').length;
         return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
             className: "result-gene",
@@ -11646,8 +11628,6 @@ const $6c5c4f90059875bf$var$GeneList = (props)=>{
                         taxName: props.grameneTaxonomy[g.taxon_id].name,
                         geneDocs: props.grameneGenes,
                         requestGene: props.doRequestGrameneGene,
-                        requestOrthologs: props.doRequestOrthologs,
-                        orthologs: props.grameneOrthologs,
                         taxLut: props.grameneTaxonomy,
                         expandedDetail: props.grameneSearch.response.numFound === 1 && g.can_show.homology ? 'homology' : null
                     }, idx)),
@@ -11659,7 +11639,7 @@ const $6c5c4f90059875bf$var$GeneList = (props)=>{
     }
     return null;
 };
-var $6c5c4f90059875bf$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectConfiguration', 'selectGrameneSearch', 'selectGrameneTaxonomy', 'selectGrameneGenes', 'selectGrameneOrthologs', 'selectGrameneSearchOffset', 'selectGrameneSearchRows', 'doRequestGrameneGene', 'doRequestOrthologs', 'doRequestResultsPage', $6c5c4f90059875bf$var$GeneList);
+var $6c5c4f90059875bf$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectConfiguration', 'selectGrameneSearch', 'selectGrameneTaxonomy', 'selectGrameneGenes', 'selectGrameneSearchOffset', 'selectGrameneSearchRows', 'doRequestGrameneGene', 'doRequestResultsPage', $6c5c4f90059875bf$var$GeneList);
 
 
 
@@ -18083,14 +18063,11 @@ const $8f8e530286a37ce9$var$AttrTableViewCmp = (props)=>{
                             return `${(0, $4b8473139e48e77e$export$50c1f966fd3af83e)(o)}: ${(0, $4b8473139e48e77e$export$433053e2c141d410)[lvl] || lvl}${sp}`;
                         },
                         comparator: (a, b)=>((0, $4b8473139e48e77e$export$a61929d6d484c6d4)[a] ?? -1) - ((0, $4b8473139e48e77e$export$a61929d6d484c6d4)[b] ?? -1),
-                        cellStyle: (p)=>{
-                            const style = {
+                        // Specific / enhanced are reported in the tooltip above rather than
+                        // with an outline, so the grid reads purely as expression level.
+                        cellStyle: (p)=>({
                                 background: p.value ? (0, $4b8473139e48e77e$export$b352e11f7a2ac9c5)[p.value] || 'transparent' : 'transparent'
-                            };
-                            if (p.data && p.data._specific.has(o)) style.boxShadow = `inset 0 0 0 2px ${0, $4b8473139e48e77e$export$39a35029fe99c21}`;
-                            else if (p.data && p.data._enhanced.has(o)) style.boxShadow = `inset 0 0 0 1px ${0, $4b8473139e48e77e$export$39a35029fe99c21}`;
-                            return style;
-                        }
+                            })
                     });
                 });
                 return;