gramene-search 2.18.3 → 2.20.0

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,
@@ -11484,10 +11483,6 @@ 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 +11641,6 @@ 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 +11652,7 @@ 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);
 
 
 
@@ -13176,7 +13169,540 @@ var $261baeb81c4d4d8a$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 
 
 
-const $0f50f369018a42ef$var$MAX_GENE_IDS = 1000; // Define the maximum number of gene IDs allowed
+
+
+
+
+
+// Conflict rows rendered before the "show N more" cap, mirroring the Refine
+// sidebar's INITIAL_VISIBLE. A large paste can produce hundreds of conflicts.
+const $3b525b9a0ec89bcb$var$INITIAL_VISIBLE = 25;
+// Candidates shown per row before collapsing. Nothing guarantees 15 is the ceiling.
+const $3b525b9a0ec89bcb$var$MAX_CANDIDATES = 50;
+// Genome bulk buttons offered. More than this and the toolbar is worse than the rows.
+const $3b525b9a0ec89bcb$var$MAX_GENOME_ACTIONS = 6;
+// A collapsible bucket with a count, following facets/FacetCounts.js FacetGroup.
+// An empty bucket renders nothing rather than an empty heading.
+const $3b525b9a0ec89bcb$var$Bucket = ({ title: title, count: count, tone: tone, defaultOpen: defaultOpen, actions: actions, children: children })=>{
+    const [open, setOpen] = (0, $gXNCa$react.useState)(!!defaultOpen);
+    if (!count) return null;
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        className: `glr-bucket glr-bucket-${tone}`,
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                className: "glr-bucket-header",
+                onClick: ()=>setOpen(!open),
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "glr-caret",
+                        children: open ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reacticonsbs.BsChevronDown), {}) : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reacticonsbs.BsChevronRight), {})
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "glr-bucket-title",
+                        children: title
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "glr-bucket-count",
+                        children: count.toLocaleString()
+                    }),
+                    actions && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "glr-bucket-actions",
+                        children: actions
+                    })
+                ]
+            }),
+            open && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                className: "glr-bucket-body",
+                children: children
+            })
+        ]
+    });
+};
+/** "sorghum_bicolort2tcas" -> "Sorghum bicolort2tcas" */ function $3b525b9a0ec89bcb$var$speciesLabel(systemName) {
+    if (!systemName) return null;
+    const s = systemName.replace(/_/g, ' ');
+    return s.charAt(0).toUpperCase() + s.slice(1);
+}
+/**
+ * Pure resolver for a validation response.
+ *
+ * `choices` is keyed by INDEX into `ambiguous`, not by the input string: a pasted
+ * token can be anything, and `obj['__proto__'] = [...]` on a plain object sets the
+ * prototype instead of a key.
+ *
+ * An index with NO entry keeps *all* of that input's matches — the "nothing is
+ * silently dropped" default. An index mapped to `[]` means the user explicitly
+ * dropped the row, which is why every read tests `undefined` rather than falsiness.
+ */ const $3b525b9a0ec89bcb$var$GeneListResolver = ({ validation: validation, choices: choices, meta: meta, onChange: onChange })=>{
+    const [query, setQuery] = (0, $gXNCa$react.useState)('');
+    const [showAll, setShowAll] = (0, $gXNCa$react.useState)(false);
+    const [expanded, setExpanded] = (0, $gXNCa$react.useState)({});
+    const { resolved: resolved, ambiguous: ambiguous, unknown: unknown } = validation;
+    const keptFor = (i, a)=>choices[i] === undefined ? a.matches : choices[i];
+    const setKept = (i, a, next)=>{
+        const c = {
+            ...choices
+        };
+        // Drop back to the default when everything is kept, so "untouched" and
+        // "explicitly kept all" stay indistinguishable and the state stays small.
+        if (next.length === a.matches.length) delete c[i];
+        else c[i] = next;
+        onChange(c);
+    };
+    const toggle = (i, a, id)=>{
+        const cur = keptFor(i, a);
+        setKept(i, a, cur.indexOf(id) === -1 ? [
+            ...cur,
+            id
+        ] : cur.filter((x)=>x !== id));
+    };
+    /**
+   * Which genomes would actually narrow something.
+   *
+   * A plain "prefer sorghum" button is useless on this index: 94 of its ~100
+   * genomes are sorghum accessions, so a conflict like Sobic.001G000200 — whose
+   * candidates are sorghum_bicolor and sorghum_bicolort2tcas — is entirely
+   * sorghum on both sides. The useful axis is the individual genome, and only
+   * those that would change a row are worth offering.
+   */ const genomeActions = (0, $gXNCa$react.useMemo)(()=>{
+        const tally = new Map();
+        ambiguous.forEach((a)=>{
+            const names = new Set();
+            a.matches.forEach((id)=>{
+                const d = meta[id];
+                if (d && d.system_name) names.add(d.system_name);
+            });
+            names.forEach((sn)=>{
+                const kept = a.matches.filter((id)=>meta[id] && meta[id].system_name === sn);
+                // Only counts if it narrows: keeping every candidate is a no-op.
+                if (kept.length && kept.length < a.matches.length) tally.set(sn, (tally.get(sn) || 0) + 1);
+            });
+        });
+        return [
+            ...tally.entries()
+        ].sort((x, y)=>y[1] - x[1]).slice(0, $3b525b9a0ec89bcb$var$MAX_GENOME_ACTIONS);
+    }, [
+        ambiguous,
+        meta
+    ]);
+    const applyGenome = (systemName)=>(e)=>{
+            e.stopPropagation();
+            const c = {
+                ...choices
+            };
+            ambiguous.forEach((a, i)=>{
+                const kept = a.matches.filter((id)=>meta[id] && meta[id].system_name === systemName);
+                // Rows with no candidate in this genome are left exactly as they are,
+                // rather than emptied.
+                if (kept.length && kept.length < a.matches.length) c[i] = kept;
+            });
+            onChange(c);
+        };
+    const bulk = (mode)=>(e)=>{
+            // These buttons sit inside the clickable header; don't collapse the section.
+            e.stopPropagation();
+            if (mode === 'all') return onChange({});
+            const c = {};
+            ambiguous.forEach((a, i)=>{
+                if (mode === 'first' && a.matches.length > 1) c[i] = [
+                    a.matches[0]
+                ];
+                if (mode === 'none') c[i] = [];
+            });
+            onChange(c);
+        };
+    const filtered = (0, $gXNCa$react.useMemo)(()=>{
+        const q = query.trim().toLowerCase();
+        const withIndex = ambiguous.map((a, i)=>({
+                a: a,
+                i: i
+            }));
+        if (!q) return withIndex;
+        return withIndex.filter(({ a: a })=>a.input.toLowerCase().indexOf(q) !== -1 || a.matches.some((id)=>id.toLowerCase().indexOf(q) !== -1));
+    }, [
+        ambiguous,
+        query
+    ]);
+    const shown = showAll ? filtered : filtered.slice(0, $3b525b9a0ec89bcb$var$INITIAL_VISIBLE);
+    const candidate = (i, a, id)=>{
+        const doc = meta[id];
+        const kept = keptFor(i, a).indexOf(id) !== -1;
+        const species = $3b525b9a0ec89bcb$var$speciesLabel(doc && doc.system_name);
+        return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("label", {
+            className: `glr-candidate${kept ? ' glr-candidate-kept' : ''}`,
+            children: [
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("input", {
+                    type: "checkbox",
+                    checked: kept,
+                    onChange: ()=>toggle(i, a, id)
+                }),
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                    className: "glr-candidate-id",
+                    children: id
+                }),
+                species ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                    className: "glr-candidate-species",
+                    children: species
+                }) : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                    className: "glr-candidate-species glr-muted",
+                    children: "\u2026"
+                }),
+                doc && doc.description && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                    className: "glr-candidate-desc",
+                    title: doc.description,
+                    children: doc.description
+                }),
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
+                    type: "button",
+                    className: "glr-only",
+                    title: "Keep only this one",
+                    onClick: ()=>setKept(i, a, [
+                            id
+                        ]),
+                    children: "only"
+                })
+            ]
+        }, id);
+    };
+    const row = ({ a: a, i: i })=>{
+        const kept = keptFor(i, a);
+        // Long candidate lists start collapsed so a 15-match row doesn't bury the rest.
+        const isOpen = expanded[i] !== undefined ? expanded[i] : a.matches.length <= 3;
+        const visible = isOpen ? a.matches.slice(0, $3b525b9a0ec89bcb$var$MAX_CANDIDATES) : [];
+        return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+            className: "glr-row",
+            children: [
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                    className: "glr-input",
+                    children: [
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
+                            type: "button",
+                            className: "glr-row-toggle",
+                            onClick: ()=>setExpanded((s)=>({
+                                        ...s,
+                                        [i]: !isOpen
+                                    })),
+                            children: isOpen ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reacticonsbs.BsChevronDown), {}) : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reacticonsbs.BsChevronRight), {})
+                        }),
+                        a.input,
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Badge), {
+                            bg: kept.length === 0 ? 'danger' : 'secondary',
+                            className: "glr-input-count",
+                            children: [
+                                kept.length,
+                                "/",
+                                a.matches.length
+                            ]
+                        })
+                    ]
+                }),
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                    className: "glr-candidates",
+                    children: isOpen ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+                        children: [
+                            visible.map((id)=>candidate(i, a, id)),
+                            a.matches.length > $3b525b9a0ec89bcb$var$MAX_CANDIDATES && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+                                className: "glr-hint",
+                                children: [
+                                    "\u2026 ",
+                                    a.matches.length - $3b525b9a0ec89bcb$var$MAX_CANDIDATES,
+                                    " more. Search to narrow."
+                                ]
+                            }),
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+                                className: "glr-row-bulk",
+                                children: [
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
+                                        type: "button",
+                                        className: "glr-only",
+                                        onClick: ()=>setKept(i, a, a.matches),
+                                        children: "all"
+                                    }),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
+                                        type: "button",
+                                        className: "glr-only",
+                                        onClick: ()=>setKept(i, a, []),
+                                        children: "none"
+                                    })
+                                ]
+                            })
+                        ]
+                    }) : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+                        className: "glr-collapsed",
+                        children: [
+                            a.matches.length,
+                            " candidates \u2014 ",
+                            kept.length === a.matches.length ? 'all kept' : `${kept.length} kept`
+                        ]
+                    })
+                })
+            ]
+        }, i);
+    };
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        className: "glr",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)($3b525b9a0ec89bcb$var$Bucket, {
+                title: "Conflicts \u2014 one identifier, several genes",
+                count: ambiguous.length,
+                tone: "warn",
+                defaultOpen: true,
+                actions: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+                    children: [
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+                            size: "sm",
+                            variant: "outline-secondary",
+                            onClick: bulk('first'),
+                            children: "Keep first"
+                        }),
+                        ' ',
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+                            size: "sm",
+                            variant: "outline-secondary",
+                            onClick: bulk('none'),
+                            children: "Drop all"
+                        }),
+                        ' ',
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+                            size: "sm",
+                            variant: "outline-secondary",
+                            onClick: bulk('all'),
+                            children: "Reset"
+                        })
+                    ]
+                }),
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("p", {
+                        className: "glr-hint",
+                        children: [
+                            "These identifiers match more than one gene. ",
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("strong", {
+                                children: "All matches are kept unless you narrow them"
+                            }),
+                            " \u2014 untick what you don't want, or use",
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
+                                children: " only"
+                            }),
+                            " to keep a single gene."
+                        ]
+                    }),
+                    genomeActions.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                        className: "glr-genomes",
+                        children: [
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                                className: "glr-hint glr-genomes-label",
+                                children: "Keep only matches from:"
+                            }),
+                            genomeActions.map(([sn, n])=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Button), {
+                                    size: "sm",
+                                    variant: "outline-primary",
+                                    className: "glr-genome-btn",
+                                    onClick: applyGenome(sn),
+                                    children: [
+                                        $3b525b9a0ec89bcb$var$speciesLabel(sn),
+                                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Badge), {
+                                            bg: "light",
+                                            text: "dark",
+                                            className: "glr-genome-count",
+                                            children: [
+                                                "narrows ",
+                                                n.toLocaleString()
+                                            ]
+                                        })
+                                    ]
+                                }, sn))
+                        ]
+                    }),
+                    ambiguous.length > $3b525b9a0ec89bcb$var$INITIAL_VISIBLE && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Control, {
+                        type: "search",
+                        size: "sm",
+                        className: "glr-search",
+                        placeholder: "Search conflicts\u2026",
+                        value: query,
+                        onChange: (e)=>{
+                            setQuery(e.target.value);
+                            setShowAll(false);
+                        }
+                    }),
+                    shown.map(row),
+                    filtered.length > shown.length && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("button", {
+                        type: "button",
+                        className: "glr-more",
+                        onClick: ()=>setShowAll(true),
+                        children: [
+                            "show ",
+                            (filtered.length - shown.length).toLocaleString(),
+                            " more"
+                        ]
+                    }),
+                    query && filtered.length === 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("p", {
+                        className: "glr-hint",
+                        children: [
+                            "No conflicts match \u201C",
+                            query,
+                            "\u201D."
+                        ]
+                    })
+                ]
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($3b525b9a0ec89bcb$var$Bucket, {
+                title: "Resolved",
+                count: resolved.length,
+                tone: "ok",
+                defaultOpen: false,
+                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                    className: "glr-resolved",
+                    children: resolved.map((r, i)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                            className: "glr-resolved-row",
+                            children: [
+                                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                                    className: "glr-resolved-input",
+                                    children: r.input
+                                }),
+                                r.input !== r.id && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+                                    children: [
+                                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                                            className: "glr-arrow",
+                                            children: "\u2192"
+                                        }),
+                                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                                            className: "glr-resolved-id",
+                                            children: r.id
+                                        })
+                                    ]
+                                })
+                            ]
+                        }, i))
+                })
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)($3b525b9a0ec89bcb$var$Bucket, {
+                title: "Not recognised",
+                count: unknown.length,
+                tone: "bad",
+                defaultOpen: false,
+                actions: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+                    size: "sm",
+                    variant: "outline-secondary",
+                    onClick: (e)=>{
+                        e.stopPropagation();
+                        navigator.clipboard && navigator.clipboard.writeText(unknown.join('\n'));
+                    },
+                    children: "Copy"
+                }),
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("p", {
+                        className: "glr-hint",
+                        children: "No gene matches these. Matching is case-sensitive for stable IDs, so a lowercased ID may not be found even when the gene exists."
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("pre", {
+                        className: "glr-unknown",
+                        children: unknown.join('\n')
+                    })
+                ]
+            })
+        ]
+    });
+};
+var $3b525b9a0ec89bcb$export$2e2bcd8739ae039 = $3b525b9a0ec89bcb$var$GeneListResolver;
+
+
+// Client for the gene-lists API ({api}/gene_lists*).
+//
+// Mirrors the shape of bundles/savedViews.js: Firebase Bearer token, one
+// status -> message mapper so every call site reports failures the same way, and
+// JSON request bodies. Deliberately a plain module rather than a redux bundle —
+// the feature is self-contained in UserGeneLists and shares no state.
+// Server-side limits, mirrored so we can say something useful instead of
+// surfacing a bare 400.
+const $4abf453405c18681$export$7fadd81f3363fc57 = 6000;
+const $4abf453405c18681$export$7f2835aa6d834dde = 255;
+// Candidate hydration passes ids through the URL. ~500 ids is a 414 (the URL
+// crosses ~8.5KB), so batch well under that.
+const $4abf453405c18681$var$HYDRATE_BATCH = 150;
+function $4abf453405c18681$export$cbb0be6dabd4295(action, status) {
+    if (status === 401) return new Error(`${action} failed \u{2014} please sign in again.`);
+    if (status === 404) return new Error(`${action} failed \u{2014} that list no longer exists.`);
+    if (status === 405) return new Error('Gene lists are not available on this server yet.');
+    if (status === 502 || status === 503) return new Error(`${action} failed \u{2014} the gene index is unreachable. Try again shortly.`);
+    return new Error(`${action} failed (${status})`);
+}
+// The API returns {message} on most 4xx; prefer it, since it names the offending
+// field (e.g. which limit was exceeded).
+async function $4abf453405c18681$var$readError(res, action) {
+    try {
+        const body = await res.json();
+        if (body && body.message) return new Error(body.message);
+    } catch (e) {
+    // not JSON — fall through to the status mapper
+    }
+    return $4abf453405c18681$export$cbb0be6dabd4295(action, res.status);
+}
+async function $4abf453405c18681$export$6c06d9a9d837c44e(api, ids) {
+    const res = await fetch(`${api}/gene_lists/validate`, {
+        method: 'POST',
+        headers: {
+            'Content-Type': 'application/json'
+        },
+        body: JSON.stringify(ids)
+    });
+    if (!res.ok) throw await $4abf453405c18681$var$readError(res, 'Validation');
+    const body = await res.json();
+    // Be strict about the contract. A server still returning the old
+    // {ids, missing, hash} shape must fail here and say so, rather than quietly
+    // validating nothing — which is exactly how the previous client broke.
+    if (!body || !Array.isArray(body.resolved)) throw new Error('Unexpected response from the validation service (is the server up to date?).');
+    return {
+        resolved: body.resolved || [],
+        ambiguous: body.ambiguous || [],
+        unknown: body.unknown || []
+    };
+}
+async function $4abf453405c18681$export$41928ff990e251ce(api, ids) {
+    const unique = [
+        ...new Set(ids)
+    ].filter(Boolean);
+    const out = {};
+    for(let i = 0; i < unique.length; i += $4abf453405c18681$var$HYDRATE_BATCH){
+        const batch = unique.slice(i, i + $4abf453405c18681$var$HYDRATE_BATCH);
+        // {!terms} takes its values literally, so no id needs escaping, and it sits in
+        // `fq`, where Solr local params are reliable.
+        const fq = encodeURIComponent(`{!terms f=id}${batch.join(',')}`);
+        // `rows` is mandatory. Without it the endpoint answers with its default of 20
+        // and the rest of the batch silently disappears.
+        const url = `${api}/search?q=*:*&fq=${fq}&rows=${batch.length}` + `&fl=id,name,system_name,description`;
+        try {
+            const res = await fetch(url);
+            if (!res.ok) continue;
+            const body = await res.json();
+            const docs = body && body.response && body.response.docs || [];
+            docs.forEach((d)=>{
+                if (d && d.id) out[d.id] = d;
+            });
+        } catch (e) {
+        // leave this batch un-hydrated
+        }
+    }
+    return out;
+}
+async function $4abf453405c18681$export$87f42b3480ee6c49(api, token, { label: label, site: site, isPublic: isPublic, ids: ids }) {
+    const res = await fetch(`${api}/gene_lists`, {
+        method: 'POST',
+        headers: {
+            'Content-Type': 'application/json',
+            Authorization: `Bearer ${token}`
+        },
+        body: JSON.stringify({
+            label: label,
+            site: site,
+            isPublic: !!isPublic,
+            ids: ids
+        })
+    });
+    if (!res.ok) throw await $4abf453405c18681$var$readError(res, 'Save');
+    return res.json();
+}
+
+
 const $0f50f369018a42ef$var$formatDate = (value)=>{
     if (!value) return '';
     const d = new Date(value);
@@ -13727,14 +14253,20 @@ const $0f50f369018a42ef$var$GeneListDisplayComponent = (props)=>{
 };
 const $0f50f369018a42ef$var$GeneListComponent = (props)=>{
     const [geneList, setGeneList] = (0, $gXNCa$react.useState)('');
-    const [listHash, setListHash] = (0, $gXNCa$react.useState)(null);
-    const [validationError, setValidationError] = (0, $gXNCa$react.useState)([]);
     const [listName, setListName] = (0, $gXNCa$react.useState)('');
     const [listIsPublic, setListIsPublic] = (0, $gXNCa$react.useState)(false);
-    const [validatedList, setValidatedList] = (0, $gXNCa$react.useState)([]);
+    // The three-bucket validate response, the user's narrowing decisions, and the
+    // hydrated gene docs used to label candidates.
+    const [validation, setValidation] = (0, $gXNCa$react.useState)(null);
+    const [choices, setChoices] = (0, $gXNCa$react.useState)({});
+    const [meta, setMeta] = (0, $gXNCa$react.useState)({});
     const [errorMessage, setErrorMessage] = (0, $gXNCa$react.useState)('');
-    const [loading, setLoading] = (0, $gXNCa$react.useState)(false); // New loading state
-    const [user, setUser] = (0, $gXNCa$react.useState)({});
+    const [notice, setNotice] = (0, $gXNCa$react.useState)('');
+    const [loading, setLoading] = (0, $gXNCa$react.useState)(false);
+    const [saving, setSaving] = (0, $gXNCa$react.useState)(false);
+    // null, not {}: the initial value is read to decide whether Save is enabled, and
+    // an empty object is truthy, which used to offer Save to a logged-out visitor.
+    const [user, setUser] = (0, $gXNCa$react.useState)(null);
     const auth = props.auth;
     (0, $gXNCa$react.useEffect)(()=>{
         if (!auth) return;
@@ -13743,6 +14275,38 @@ const $0f50f369018a42ef$var$GeneListComponent = (props)=>{
     }, [
         auth
     ]);
+    // The single source of truth for what gets saved. An ambiguous input the user
+    // never touched contributes ALL of its matches, so nothing is silently dropped;
+    // narrowing is a choice, not a requirement.
+    // `choices[i] === undefined` means untouched -> keep all. `choices[i] === []`
+    // means the user explicitly dropped the row, so this must NOT be `|| a.matches`:
+    // an empty array is falsy, and that would silently re-add everything they just
+    // removed.
+    const keptFor = (i, a)=>choices[i] === undefined ? a.matches : choices[i];
+    const idsToSave = (0, $gXNCa$react.useMemo)(()=>{
+        if (!validation) return [];
+        const out = validation.resolved.map((r)=>r.id);
+        validation.ambiguous.forEach((a, i)=>out.push(...keptFor(i, a)));
+        // Mandatory, not tidiness: the same gene reaches this list twice routinely —
+        // two inputs can resolve to one id, and a resolved id can also appear among
+        // another input's candidates. Duplicates would inflate n_genes and change the
+        // server's content hash, breaking the save endpoint's idempotency.
+        return [
+            ...new Set(out)
+        ];
+    }, [
+        validation,
+        choices
+    ]);
+    // How much of the total came from conflicts, for the summary line — with
+    // keep-all-by-default a single identifier can contribute 15 genes.
+    const fromConflicts = (0, $gXNCa$react.useMemo)(()=>{
+        if (!validation) return 0;
+        return validation.ambiguous.reduce((n, a, i)=>n + keptFor(i, a).length, 0);
+    }, [
+        validation,
+        choices
+    ]);
     // Function to handle gene list input
     const handleGeneListChange = (event)=>{
         setGeneList(event.target.value);
@@ -13759,65 +14323,66 @@ const $0f50f369018a42ef$var$GeneListComponent = (props)=>{
     };
     // Function to submit gene list for validation
     const handleSubmit = async ()=>{
-        const geneArray = geneList.split('\n').filter(Boolean); // Convert the gene list into an array and filter out empty values
-        if (geneArray.length > $0f50f369018a42ef$var$MAX_GENE_IDS) {
-            setErrorMessage(`You have exceeded the maximum limit of ${$0f50f369018a42ef$var$MAX_GENE_IDS} gene IDs.`);
+        // The server only drops blanks and duplicates; splitting and trimming is ours
+        // to do. Accept commas, tabs and semicolons as well as newlines.
+        const geneArray = [
+            ...new Set(geneList.split(/[\s,;]+/).map((s)=>s.trim()).filter(Boolean))
+        ];
+        if (geneArray.length === 0) {
+            setErrorMessage('Paste at least one gene identifier.');
+            return;
+        }
+        if (geneArray.length > (0, $4abf453405c18681$export$7fadd81f3363fc57)) {
+            setErrorMessage(`That is ${geneArray.length.toLocaleString()} identifiers; the limit is ${(0, $4abf453405c18681$export$7fadd81f3363fc57).toLocaleString()}.`);
             return;
         }
-        setErrorMessage(''); // Reset error message if validation passes
-        setLoading(true); // Set loading state to true to show progress
+        setErrorMessage('');
+        setNotice('');
+        setLoading(true);
         try {
-            const response = await fetch(`${props.api}/gene_lists/validate`, {
-                method: 'POST',
-                headers: {
-                    'Content-Type': 'application/json'
-                },
-                body: JSON.stringify(geneArray)
-            });
-            const result = await response.json();
-            if (result.hash) {
-                setListHash(result.hash);
-                setValidatedList(result.ids);
-                setValidationError(result.missing);
-            } else // Handle errors from validation
-            alert('Error during validation.');
+            const result = await (0, $4abf453405c18681$export$6c06d9a9d837c44e)(props.api, geneArray);
+            setValidation(result);
+            setChoices({});
+            // Candidates are only choosable if the user can see what they are, so pull
+            // species/description for every candidate id. Best-effort and non-blocking:
+            // the resolver renders bare ids until this lands.
+            const candidateIds = result.ambiguous.reduce((acc, a)=>acc.concat(a.matches), []);
+            if (candidateIds.length) (0, $4abf453405c18681$export$41928ff990e251ce)(props.api, candidateIds).then(setMeta).catch(()=>{});
+            else setMeta({});
         } catch (error) {
-            alert('There was an error with the validation service.', error);
+            setValidation(null);
+            setErrorMessage(error.message || 'There was an error with the validation service.');
         } finally{
-            setLoading(false); // Set loading to false when the request is complete
+            setLoading(false);
         }
     };
     // Function to save the validated gene list
     const handleSaveList = async ()=>{
-        const queryParams = {
-            label: listName,
-            hash: listHash,
-            site: props.site,
-            n_genes: validatedList.length,
-            isPublic: listIsPublic
-        };
-        const queryString = new URLSearchParams(queryParams).toString();
-        const token = await user.getIdToken();
+        setErrorMessage('');
+        setNotice('');
+        setSaving(true);
         try {
-            const response = await fetch(`${props.api}/gene_lists?${queryString}`, {
-                method: 'POST',
-                headers: {
-                    "Content-Type": "application/json",
-                    "Authorization": `Bearer ${token}`
-                }
+            // Inside the try: getIdToken() rejects when the session has expired, and
+            // that used to escape as an unhandled rejection with no UI feedback.
+            const token = await user.getIdToken();
+            const result = await (0, $4abf453405c18681$export$87f42b3480ee6c49)(props.api, token, {
+                label: listName,
+                site: props.site,
+                isPublic: listIsPublic,
+                ids: idsToSave
             });
-            if (!response.ok) throw new Error('Failed to save list');
-            const result = await response.json();
-            console.log(result);
             setGeneList('');
-            setListHash(null);
-            setValidatedList([]);
-            setValidationError([]);
+            setValidation(null);
+            setChoices({});
+            setMeta({});
             setListName('');
             setListIsPublic(false);
+            setNotice(`Saved \u{201C}${listName}\u{201D} \u{2014} ${(result.n_genes || idsToSave.length).toLocaleString()} genes.`);
             if (props.onListSaved) props.onListSaved();
         } catch (error) {
-            console.error("There was an problem with fetch", error);
+            setErrorMessage(error.message || 'Failed to save the gene list.');
+        } finally{
+            setSaving(false);
         }
     };
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
@@ -13836,7 +14401,7 @@ const $0f50f369018a42ef$var$GeneListComponent = (props)=>{
                                 rows: 10,
                                 value: geneList,
                                 onChange: handleGeneListChange,
-                                placeholder: `Paste or drop your gene list here (Maximum: ${$0f50f369018a42ef$var$MAX_GENE_IDS} IDs)`,
+                                placeholder: `Paste or drop your gene list here (Maximum: ${(0, $4abf453405c18681$export$7fadd81f3363fc57)} IDs)`,
                                 onDrop: handleDrop,
                                 onDragOver: handleDragOver
                             })
@@ -13844,8 +14409,16 @@ const $0f50f369018a42ef$var$GeneListComponent = (props)=>{
                     }),
                     errorMessage && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Alert), {
                         variant: "danger",
+                        dismissible: true,
+                        onClose: ()=>setErrorMessage(''),
                         children: errorMessage
                     }),
+                    notice && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Alert), {
+                        variant: "success",
+                        dismissible: true,
+                        onClose: ()=>setNotice(''),
+                        children: notice
+                    }),
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
                         variant: "primary",
                         onClick: handleSubmit,
@@ -13869,53 +14442,55 @@ const $0f50f369018a42ef$var$GeneListComponent = (props)=>{
                     })
                 ]
             }),
-            !loading && listHash && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-                className: "validation-summary mt-3 p-3 border rounded bg-light",
+            !loading && validation && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
                 children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $3b525b9a0ec89bcb$export$2e2bcd8739ae039), {
+                        validation: validation,
+                        choices: choices,
+                        meta: meta,
+                        onChange: setChoices
+                    }),
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                        className: "glr-summary",
                         children: [
-                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
-                                className: "text-success",
-                                children: [
-                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("strong", {
-                                        children: validatedList.length
-                                    }),
-                                    " valid"
-                                ]
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                                className: "glr-summary-total",
+                                children: idsToSave.length.toLocaleString()
                             }),
-                            validationError.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-                                className: "text-danger mt-1",
+                            ' ',
+                            "gene",
+                            idsToSave.length === 1 ? '' : 's',
+                            " will be saved",
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                                className: "glr-summary-detail",
                                 children: [
-                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("strong", {
-                                        children: validationError.length
+                                    validation.resolved.length.toLocaleString(),
+                                    " identifier",
+                                    validation.resolved.length === 1 ? '' : 's',
+                                    " matched exactly one gene",
+                                    validation.ambiguous.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+                                        children: [
+                                            '; ',
+                                            validation.ambiguous.length.toLocaleString(),
+                                            " conflicting identifier",
+                                            validation.ambiguous.length === 1 ? '' : 's',
+                                            " contributing",
+                                            ' ',
+                                            fromConflicts.toLocaleString(),
+                                            " candidate",
+                                            fromConflicts === 1 ? '' : 's',
+                                            Object.keys(choices).length > 0 && ` (${Object.keys(choices).length.toLocaleString()} narrowed)`
+                                        ]
                                     }),
-                                    " not found"
+                                    '. ',
+                                    "Genes matched more than once are counted once."
                                 ]
                             })
                         ]
-                    }),
-                    validationError.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("details", {
-                        className: "mt-2",
-                        children: [
-                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("summary", {
-                                style: {
-                                    cursor: 'pointer'
-                                },
-                                children: "Show unrecognized IDs"
-                            }),
-                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("pre", {
-                                className: "small mt-2 mb-0",
-                                style: {
-                                    maxHeight: 150,
-                                    overflow: 'auto'
-                                },
-                                children: validationError.join('\n')
-                            })
-                        ]
                     })
                 ]
             }),
-            !loading && validatedList.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+            !loading && idsToSave.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
                 className: "save-list mt-4",
                 children: [
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Form).Group, {
@@ -13942,7 +14517,8 @@ const $0f50f369018a42ef$var$GeneListComponent = (props)=>{
                     user ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
                         variant: "primary",
                         onClick: handleSaveList,
-                        children: "Save Gene List"
+                        disabled: saving || !listName.trim(),
+                        children: saving ? "Saving\u2026" : 'Save Gene List'
                     }) : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
                         variant: "secondary",
                         disabled: true,