gramene-search 2.14.0 → 2.15.0

package/dist/index.js

@@ -219,6 +219,7 @@ $parcel$export(module.exports, "resultSummary", () => $27617dbc24e7faf0$export$2
 $parcel$export(module.exports, "suggestions", () => $541b8b0d8c5501d2$export$2e2bcd8739ae039);
 $parcel$export(module.exports, "Status", () => $693dd8c7a5607c3a$export$96e9906d6d93a972);
 $parcel$export(module.exports, "Filters", () => $693dd8c7a5607c3a$export$92a576f896a9bf72);
+$parcel$export(module.exports, "Facets", () => $7d7b7dad5e71dfd3$export$2e2bcd8739ae039);
 $parcel$export(module.exports, "Results", () => $693dd8c7a5607c3a$export$4a34de49b46a2bfa);
 $parcel$export(module.exports, "Views", () => $693dd8c7a5607c3a$export$5cb791131c501f6a);
 $parcel$export(module.exports, "Auth", () => $c5d403787de8b05f$export$2e2bcd8739ae039);
@@ -4744,12 +4745,12 @@ const $4b8473139e48e77e$export$a61929d6d484c6d4 = $4b8473139e48e77e$export$4bb93
 }, {});
 const $4b8473139e48e77e$export$c6dbe9be8c8b382e = {
     up: {
-        bg: '#fdecea',
-        fg: '#c0392b'
-    },
-    down: {
         bg: '#eaf2fb',
         fg: '#2e6fae'
+    },
+    down: {
+        bg: '#fdecea',
+        fg: '#c0392b'
     }
 };
 const $4b8473139e48e77e$export$39a35029fe99c21 = '#d35400'; // specific-to dot / enhanced-in outline
@@ -5061,6 +5062,188 @@ var $12feb7ca48271e17$export$2e2bcd8739ae039 = $12feb7ca48271e17$var$attrTable;
 
 
 
+const $6c52be7952d5ec43$export$f3878c70e70de19e = [
+    {
+        field: 'capabilities',
+        heading: 'Available data',
+        hide: [
+            'expression_attributes',
+            'location',
+            'taxonomy',
+            'xrefs',
+            'familyRoot',
+            'MAKER',
+            'Grassius'
+        ],
+        // Per-value display overrides (raw value -> label). Anything not listed falls
+        // back to underscores->spaces. The raw value is still what gets filtered on.
+        labels: {
+            expression: 'Expression',
+            homology: 'Homology',
+            domains: 'Domains',
+            grassius_homolog: 'Grassius',
+            GO: 'Gene Ontology',
+            PO: 'Plant Ontology',
+            TO: 'Trait Ontology',
+            QTL_TO: 'QTL',
+            VEP: 'Loss-of-function variants',
+            pubs: 'Curated in literature'
+        }
+    },
+    {
+        field: 'expr_class__attr_ss',
+        heading: 'Expression class'
+    },
+    {
+        field: 'grassius_homolog__attr_ss',
+        heading: 'TF family (GRASSIUS)'
+    }
+];
+const $6c52be7952d5ec43$var$FACET_FIELDS = $6c52be7952d5ec43$export$f3878c70e70de19e.map((g)=>g.field);
+// field -> Set of raw values to omit from the rendered group.
+const $6c52be7952d5ec43$var$HIDE_BY_FIELD = {};
+$6c52be7952d5ec43$export$f3878c70e70de19e.forEach((g)=>{
+    if (g.hide && g.hide.length) $6c52be7952d5ec43$var$HIDE_BY_FIELD[g.field] = new Set(g.hide);
+});
+// The output key of a Solr facet defaults to the field name, so no {!key=...}
+// local params are needed — just one facet.field per field.
+const $6c52be7952d5ec43$var$FACET_PARAMS = $6c52be7952d5ec43$var$FACET_FIELDS.map((f)=>`facet.field=${f}`).join('&');
+let $6c52be7952d5ec43$var$fetchPendingId = 0;
+// Same rule the main search uses: only constrain by taxon_id when the user has
+// actually subset the visible genomes (see bundles/api.js). Keeps counts in step
+// with the visible result set without bloating the URL.
+function $6c52be7952d5ec43$var$genomeSubset(g, m) {
+    const maps = m || {};
+    const visibleTaxa = Object.keys(maps).filter((tid)=>!maps[tid].hidden);
+    const activeVisible = Object.keys(g && g.active || {}).filter((tid)=>maps[tid] && !maps[tid].hidden);
+    const subset = activeVisible.length > 0 && activeVisible.length < visibleTaxa.length;
+    const sorted = activeVisible.slice().sort();
+    return {
+        fq: subset ? `&fq=taxon_id:(${sorted.join(' OR ')})` : '',
+        key: subset ? sorted.join(',') : ''
+    };
+}
+function $6c52be7952d5ec43$var$computeSignature(q, g, m) {
+    return `${q}|${$6c52be7952d5ec43$var$genomeSubset(g, m).key}`;
+}
+const $6c52be7952d5ec43$var$facetCounts = {
+    name: 'facetCounts',
+    getReducer: ()=>{
+        const initialState = {
+            status: 'idle',
+            signature: null,
+            groups: {},
+            error: null,
+            requestId: 0,
+            open: false
+        };
+        return (state = initialState, { type: type, payload: payload })=>{
+            switch(type){
+                case 'FACETCOUNTS_TOGGLE_OPEN':
+                    return {
+                        ...state,
+                        open: typeof payload === 'boolean' ? payload : !state.open
+                    };
+                case 'FACETCOUNTS_FETCH_STARTED':
+                    // Keep the previous groups visible during a refetch (smooth update);
+                    // they're replaced when the new counts land.
+                    return {
+                        ...state,
+                        status: 'loading',
+                        error: null,
+                        signature: payload.signature,
+                        requestId: payload.requestId
+                    };
+                case 'FACETCOUNTS_FETCH_DONE':
+                    if (payload.requestId !== state.requestId) return state; // superseded
+                    return {
+                        ...state,
+                        status: 'ready',
+                        groups: payload.groups
+                    };
+                case 'FACETCOUNTS_FETCH_FAILED':
+                    if (payload.requestId !== state.requestId) return state;
+                    return {
+                        ...state,
+                        status: 'error',
+                        error: payload.error
+                    };
+                default:
+                    return state;
+            }
+        };
+    },
+    doToggleFacetCounts: (open)=>({ dispatch: dispatch })=>dispatch({
+                type: 'FACETCOUNTS_TOGGLE_OPEN',
+                payload: open
+            }),
+    doFetchFacetCounts: ()=>({ dispatch: dispatch, store: store })=>{
+            const q = store.selectGrameneFiltersQueryString();
+            const { fq: fq } = $6c52be7952d5ec43$var$genomeSubset(store.selectGrameneGenomes(), store.selectGrameneMaps());
+            const signature = $6c52be7952d5ec43$var$computeSignature(q, store.selectGrameneGenomes(), store.selectGrameneMaps());
+            const requestId = ++$6c52be7952d5ec43$var$fetchPendingId;
+            dispatch({
+                type: 'FACETCOUNTS_FETCH_STARTED',
+                payload: {
+                    requestId: requestId,
+                    signature: signature
+                }
+            });
+            const api = store.selectGrameneAPI();
+            const url = `${api}/search?q=${q}${fq}&rows=0&facet=true&facet.mincount=1&facet.limit=-1&${$6c52be7952d5ec43$var$FACET_PARAMS}`;
+            fetch(url).then((r)=>r.json()).then((json)=>{
+                if (requestId !== $6c52be7952d5ec43$var$fetchPendingId) return;
+                const ff = json.facet_counts && json.facet_counts.facet_fields || {};
+                const groups = {};
+                $6c52be7952d5ec43$var$FACET_FIELDS.forEach((f)=>{
+                    const arr = ff[f] || [];
+                    const hidden = $6c52be7952d5ec43$var$HIDE_BY_FIELD[f];
+                    const vals = [];
+                    for(let i = 0; i < arr.length; i += 2){
+                        if (hidden && hidden.has(arr[i])) continue;
+                        vals.push({
+                            value: arr[i],
+                            count: arr[i + 1]
+                        });
+                    }
+                    groups[f] = vals;
+                });
+                dispatch({
+                    type: 'FACETCOUNTS_FETCH_DONE',
+                    payload: {
+                        requestId: requestId,
+                        groups: groups
+                    }
+                });
+            }).catch((err)=>{
+                dispatch({
+                    type: 'FACETCOUNTS_FETCH_FAILED',
+                    payload: {
+                        requestId: requestId,
+                        error: String(err)
+                    }
+                });
+            });
+        },
+    selectFacetCounts: (state)=>state.facetCounts,
+    selectFacetCountsOpen: (state)=>state.facetCounts.open,
+    selectFacetCountsGroups: (state)=>state.facetCounts.groups,
+    // Fetch only while the section is open, once per unique (query, genomes).
+    reactFacetCountsFetch: (0, $gXNCa$reduxbundler.createSelector)('selectFacetCounts', 'selectGrameneFiltersStatus', 'selectGrameneFiltersQueryString', 'selectGrameneGenomes', 'selectGrameneMaps', (fc, filtersStatus, q, g, m)=>{
+        if (!fc || !fc.open) return;
+        if (filtersStatus === 'init') return;
+        if (fc.status === 'loading') return;
+        const sig = $6c52be7952d5ec43$var$computeSignature(q, g, m);
+        if (fc.signature === sig && (fc.status === 'ready' || fc.status === 'error')) return;
+        return {
+            actionCreator: 'doFetchFacetCounts'
+        };
+    })
+};
+var $6c52be7952d5ec43$export$2e2bcd8739ae039 = $6c52be7952d5ec43$var$facetCounts;
+
+
+
 // Ontology over-representation analysis (clusterProfiler::enrichGO-style).
 //
 // For each species tab we run:
@@ -6818,6 +7001,7 @@ var $5df6c55c1bef3469$export$2e2bcd8739ae039 = [
     (0, $c921a0d2b34aadb6$export$2e2bcd8739ae039),
     (0, $4f15cd8a7d970b18$export$2e2bcd8739ae039),
     (0, $12feb7ca48271e17$export$2e2bcd8739ae039),
+    (0, $6c52be7952d5ec43$export$2e2bcd8739ae039),
     (0, $d365d8c287ab0c94$export$2e2bcd8739ae039),
     (0, $7f865ea0feda21af$export$2e2bcd8739ae039),
     (0, $6048209b532f201d$export$2e2bcd8739ae039),
@@ -19693,6 +19877,149 @@ var $15504f5eba8e73bd$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 
 
 
+// How many values to show per group before a "show N more" toggle. GRASSIUS has
+// ~90 TF families, so an uncapped list would swamp the sidebar.
+const $7d7b7dad5e71dfd3$var$INITIAL_VISIBLE = 12;
+// Display label for a raw facet value: a per-group override (group.labels) if
+// present, else underscores -> spaces. The raw value is still what gets filtered.
+const $7d7b7dad5e71dfd3$var$labelFor = (group, value)=>group.labels && group.labels[value] || String(value).replace(/_/g, ' ');
+// One collapsible group = one facet field. Values arrive pre-sorted by count
+// (Solr default facet.sort). Clicking a count adds the filter.
+const $7d7b7dad5e71dfd3$var$FacetGroup = ({ group: group, values: values, onAdd: onAdd })=>{
+    const [open, setOpen] = (0, $gXNCa$react.useState)(true);
+    const [showAll, setShowAll] = (0, $gXNCa$react.useState)(false);
+    const shown = showAll ? values : values.slice(0, $7d7b7dad5e71dfd3$var$INITIAL_VISIBLE);
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        className: "facet-group",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                className: "facet-group-header",
+                onClick: ()=>setOpen(!open),
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "facet-group-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: "facet-group-title",
+                        children: group.heading
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "facet-group-nvals",
+                        children: values.length
+                    })
+                ]
+            }),
+            open && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                className: "facet-group-body",
+                children: [
+                    values.length === 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                        className: "facet-empty",
+                        children: "none in this result set"
+                    }),
+                    shown.map(({ value: value, count: count })=>{
+                        const label = $7d7b7dad5e71dfd3$var$labelFor(group, value);
+                        return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                            className: "facet-row",
+                            children: [
+                                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                                    className: "facet-val",
+                                    title: label,
+                                    children: label
+                                }),
+                                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
+                                    type: "button",
+                                    className: "facet-count",
+                                    title: `Add filter: ${group.heading} = ${label}`,
+                                    onClick: ()=>onAdd(group.field, group.heading, value, label),
+                                    children: count.toLocaleString()
+                                })
+                            ]
+                        }, value);
+                    }),
+                    values.length > $7d7b7dad5e71dfd3$var$INITIAL_VISIBLE && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
+                        type: "button",
+                        className: "facet-more",
+                        onClick: ()=>setShowAll(!showAll),
+                        children: showAll ? 'show less' : `show ${values.length - $7d7b7dad5e71dfd3$var$INITIAL_VISIBLE} more`
+                    })
+                ]
+            })
+        ]
+    });
+};
+const $7d7b7dad5e71dfd3$var$FacetsCmp = (props)=>{
+    const { facetCounts: facetCounts, configuration: configuration, doToggleFacetCounts: doToggleFacetCounts, doAcceptGrameneSuggestion: doAcceptGrameneSuggestion } = props;
+    const open = facetCounts.open;
+    const status = facetCounts.status;
+    const groups = facetCounts.groups || {};
+    const containerClass = configuration && configuration.id === 'sorghum' ? 'sorghumbase-facet-container' : 'gramene-facet-container';
+    const hasData = (0, $6c52be7952d5ec43$export$f3878c70e70de19e).some((g)=>(groups[g.field] || []).length > 0);
+    const onAdd = (field, heading, value, label)=>{
+        doAcceptGrameneSuggestion({
+            fq_field: field,
+            fq_value: value,
+            category: heading,
+            name: label
+        });
+    };
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: containerClass,
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+            className: "sidebar-section",
+            children: [
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                    className: "sidebar-section-header",
+                    onClick: ()=>doToggleFacetCounts(!open),
+                    children: [
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("b", {
+                            children: "Refine"
+                        }),
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                            className: "sidebar-section-actions",
+                            children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                                className: "sidebar-section-toggle",
+                                children: open ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reacticonsbs.BsChevronDown), {}) : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reacticonsbs.BsChevronRight), {})
+                            })
+                        })
+                    ]
+                }),
+                open && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                    className: "sidebar-section-body",
+                    children: [
+                        !hasData && status === 'error' && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                            className: "facet-status",
+                            children: "counts unavailable"
+                        }),
+                        !hasData && status !== 'error' && status !== 'ready' && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                            className: "facet-status",
+                            children: "counting\u2026"
+                        }),
+                        !hasData && status === 'ready' && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                            className: "facet-status",
+                            children: "no categories for this result set"
+                        }),
+                        hasData && (0, $6c52be7952d5ec43$export$f3878c70e70de19e).map((g)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($7d7b7dad5e71dfd3$var$FacetGroup, {
+                                group: g,
+                                values: groups[g.field] || [],
+                                onAdd: onAdd
+                            }, g.field))
+                    ]
+                })
+            ]
+        })
+    });
+};
+const $7d7b7dad5e71dfd3$var$Facets = (0, $gXNCa$reduxbundlerreact.connect)('selectFacetCounts', 'selectConfiguration', 'doToggleFacetCounts', 'doAcceptGrameneSuggestion', $7d7b7dad5e71dfd3$var$FacetsCmp);
+var $7d7b7dad5e71dfd3$export$2e2bcd8739ae039 = $7d7b7dad5e71dfd3$var$Facets;
+
+
+
+
+
+
+
+
 
 // "Save this view" UI — sits inside the Auth sidebar panel.
 //