gramene-search 2.37.0 → 2.38.1

package/dist/index.js

@@ -5236,16 +5236,17 @@ const $4b8473139e48e77e$export$705aff68da3ddba0 = [
 // Paging mirrors exprViz's doFetchExprVizData: a recursive fetchPage(offset)
 // with a request-id guard so a superseded fetch can never write stale rows.
 //
-// The offered columns are deliberately limited to two field-catalog groups —
-// Core identifiers and Expression attributes — and *all* of them are fetched up
-// front. That keeps the column picker a pure visibility control: toggling a
-// column is instant and never triggers a refetch.
+// The offered columns are deliberately limited to a few field-catalog groups —
+// Core identifiers, Expression attributes and MAKER transcript metrics — and
+// *all* of them are fetched up front. That keeps the column picker a pure
+// visibility control: toggling a column is instant and never triggers a refetch.
 const $12feb7ca48271e17$var$PAGE_SIZE = 1000;
 const $12feb7ca48271e17$var$MAX_GENES = 5000;
 // The catalog groups whose fields the column picker offers.
 const $12feb7ca48271e17$export$53e90de8d659db95 = [
     'core',
-    'exprattrs'
+    'exprattrs',
+    'MAKER'
 ];
 // The 'core' group's fields (bundles/../fieldCatalog.overlay.json).
 const $12feb7ca48271e17$export$9d77d82cc773e55e = [
@@ -5260,12 +5261,28 @@ const $12feb7ca48271e17$export$9d77d82cc773e55e = [
     'taxon_id',
     'db_type'
 ];
+// The 'MAKER' group's fields: MAKER's annotation quality metrics (AED and the
+// quality index QI1-QI9). Only some releases have them (e.g. SorghumBase); Solr
+// returns nothing for them elsewhere, and the picker then hides the empty group.
+const $12feb7ca48271e17$export$3ae897f4a2495276 = [
+    'MAKER__AED__attr_f',
+    'MAKER__QI1__attr_i',
+    'MAKER__QI2__attr_f',
+    'MAKER__QI3__attr_f',
+    'MAKER__QI4__attr_f',
+    'MAKER__QI5__attr_f',
+    'MAKER__QI6__attr_f',
+    'MAKER__QI7__attr_i',
+    'MAKER__QI8__attr_i',
+    'MAKER__QI9__attr_i'
+];
 // Always fetched, so visibility toggles never need the network. taxon_id is
 // needed by the genome filter even when its column is hidden.
 const $12feb7ca48271e17$var$FETCH_FIELDS = [
     ...new Set([
         ...$12feb7ca48271e17$export$9d77d82cc773e55e,
-        ...(0, $4b8473139e48e77e$export$705aff68da3ddba0)
+        ...(0, $4b8473139e48e77e$export$705aff68da3ddba0),
+        ...$12feb7ca48271e17$export$3ae897f4a2495276
     ])
 ];
 // Default columns, in display order. The two stress fields are adjacent so the
@@ -13316,6 +13333,7 @@ function $76e15aea9236bd47$var$findRoots(tax) {
 }
 // Post-order: attach .leafIds (taxon_ids of maps in subtree) and .isLeaf
 function $76e15aea9236bd47$var$annotate(node, tax, maps) {
+    maps = maps || {};
     const leafIds = [];
     if (maps[node._id]) {
         node.isLeaf = true;
@@ -13329,9 +13347,20 @@ function $76e15aea9236bd47$var$annotate(node, tax, maps) {
     });
     node.leafIds = leafIds;
 }
+// The taxonomy's root nodes, annotated with the genomes (maps) under them. The
+// modal is mounted with the search status, so the taxonomy and the maps can
+// arrive in either order: missing maps count as no genomes, and the roots are
+// rebuilt when either changes.
+function $76e15aea9236bd47$var$buildRoots({ grameneMaps: grameneMaps, grameneTaxonomy: grameneTaxonomy }) {
+    if (!grameneTaxonomy) return [];
+    const roots = $76e15aea9236bd47$var$findRoots(grameneTaxonomy);
+    roots.forEach((r)=>$76e15aea9236bd47$var$annotate(r, grameneTaxonomy, grameneMaps || {}));
+    return roots;
+}
 // Walk down the spine through single-child internals until a branch point,
 // leaf, or node that is itself a genome.
 function $76e15aea9236bd47$var$compressChain(node, tax, maps) {
+    maps = maps || {};
     const chain = [
         node
     ];
@@ -13483,17 +13512,11 @@ function $76e15aea9236bd47$var$computeOpenState(props) {
 class $76e15aea9236bd47$var$TaxonomyModal extends (0, ($parcel$interopDefault($gXNCa$react))).Component {
     constructor(props){
         super(props);
-        const { grameneMaps: grameneMaps, grameneTaxonomy: grameneTaxonomy } = props;
-        let roots = [];
-        if (grameneTaxonomy) {
-            roots = $76e15aea9236bd47$var$findRoots(grameneTaxonomy);
-            roots.forEach((r)=>$76e15aea9236bd47$var$annotate(r, grameneTaxonomy, grameneMaps));
-        }
         const { selected: selected, expanded: expanded } = $76e15aea9236bd47$var$computeOpenState(props);
         this.state = {
             selected: selected,
             expanded: expanded,
-            roots: roots,
+            roots: $76e15aea9236bd47$var$buildRoots(props),
             query: '',
             highlightId: null,
             activeIdx: 0
@@ -13538,6 +13561,16 @@ class $76e15aea9236bd47$var$TaxonomyModal extends (0, ($parcel$interopDefault($g
         }
     }
     componentDidUpdate(prevProps, prevState) {
+        // Maps or taxonomy arrived (or changed): rebuild the tree and reseed the
+        // selection, which was empty if the modal mounted before the maps loaded.
+        if (prevProps.grameneMaps !== this.props.grameneMaps || prevProps.grameneTaxonomy !== this.props.grameneTaxonomy) {
+            const { selected: selected, expanded: expanded } = $76e15aea9236bd47$var$computeOpenState(this.props);
+            this.setState({
+                roots: $76e15aea9236bd47$var$buildRoots(this.props),
+                selected: selected,
+                expanded: expanded
+            });
+        }
         // On each hidden→shown transition, reseed selection from current active
         // genomes and expand every ancestor so selected taxa are visible.
         const wasShown = prevProps.grameneGenomes && prevProps.grameneGenomes.show;
@@ -13609,7 +13642,7 @@ class $76e15aea9236bd47$var$TaxonomyModal extends (0, ($parcel$interopDefault($g
     }
     selectAll() {
         const s = new Set();
-        Object.values(this.props.grameneMaps).forEach((m)=>{
+        Object.values(this.props.grameneMaps || {}).forEach((m)=>{
             if (!m.hidden) s.add(m.taxon_id);
         });
         this.setState({
@@ -13626,7 +13659,7 @@ class $76e15aea9236bd47$var$TaxonomyModal extends (0, ($parcel$interopDefault($g
         this.state.selected.forEach((id)=>{
             active[id] = true;
         });
-        if (Object.keys(active).length === 0) Object.values(this.props.grameneMaps).forEach((m)=>{
+        if (Object.keys(active).length === 0) Object.values(this.props.grameneMaps || {}).forEach((m)=>{
             if (!m.hidden) active[m.taxon_id] = true;
         });
         this.props.doUpdateGrameneGenomes(active);
@@ -13644,7 +13677,7 @@ class $76e15aea9236bd47$var$TaxonomyModal extends (0, ($parcel$interopDefault($g
         const someOn = selCount > 0 && !allOn;
         const visibleKids = (terminal.children || []).map((cid)=>grameneTaxonomy[cid]).filter((c)=>c && c.leafIds.length > 0);
         const hasKids = visibleKids.length > 0;
-        const terminalIsGenome = !!grameneMaps[terminal._id];
+        const terminalIsGenome = !!(grameneMaps && grameneMaps[terminal._id]);
         const isOpen = expanded.has(terminal._id);
         // Deepest clade colour in the chain wins; falls back to inherited.
         const color = chain.reduce((acc, n)=>$76e15aea9236bd47$var$CLADE_COLORS[n.name] || acc, inheritedColor);
@@ -18705,6 +18738,84 @@ const $8f8e530286a37ce9$var$WIDTHS = {
     expr_enhanced_in__attr_ss: 150,
     expr_high_in__attr_ss: 150
 };
+// MAKER annotation metrics: AED and the QI fractions are 0-1 (2 decimals); the
+// other QIs are lengths or counts (integers).
+const $8f8e530286a37ce9$var$MAKER_SET = new Set((0, $12feb7ca48271e17$export$3ae897f4a2495276));
+const $8f8e530286a37ce9$var$fmtMaker = (f, v)=>{
+    if (v == null || v === '' || !Number.isFinite(+v)) return '';
+    return f.endsWith('__attr_f') ? (+v).toFixed(2) : String(Math.round(+v));
+};
+const $8f8e530286a37ce9$var$makerShortName = (f)=>f.replace(/^MAKER__/, '').replace(/__attr_[a-z]$/, '');
+// AED gets an explanation; the QIs their catalog label, e.g. "QI1: Length of the 5' UTR".
+const $8f8e530286a37ce9$var$makerTooltip = (f, label)=>f === 'MAKER__AED__attr_f' ? 'MAKER Annotation Edit Distance: 0 = fully supported by evidence, 1 = no support' : label;
+// Summary-statistics rows, pinned above the genes. The header row collapses the
+// rest; stats cover every loaded gene, for each visible column whose values are
+// all numbers (taxon_id is an identifier, not a measurement).
+const $8f8e530286a37ce9$var$STAT_ROWS = [
+    {
+        key: 'n',
+        label: 'N'
+    },
+    {
+        key: 'min',
+        label: 'Min'
+    },
+    {
+        key: 'max',
+        label: 'Max'
+    },
+    {
+        key: 'median',
+        label: 'Median'
+    },
+    {
+        key: 'mean',
+        label: 'Mean'
+    },
+    {
+        key: 'sd',
+        label: 'Std dev'
+    }
+];
+const $8f8e530286a37ce9$var$NOT_MEASUREMENTS = new Set([
+    'taxon_id'
+]);
+const $8f8e530286a37ce9$var$numericFieldsOf = (rows, fields)=>fields.filter((f)=>{
+        if ($8f8e530286a37ce9$var$NOT_MEASUREMENTS.has(f)) return false;
+        let numbers = 0;
+        for (const r of rows){
+            const v = r[f];
+            if (v == null || v === '') continue;
+            if (typeof v !== 'number' || !Number.isFinite(v)) return false;
+            numbers++;
+        }
+        return numbers > 0;
+    });
+const $8f8e530286a37ce9$var$statsOf = (values)=>{
+    const n = values.length;
+    if (!n) return {
+        n: 0
+    };
+    const sorted = values.slice().sort((a, b)=>a - b);
+    const mean = values.reduce((a, b)=>a + b, 0) / n;
+    const median = n % 2 ? sorted[(n - 1) / 2] : (sorted[n / 2 - 1] + sorted[n / 2]) / 2;
+    const sd = n > 1 ? Math.sqrt(values.reduce((a, v)=>a + (v - mean) * (v - mean), 0) / (n - 1)) : null;
+    return {
+        n: n,
+        min: sorted[0],
+        max: sorted[n - 1],
+        median: median,
+        mean: mean,
+        sd: sd
+    };
+};
+// Mean and std dev of a whole-number column still need decimals.
+const $8f8e530286a37ce9$var$fmtDecimal = (v)=>{
+    if (v == null || !Number.isFinite(v)) return '';
+    const a = Math.abs(v);
+    return a !== 0 && (a < 0.01 || a >= 1e6) ? v.toPrecision(3) : v.toFixed(2);
+};
+const $8f8e530286a37ce9$var$isIntegerField = (f, rows)=>f.endsWith('__attr_i') || rows.every((r)=>r[f] == null || Number.isInteger(r[f]));
 const $8f8e530286a37ce9$var$joinValues = (p)=>Array.isArray(p.value) ? p.value.map((v)=>String(v).replace(/_/g, ' ')).join(', ') : p.value ?? '';
 const $8f8e530286a37ce9$var$StressChip = ({ c: c, dir: dir })=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
         style: {
@@ -18775,6 +18886,7 @@ const $8f8e530286a37ce9$var$AttrTableViewCmp = (props)=>{
     const [fieldQuery, setFieldQuery] = (0, $gXNCa$react.useState)('');
     const [popover, setPopover] = (0, $gXNCa$react.useState)(null);
     const popRef = (0, $gXNCa$react.useRef)(null);
+    const [statsOpen, setStatsOpen] = (0, $gXNCa$react.useState)(true);
     const { docs: docs, total: total, truncated: truncated, status: status, error: error, visibleFields: visibleFields } = attrTable;
     const visibleSet = (0, $gXNCa$react.useMemo)(()=>new Set(visibleFields), [
         visibleFields
@@ -18809,15 +18921,13 @@ const $8f8e530286a37ce9$var$AttrTableViewCmp = (props)=>{
     }, [
         docs
     ]);
-    // Only the Core identifiers + Expression attributes groups are offered.
+    // Only the groups the bundle fetches are offered (Core identifiers, Expression
+    // attributes, MAKER transcript metrics); the catalog drops groups a site lacks.
     const pickerCatalog = (0, $gXNCa$react.useMemo)(()=>{
         if (!fieldCatalog || !fieldCatalog.groups) return null;
         return {
             ...fieldCatalog,
-            groups: fieldCatalog.groups.filter((g)=>[
-                    'core',
-                    'exprattrs'
-                ].includes(g.id))
+            groups: fieldCatalog.groups.filter((g)=>(0, $12feb7ca48271e17$export$53e90de8d659db95).includes(g.id))
         };
     }, [
         fieldCatalog
@@ -18844,10 +18954,11 @@ const $8f8e530286a37ce9$var$AttrTableViewCmp = (props)=>{
                         headerTooltip: (0, $4b8473139e48e77e$export$50c1f966fd3af83e)(o),
                         width: 22,
                         minWidth: 18,
-                        valueGetter: (p)=>p.data && p.data._organ[o] || '',
+                        valueGetter: (p)=>p.data && p.data._organ && p.data._organ[o] || '',
                         valueFormatter: ()=>'',
                         tooltipValueGetter: (p)=>{
-                            const lvl = p.data && p.data._organ[o];
+                            if (p.node && p.node.rowPinned) return undefined;
+                            const lvl = p.data && p.data._organ && p.data._organ[o];
                             if (!lvl) return `${(0, $4b8473139e48e77e$export$50c1f966fd3af83e)(o)}: not assayed`;
                             const sp = p.data._specific.has(o) ? " \xb7 specific" : p.data._enhanced.has(o) ? " \xb7 enhanced" : '';
                             return `${(0, $4b8473139e48e77e$export$50c1f966fd3af83e)(o)}: ${(0, $4b8473139e48e77e$export$433053e2c141d410)[lvl] || lvl}${sp}`;
@@ -18900,6 +19011,18 @@ const $8f8e530286a37ce9$var$AttrTableViewCmp = (props)=>{
                 });
                 return;
             }
+            if ($8f8e530286a37ce9$var$MAKER_SET.has(f)) {
+                cols.push({
+                    colId: f,
+                    field: f,
+                    headerName: labelOf(f),
+                    headerTooltip: $8f8e530286a37ce9$var$makerTooltip(f, labelOf(f)),
+                    width: 110,
+                    type: 'numericColumn',
+                    valueFormatter: (p)=>$8f8e530286a37ce9$var$fmtMaker(f, p.value)
+                });
+                return;
+            }
             cols.push({
                 colId: f,
                 field: f,
@@ -18919,6 +19042,110 @@ const $8f8e530286a37ce9$var$AttrTableViewCmp = (props)=>{
         tpmRange,
         fieldCatalogByName
     ]);
+    // Visible columns whose values are all numbers get summary statistics.
+    const numericFields = (0, $gXNCa$react.useMemo)(()=>{
+        const fields = columnDefs.filter((c)=>c.field).map((c)=>c.field);
+        return new Set($8f8e530286a37ce9$var$numericFieldsOf(rows, fields));
+    }, [
+        columnDefs,
+        rows
+    ]);
+    const stats = (0, $gXNCa$react.useMemo)(()=>{
+        const out = {};
+        numericFields.forEach((f)=>{
+            out[f] = $8f8e530286a37ce9$var$statsOf(rows.map((r)=>r[f]).filter((v)=>typeof v === 'number' && Number.isFinite(v)));
+        });
+        return out;
+    }, [
+        numericFields,
+        rows
+    ]);
+    const pinnedTopRows = (0, $gXNCa$react.useMemo)(()=>{
+        if (!numericFields.size || !rows.length) return [];
+        const header = {
+            _stat: 'header'
+        };
+        if (!statsOpen) return [
+            header
+        ];
+        return [
+            header,
+            ...$8f8e530286a37ce9$var$STAT_ROWS.map(({ key: key, label: label })=>{
+                const row = {
+                    _stat: key,
+                    _statLabel: label
+                };
+                numericFields.forEach((f)=>{
+                    row[f] = stats[f][key];
+                });
+                return row;
+            })
+        ];
+    }, [
+        numericFields,
+        stats,
+        statsOpen,
+        rows.length
+    ]);
+    // The first column carries the stats rows' labels; numeric columns show their
+    // statistics, formatted like the column (N as a count, mean/sd with decimals).
+    const gridColumnDefs = (0, $gXNCa$react.useMemo)(()=>columnDefs.map((col, i)=>{
+            const first = i === 0;
+            const numeric = !!col.field && numericFields.has(col.field);
+            if (!first && !numeric) return col;
+            const intField = numeric && $8f8e530286a37ce9$var$isIntegerField(col.field, rows);
+            const statText = (p)=>{
+                const v = p.value;
+                if (v == null || v === '') return '';
+                const k = p.data._stat;
+                if (k === 'n') return Number(v).toLocaleString();
+                if (k === 'mean' || k === 'sd' || k === 'median' && intField && !Number.isInteger(v)) return col.field === 'expr_max_tpm__attr_f' ? (0, $4b8473139e48e77e$export$8eaa32ef86afdd9c)(v) : $8f8e530286a37ce9$var$fmtDecimal(v);
+                return col.valueFormatter ? col.valueFormatter({
+                    ...p,
+                    value: v
+                }) : String(v);
+            };
+            return {
+                ...col,
+                valueFormatter: (p)=>{
+                    if (!(p.node && p.node.rowPinned)) return col.valueFormatter ? col.valueFormatter(p) : p.value;
+                    return numeric ? statText(p) : '';
+                },
+                cellStyle: (p)=>p.node && p.node.rowPinned ? null : typeof col.cellStyle === 'function' ? col.cellStyle(p) : col.cellStyle,
+                cellRenderer: (p)=>{
+                    if (p.node && p.node.rowPinned) {
+                        const k = p.data._stat;
+                        if (first && k === 'header') return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+                            className: "attrtable-stats-toggle",
+                            title: statsOpen ? 'Hide summary statistics' : 'Show summary statistics',
+                            children: [
+                                statsOpen ? "\u25BE" : "\u25B8",
+                                " Summary statistics (",
+                                rows.length.toLocaleString(),
+                                " genes)"
+                            ]
+                        });
+                        if (first) {
+                            const value = numeric ? statText(p) : '';
+                            return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+                                className: "attrtable-stats-label",
+                                children: [
+                                    p.data._statLabel,
+                                    value ? `: ${value}` : ''
+                                ]
+                            });
+                        }
+                        return k === 'header' ? '' : p.valueFormatted;
+                    }
+                    return col.cellRenderer ? /*#__PURE__*/ (0, ($parcel$interopDefault($gXNCa$react))).createElement(col.cellRenderer, p) : p.valueFormatted ?? p.value;
+                }
+            };
+        }), [
+        columnDefs,
+        numericFields,
+        rows,
+        statsOpen
+    ]);
     // Build the click-popover for a cell: a title (the column meaning) and one
     // filterable item per value. Each item carries the fq_field / fq_value the
     // "add filter" button hands to doAcceptGrameneSuggestion.
@@ -18987,6 +19214,27 @@ const $8f8e530286a37ce9$var$AttrTableViewCmp = (props)=>{
                 ]
             };
         }
+        if ($8f8e530286a37ce9$var$MAKER_SET.has(colId)) {
+            // AED: lower is better supported, so offer "at most"; the QI metrics "at least".
+            const v = data[colId];
+            if (!Number.isFinite(+v)) return {
+                title: labelOf(colId),
+                items: []
+            };
+            const shown = $8f8e530286a37ce9$var$fmtMaker(colId, +v);
+            const short = $8f8e530286a37ce9$var$makerShortName(colId);
+            return colId === 'MAKER__AED__attr_f' ? {
+                title: labelOf(colId),
+                items: [
+                    mk(`\u{2264} ${shown}`, colId, `[* TO ${v}]`, 'MAKER', `${short} \u{2264} ${shown}`)
+                ]
+            } : {
+                title: labelOf(colId),
+                items: [
+                    mk(`\u{2265} ${shown}`, colId, `[${v} TO *]`, 'MAKER', `${short} \u{2265} ${shown}`)
+                ]
+            };
+        }
         // Generic (Expression class, and any core / added attribute).
         const label = labelOf(colId);
         const raw = data[colId];
@@ -18999,6 +19247,11 @@ const $8f8e530286a37ce9$var$AttrTableViewCmp = (props)=>{
         };
     };
     const onCellClicked = (e)=>{
+        if (e.node && e.node.rowPinned) {
+            if (e.data && e.data._stat === 'header') setStatsOpen((v)=>!v);
+            setPopover(null);
+            return;
+        }
         const desc = buildCellPopover(e.column.getColId(), e.data);
         if (!desc || !desc.items.length) {
             setPopover(null);
@@ -19161,7 +19414,9 @@ const $8f8e530286a37ce9$var$AttrTableViewCmp = (props)=>{
                 className: `ag-theme-quartz attrtable-aggrid${organShown ? ' attrtable-tall-header' : ''}`,
                 children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$aggridreact.AgGridReact), {
                     rowData: rows,
-                    columnDefs: columnDefs,
+                    columnDefs: gridColumnDefs,
+                    pinnedTopRowData: pinnedTopRows,
+                    getRowClass: (p)=>p.node.rowPinned ? p.data._stat === 'header' ? 'attrtable-stats-header' : 'attrtable-stats-row' : undefined,
                     defaultColDef: $8f8e530286a37ce9$var$DEFAULT_COL_DEF,
                     animateRows: false,
                     suppressFieldDotNotation: true,