gramene-search 2.15.6 → 2.16.0

package/dist/index.js

@@ -850,6 +850,38 @@ function $af4441dd29af05df$var$markSubtree(node, source, invert) {
         $af4441dd29af05df$var$markSubtree(child, source, invert);
     });
 }
+const $af4441dd29af05df$export$da3188ffd2da2525 = {
+    orthologs: {
+        label: 'orthologs',
+        // Edge fields: a seed gene's homology__all_orthologs values are the ids of its
+        // orthologs. Same field already queried directly in bundles/api.js.
+        from: 'homology__all_orthologs',
+        to: 'id'
+    },
+    paralogs: {
+        label: 'paralogs',
+        // Within-species, so this stays inside the seed's own genome — a much smaller
+        // expansion than orthologs (11 vs 70 for msd2).
+        from: 'homology__within_species_paralog',
+        to: 'id'
+    }
+};
+function $af4441dd29af05df$export$a6dc3fef1cecdf28(node) {
+    const type = node && node.expand;
+    return typeof type === 'string' && type ? type : null;
+}
+function $af4441dd29af05df$export$c8b6102be216752a(token) {
+    return String(token).replace(/[^A-Za-z0-9_-]/g, '-');
+}
+function $af4441dd29af05df$export$fb4df7b076406c76(subquery) {
+    return String(subquery).replace(/\\/g, '\\\\').replace(/"/g, '\\"');
+}
+function $af4441dd29af05df$export$90cfa1f3fbcb6430(node) {
+    const type = $af4441dd29af05df$export$a6dc3fef1cecdf28(node);
+    if (!type) return null;
+    const spec = $af4441dd29af05df$export$da3188ffd2da2525[type];
+    return `EXPAND: ${spec ? spec.label : type}`;
+}
 function $af4441dd29af05df$var$reindexTree(node, idx) {
     node.leftIdx = idx;
     idx++;
@@ -988,11 +1020,33 @@ const $af4441dd29af05df$var$grameneFilters = {
                             searchOffset: 0
                         });
                         let node = $af4441dd29af05df$var$findNodeWithLeftIdx(newState, payload.leftIdx);
-                        node.operation = node.operation === 'AND' ? 'OR' : 'AND';
+                        // Set an explicit operation when one is supplied; otherwise keep the
+                        // historical AND<->OR flip for callers that just pass the node.
+                        node.operation = payload.newOperation ? payload.newOperation : node.operation === 'AND' ? 'OR' : 'AND';
                         $af4441dd29af05df$var$markSubtree(newState, node, false);
                         return newState;
                     }
                     break;
+                case 'GRAMENE_FILTER_EXPANSION_SET':
+                    {
+                        // Setting or clearing an expansion is just a field on the node — the tree
+                        // shape is untouched, so there is nothing to reindex and no special case
+                        // for the root. `payload.expand` of null/undefined removes it.
+                        newState = Object.assign({}, state, {
+                            status: 'search',
+                            showMarked: true,
+                            searchOffset: 0
+                        });
+                        let node = $af4441dd29af05df$var$findNodeWithLeftIdx(newState, payload.leftIdx);
+                        if (!node) break;
+                        // Leave showMenu alone, as GRAMENE_FILTER_NEGATED does. The radios are a
+                        // setting rather than a command, so the menu stays open and the selection
+                        // updates in place — you can switch type or clear without reopening it.
+                        if (payload.expand) node.expand = payload.expand;
+                        else delete node.expand;
+                        $af4441dd29af05df$var$markSubtree(newState, node, false);
+                        return newState;
+                    }
                 case 'GRAMENE_FILTER_MOVED':
                     {
                         newState = Object.assign({}, state, {
@@ -1163,6 +1217,48 @@ const $af4441dd29af05df$var$grameneFilters = {
                 ]
             });
         },
+    // Expand a node (leaf or group) along a relationship, e.g. "orthologs of this".
+    doExpandGrameneFilter: (filter, type)=>({ dispatch: dispatch })=>{
+            dispatch({
+                type: 'BATCH_ACTIONS',
+                actions: [
+                    {
+                        type: 'GRAMENE_SEARCH_CLEARED'
+                    },
+                    {
+                        type: 'GRAMENE_TAXONOMY_CLEARED'
+                    },
+                    {
+                        type: 'GRAMENE_FILTER_EXPANSION_SET',
+                        payload: {
+                            leftIdx: filter.leftIdx,
+                            expand: type
+                        }
+                    }
+                ]
+            });
+        },
+    // Clear a node's expansion, leaving the node and its filters in place.
+    doRemoveGrameneExpansion: (filter)=>({ dispatch: dispatch })=>{
+            dispatch({
+                type: 'BATCH_ACTIONS',
+                actions: [
+                    {
+                        type: 'GRAMENE_SEARCH_CLEARED'
+                    },
+                    {
+                        type: 'GRAMENE_TAXONOMY_CLEARED'
+                    },
+                    {
+                        type: 'GRAMENE_FILTER_EXPANSION_SET',
+                        payload: {
+                            leftIdx: filter.leftIdx,
+                            expand: null
+                        }
+                    }
+                ]
+            });
+        },
     doMoveOrCopyGrameneFilter: (target)=>({ dispatch: dispatch, getState: getState })=>{
             const state = getState();
             if (state.grameneFilters.moveCopyMode) {
@@ -1301,18 +1397,45 @@ const $af4441dd29af05df$var$grameneFilters = {
         const isQuery = new RegExp(/\([a-zA-Z0-9_]+:[a-zA-Z0-9_]+\s/);
         const isRegionQuery = new RegExp(/^\(map:/);
         const idWithColon = new RegExp(/^[a-zA-Z0-9_]+:[a-zA-Z0-9_]+$/);
+        // The node's own clause, before negation and before any expansion.
+        function ownQuery(node) {
+            if (node.hasOwnProperty('children')) {
+                // Only AND and OR are valid infix operators. Anything else — a token from a
+                // newer client arriving via ?filters= or a saved view — would otherwise be
+                // interpolated raw and produce a Solr 400, which surfaces as blank results
+                // across every view rather than as an error.
+                const op = node.operation === 'AND' || node.operation === 'OR' ? node.operation : 'OR';
+                const kids = Array.isArray(node.children) ? node.children : [];
+                return `(${kids.map((c)=>getQuery(c)).sort().join(` ${op} `)})`;
+            }
+            // this node is a suggestion
+            if (node.fq_field === 'location' && isRegionQuery.test(node.fq_value)) return `${node.fq_value}`;
+            if (isQuery.test(node.fq_value)) return `${node.fq_value.replace(/:/g, '\\:')}`;
+            if (hasSpaces.test(node.fq_value)) return `${node.fq_field}:"${node.fq_value}"`;
+            else if (idWithColon.test(node.fq_value)) return `${node.fq_field}:${node.fq_value.replace(/:/g, '\\:')}`;
+            else return `${node.fq_field}:${node.fq_value}`;
+        }
         function getQuery(node) {
             const negate = node.negate ? 'NOT ' : '';
-            if (node.hasOwnProperty('children')) // do some recursion
-            return `${negate}(${node.children.map((c)=>getQuery(c)).sort().join(` ${node.operation} `)})`;
-            else {
-                // this node is a suggestion
-                if (node.fq_field === 'location' && isRegionQuery.test(node.fq_value)) return `${negate}${node.fq_value}`;
-                if (isQuery.test(node.fq_value)) return `${negate}${node.fq_value.replace(/:/g, '\\:')}`;
-                if (hasSpaces.test(node.fq_value)) return `${negate}${node.fq_field}:"${node.fq_value}"`;
-                else if (idWithColon.test(node.fq_value)) return `${negate}${node.fq_field}:${node.fq_value.replace(/:/g, '\\:')}`;
-                else return `${negate}${node.fq_field}:${node.fq_value}`;
-            }
+            const clause = ownQuery(node);
+            const expType = $af4441dd29af05df$export$a6dc3fef1cecdf28(node);
+            // No expansion on this node: unchanged from before.
+            if (!expType) return `${negate}${clause}`;
+            const spec = $af4441dd29af05df$export$da3188ffd2da2525[expType];
+            // Unknown expansion type — e.g. a link shared from a newer client. Degrade to
+            // the un-expanded clause rather than emitting something broken.
+            if (!spec) return `${negate}${clause}`;
+            // An expansion of nothing must match nothing; '*:*' here would turn an empty
+            // group into "every gene in the index".
+            if (!clause || clause === '()') return `${negate}(*:* AND NOT *:*)`;
+            // The braces MUST stay inside a quoted `_query_` value. A bare `{!graph ...}`
+            // in `q` is unreliable and fails *silently* — observed returning 0 rows in
+            // some shapes and millions in others, always HTTP 200, depending on the seed
+            // and the endpoint in front of Solr. Don't factor `graph` out to module scope
+            // where it could be used somewhere that isn't wrapped this way.
+            const graph = `{!graph from=${spec.from} to=${spec.to} maxDepth=1 returnRoot=true}`;
+            // Negation applies to the expanded set: "NOT an ortholog of msd2".
+            return `${negate}(_query_:"${graph}${$af4441dd29af05df$export$fb4df7b076406c76(clause)}")`;
         }
         if (state.grameneFilters.rightIdx === 1) return '*:*';
         return `*:* AND (${getQuery(state.grameneFilters)})`;
@@ -5226,6 +5349,9 @@ const $6c52be7952d5ec43$var$facetCounts = {
                     const vals = [];
                     for(let i = 0; i < arr.length; i += 2){
                         if (hidden && hidden.has(arr[i])) continue;
+                        // facet.mincount=1 already excludes empty buckets; belt and braces so
+                        // a zero can never reach the sidebar if that param is ever relaxed.
+                        if (!(arr[i + 1] > 0)) continue;
                         vals.push({
                             value: arr[i],
                             count: arr[i + 1]
@@ -6267,6 +6393,7 @@ const $472fe3745b238881$var$FILTER_NODE_KEEP = [
     'rightIdx',
     'operation',
     'negate',
+    'expand',
     'fq_field',
     'fq_value',
     'name',
@@ -6276,6 +6403,7 @@ const $472fe3745b238881$var$FILTER_NODE_KEEP = [
 const $472fe3745b238881$var$FILTER_ROOT_KEEP = [
     'operation',
     'negate',
+    'expand',
     'leftIdx',
     'rightIdx',
     'children',
@@ -7776,8 +7904,13 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
     }, [
         props.expressionStudies
     ]);
+    // Which Expression Atlas instance the embedded widget should query. The
+    // widget falls back to its own default when `atlasUrl` is absent, so sites
+    // that don't configure one are unaffected — only pass it when set.
+    const atlasUrl = props.configuration && props.configuration.atlasUrl || null;
+    const atlasParam = atlasUrl ? `&atlasUrl=${encodeURIComponent(atlasUrl)}` : '';
     let paralogs_url;
-    let gene_url = `https://dev.gramene.org/static/atlasWidget.html?genes=${gene.atlas_id || gene._id}&localAPI=${isLocal}`;
+    let gene_url = `https://dev.gramene.org/static/atlasWidget.html?genes=${gene.atlas_id || gene._id}&localAPI=${isLocal}${atlasParam}`;
     let paralogs = [];
     const haveParalogs = props.grameneParalogs && props.grameneParalogs[gene._id];
     if (haveParalogs) paralogs = props.grameneParalogs[gene._id];
@@ -7790,7 +7923,7 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
     // if (gene.homology && gene.homology.homologous_genes && gene.homology.homologous_genes.within_species_paralog) {
     //   paralogs = gene.homology.homologous_genes.within_species_paralog;
     // }
-    if (paralogs.length > 0 && atlasExperiment) paralogs_url = `https://dev.gramene.org/static/atlasWidget.html?genes=${paralogs.join(' ')}&experiment=${atlasExperiment}&localAPI=${isLocal}`;
+    if (paralogs.length > 0 && atlasExperiment) paralogs_url = `https://dev.gramene.org/static/atlasWidget.html?genes=${paralogs.join(' ')}&experiment=${atlasExperiment}&localAPI=${isLocal}${atlasParam}`;
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Tabs), {
         activeKey: activeTab,
         onSelect: (k)=>setActiveTab(k),
@@ -7845,7 +7978,7 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
         ]
     });
 };
-var $9e29a4f60318db7a$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneParalogs', 'selectExpressionStudies', 'selectUiViewState', 'doRequestParalogs', 'doFetchExpressionStudies', 'doSetExpressionState', //'doRequestParalogExpression',
+var $9e29a4f60318db7a$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectConfiguration', 'selectGrameneParalogs', 'selectExpressionStudies', 'selectUiViewState', 'doRequestParalogs', 'doFetchExpressionStudies', 'doSetExpressionState', //'doRequestParalogExpression',
 $9e29a4f60318db7a$var$Detail);
 
 
@@ -19945,10 +20078,6 @@ const $7d7b7dad5e71dfd3$var$FacetGroup = ({ group: group, values: values, onAdd:
             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", {
@@ -20031,11 +20160,17 @@ const $7d7b7dad5e71dfd3$var$FacetsCmp = (props)=>{
                             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, {
+                        hasData && (0, $6c52be7952d5ec43$export$f3878c70e70de19e).map((g)=>{
+                            // A field with nothing in this result set is dropped rather than
+                            // rendered as an empty group — an all-zero heading is noise.
+                            const values = groups[g.field] || [];
+                            if (values.length === 0) return null;
+                            return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($7d7b7dad5e71dfd3$var$FacetGroup, {
                                 group: g,
-                                values: groups[g.field] || [],
+                                values: values,
                                 onAdd: onAdd
-                            }, g.field))
+                            }, g.field);
+                        })
                     ]
                 })
             ]
@@ -20053,6 +20188,7 @@ var $7d7b7dad5e71dfd3$export$2e2bcd8739ae039 = $7d7b7dad5e71dfd3$var$Facets;
 
 
 
+
 // "Save this view" UI — sits inside the Auth sidebar panel.
 //
 // Sign-in-gated by Auth.js (we only mount this when `user` is truthy). Opens
@@ -20496,7 +20632,10 @@ function $693dd8c7a5607c3a$var$logAction(action) {
 }
 const $693dd8c7a5607c3a$var$Filter = ({ node: node, moveCopyMode: moveCopyMode, showMarked: showMarked, actions: actions })=>{
     let classes = 'gramene-filter gramene-filter';
-    if (node.operation) classes = `${classes}-${node.operation}`;
+    if (node.operation) classes = `${classes}-${(0, $af4441dd29af05df$export$c8b6102be216752a)(node.operation)}`;
+    // An expansion decorates whatever node it sits on, leaf or group — same as negate.
+    const expType = (0, $af4441dd29af05df$export$a6dc3fef1cecdf28)(node);
+    if (expType) classes = `${classes} gramene-filter-EXPAND gramene-filter-EXPAND-${(0, $af4441dd29af05df$export$c8b6102be216752a)(expType)}`;
     if (node.negate) classes = `${classes} gramene-filter-NOT`;
     if (showMarked && node.marked) classes = `${classes} gramene-filter-marked`;
     let content = '';
@@ -20517,6 +20656,40 @@ const $693dd8c7a5607c3a$var$Filter = ({ node: node, moveCopyMode: moveCopyMode,
                 })
             ]
         }, key++));
+        // A node carries at most one expansion, so the types are radios rather than
+        // separate commands. Any node can carry one, leaf or group — attaching it to a
+        // group means "expand whatever this group matches".
+        menuItems.push(/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("li", {
+            className: "gramene-filter-menu-label",
+            children: "expand filter(s)"
+        }, key++));
+        Object.keys((0, $af4441dd29af05df$export$da3188ffd2da2525)).forEach((type)=>{
+            const checked = expType === type;
+            menuItems.push(/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("li", {
+                className: "gramene-filter-menu-radio",
+                onClick: ()=>{
+                    // Re-picking the active type clears it — the only way to remove an
+                    // expansion from the root, which has no `delete`.
+                    if (checked) {
+                        $693dd8c7a5607c3a$var$logAction(`Remove expansion`);
+                        actions.removeExpansion(node);
+                    } else {
+                        $693dd8c7a5607c3a$var$logAction(`Expand by ${type}`);
+                        actions.expand(node, type);
+                    }
+                },
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("input", {
+                        type: "radio",
+                        readOnly: true,
+                        checked: checked,
+                        onChange: ()=>{},
+                        name: `gramene-expand-${node.leftIdx}`
+                    }),
+                    (0, $af4441dd29af05df$export$da3188ffd2da2525)[type].label
+                ]
+            }, key++));
+        });
         if (node.leftIdx > 0) {
             menuItems.push(/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("li", {
                 onClick: ()=>{
@@ -20586,6 +20759,13 @@ const $693dd8c7a5607c3a$var$Filter = ({ node: node, moveCopyMode: moveCopyMode,
             })
         });
     }
+    // Shown above the node's own label, since the expansion applies to whatever that
+    // node resolves to rather than replacing it.
+    const expBadge = expType ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+        className: "gramene-filter-expansion",
+        onClick: ()=>actions.toggleMenu(node),
+        children: (0, $af4441dd29af05df$export$90cfa1f3fbcb6430)(node)
+    }) : null;
     if (node.operation) {
         children = node.children.map((child, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($693dd8c7a5607c3a$var$Filter, {
                 moveCopyMode: moveCopyMode,
@@ -20595,6 +20775,7 @@ const $693dd8c7a5607c3a$var$Filter = ({ node: node, moveCopyMode: moveCopyMode,
             }, idx));
         content = /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
             children: [
+                expBadge,
                 /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
                     className: "gramene-filter-operation",
                     onClick: ()=>actions.toggleMenu(node),
@@ -20603,13 +20784,18 @@ const $693dd8c7a5607c3a$var$Filter = ({ node: node, moveCopyMode: moveCopyMode,
                 warning
             ]
         });
-    } else content = /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
-        className: "gramene-filter-text",
-        onClick: ()=>actions.toggleMenu(node),
+    } else content = /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
         children: [
-            node.category,
-            " |\xa0",
-            node.name
+            expBadge,
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+                className: "gramene-filter-text",
+                onClick: ()=>actions.toggleMenu(node),
+                children: [
+                    node.category,
+                    " |\xa0",
+                    node.name
+                ]
+            })
         ]
     });
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
@@ -20627,6 +20813,8 @@ const $693dd8c7a5607c3a$var$FiltersCmp = (props)=>{
         negate: props.doNegateGrameneFilter,
         deleteNode: props.doDeleteGrameneFilter,
         changeOperation: props.doChangeGrameneFilterOperation,
+        expand: props.doExpandGrameneFilter,
+        removeExpansion: props.doRemoveGrameneExpansion,
         selectTarget: props.doMoveOrCopyGrameneFilter,
         markTargets: props.doMarkGrameneFilterTargets,
         unmarkTargets: props.doUnmarkGrameneFilterTargets,
@@ -20667,7 +20855,7 @@ const $693dd8c7a5607c3a$var$FiltersCmp = (props)=>{
         })
     });
 };
-const $693dd8c7a5607c3a$export$92a576f896a9bf72 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneFilters', 'selectConfiguration', 'doNegateGrameneFilter', 'doDeleteGrameneFilter', 'doChangeGrameneFilterOperation', 'doMoveOrCopyGrameneFilter', 'doMarkGrameneFilterTargets', 'doUnmarkGrameneFilterTargets', 'doToggleGrameneFilterMenu', 'doClearGrameneFilters', $693dd8c7a5607c3a$var$FiltersCmp);
+const $693dd8c7a5607c3a$export$92a576f896a9bf72 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneFilters', 'selectConfiguration', 'doNegateGrameneFilter', 'doDeleteGrameneFilter', 'doChangeGrameneFilterOperation', 'doExpandGrameneFilter', 'doRemoveGrameneExpansion', 'doMoveOrCopyGrameneFilter', 'doMarkGrameneFilterTargets', 'doUnmarkGrameneFilterTargets', 'doToggleGrameneFilterMenu', 'doClearGrameneFilters', $693dd8c7a5607c3a$var$FiltersCmp);
 const $693dd8c7a5607c3a$var$ResultsCmp = (props)=>{
     let activeViews = props.grameneViews.options;
     return props.grameneFilters.rightIdx > 0 ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {