gramene-search 2.23.0 → 2.24.0

package/dist/index.js

@@ -31,6 +31,7 @@ var $gXNCa$reactsimpletreemenu = require("react-simple-tree-menu");
 require("@fortawesome/fontawesome-free/css/all.min.css");
 var $gXNCa$gramenedbxrefs = require("gramene-dbxrefs");
 var $gXNCa$reacticonsai = require("react-icons/ai");
+var $gXNCa$grameneprimers = require("gramene-primers");
 var $gXNCa$gramenesearchvis = require("gramene-search-vis");
 var $gXNCa$numeral = require("numeral");
 var $gXNCa$firebaseauth = require("firebase/auth");
@@ -6280,6 +6281,15 @@ var $d365d8c287ab0c94$export$2e2bcd8739ae039 = $d365d8c287ab0c94$var$ontologyEnr
 //     ('gene'|'paralogs'|'eFP'), atlasExperiment (selected GXA experiment id),
 //     barStudy (selected eFP/BAR study). Driven in controlled mode from this so a
 //     saved view restores the chosen sub-tab and study.
+//   - primers: the Primers detail's PrimerDesignerState (gramene-primers), a
+//     serializable {v: 1, mode, transcriptId, flankUp, flankDown, region,
+//     target, included, excluded, junctionSpanning, avoidRepeats, preset,
+//     params, designed, selectedRank, checkedRanks, check: {checks, genomes,
+//     params, jobId, submitted}, view}. Replaced wholesale on every change and
+//     driven in controlled mode, so a saved view re-runs the design and
+//     re-attaches to the check job. A pasted `sequence` is kept here so it
+//     survives a detail-tab switch; viewSnapshot drops it from saved views.
+//     Design responses and check results are never stored.
 //
 // What does NOT live here:
 //   - derived/computed state like `details` (per-render config from
@@ -6403,6 +6413,12 @@ const $7f865ea0feda21af$var$uiViewState = {
                     // payload: { geneId, patch }  -- merges into the expression slice
                     // (e.g. { activeTab }, { atlasExperiment }, { barStudy })
                     return $7f865ea0feda21af$var$setExpression(state, payload.geneId, payload.patch);
+                case 'UI_PRIMERS_SET':
+                    // payload: { geneId, state }  -- replaces the primers slice with the
+                    // full PrimerDesignerState emitted by <PrimerDesigner> (not merged)
+                    return $7f865ea0feda21af$var$setGene(state, payload.geneId, {
+                        primers: payload.state
+                    });
                 case 'UI_VIEW_STATE_REPLACED':
                     // payload: { byGene }  -- used by the snapshot loader in a later phase
                     return {
@@ -6476,6 +6492,15 @@ const $7f865ea0feda21af$var$uiViewState = {
                 }
             });
         },
+    doSetPrimersState: ({ geneId: geneId, state: state })=>({ dispatch: dispatch })=>{
+            dispatch({
+                type: 'UI_PRIMERS_SET',
+                payload: {
+                    geneId: geneId,
+                    state: state
+                }
+            });
+        },
     doReplaceUiViewState: (byGene)=>({ dispatch: dispatch })=>{
             dispatch({
                 type: 'UI_VIEW_STATE_REPLACED',
@@ -6567,7 +6592,9 @@ var $6048209b532f201d$export$2e2bcd8739ae039 = $6048209b532f201d$var$taxTreeView
 //       fullscreen: boolean,
 //       homology: { viewer, height, tbrowse: <ViewState> } | undefined,
 //       sequences: { tab, tid, upstream, downstream } | undefined,
-//       expression: { activeTab, atlasExperiment, barStudy } | undefined
+//       expression: { activeTab, atlasExperiment, barStudy } | undefined,
+//       primers: <gramene-primers PrimerDesignerState, {v: 1, ...}, without
+//                 the pasted `sequence`> | undefined
 //     }, ...
 //   ]
 // }
@@ -6622,8 +6649,18 @@ const $472fe3745b238881$var$isMeaningfulGene = (entry)=>{
     if (entry.homology && (entry.homology.viewer !== undefined || entry.homology.height !== undefined || entry.homology.tbrowse !== undefined)) return true;
     if (entry.sequences && Object.keys(entry.sequences).length) return true;
     if (entry.expression && Object.keys(entry.expression).length) return true;
+    if (entry.primers && Object.keys(entry.primers).length) return true;
     return false;
 };
+// The Primers slice keeps a pasted sequence in memory (so it survives a detail
+// tab switch), but a saved view must not carry it: it can be long and is the
+// user's own data. A restored sequence-mode design then waits for a new paste
+// (gramene-primers does not re-run a design whose inputs are incomplete).
+const $472fe3745b238881$var$snapshotPrimers = (primers)=>{
+    if (!primers || !Object.keys(primers).length) return undefined;
+    const { sequence: sequence, ...rest } = primers;
+    return rest;
+};
 const $472fe3745b238881$var$viewSnapshot = {
     name: 'viewSnapshot',
     // No reducer — this bundle is pure derivation + dispatch orchestration.
@@ -6687,6 +6724,9 @@ const $472fe3745b238881$var$viewSnapshot = {
                     } : {},
                     expression: e.expression ? {
                         ...e.expression
+                    } : {},
+                    primers: e.primers ? {
+                        ...e.primers
                     } : {}
                 };
             }
@@ -6759,7 +6799,8 @@ function $472fe3745b238881$var$buildSnapshot(state) {
             } : undefined,
             expression: e.expression && Object.keys(e.expression).length ? {
                 ...e.expression
-            } : undefined
+            } : undefined,
+            primers: $472fe3745b238881$var$snapshotPrimers(e.primers)
         }));
     else snap.expandedDetails = [];
     // Expression-visualization view config. Capture only the selection/config
@@ -10206,6 +10247,21 @@ var $54c74a4689d5a778$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 
 
 
+// Grid row height. Overrides the ag-theme-quartz default (42px) via the
+// `rowHeight` prop, and drives the container height calc below so the two
+// can't drift apart.
+const $283508ffcf8a47c4$var$ROW_HEIGHT = 36;
+// Header allowance in the container height calc (quartz header ≈ 49px).
+const $283508ffcf8a47c4$var$HEADER_HEIGHT_ALLOWANCE = 50;
+// Compact "Search" button so it sits comfortably inside a ROW_HEIGHT row —
+// react-bootstrap's `size="sm"` alone is ~31px, which crowds a 36px row.
+// Bump padding/fontSize here if the button should be taller.
+const $283508ffcf8a47c4$var$SEARCH_BUTTON_STYLE = {
+    whiteSpace: 'nowrap',
+    lineHeight: 1.4,
+    padding: '1px 8px',
+    fontSize: 12
+};
 const $283508ffcf8a47c4$var$ggURL = {
     xIRRI: 'https://gringlobal.irri.org/gringlobal/accessiondetail?id=',
     IRRI: 'https://www.irri.org/genesys-rice#/a/',
@@ -10500,6 +10556,7 @@ const $283508ffcf8a47c4$var$GridWithGroups = ({ groups: groups, gene_id: gene_id
                     currentURL.searchParams.set('name', accession.germplasm.ens_id);
                     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
                         size: "sm",
+                        style: $283508ffcf8a47c4$var$SEARCH_BUTTON_STYLE,
                         href: currentURL.toString(),
                         children: "Search"
                     });
@@ -10519,7 +10576,7 @@ const $283508ffcf8a47c4$var$GridWithGroups = ({ groups: groups, gene_id: gene_id
         }
     };
     const nVisible = getVisibleRowData().length;
-    const tableHeight = 50 + Math.min(nVisible, 10) * 42;
+    const tableHeight = $283508ffcf8a47c4$var$HEADER_HEIGHT_ALLOWANCE + Math.min(nVisible, 10) * $283508ffcf8a47c4$var$ROW_HEIGHT;
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
         style: {
             overflowX: "auto",
@@ -10537,8 +10594,20 @@ const $283508ffcf8a47c4$var$GridWithGroups = ({ groups: groups, gene_id: gene_id
                 rowData: getVisibleRowData(),
                 columnDefs: columnDefs,
                 getRowNodeId: (data)=>data.id,
-                animateRows: true,
-                defaultColDef: defaultColDef
+                rowHeight: $283508ffcf8a47c4$var$ROW_HEIGHT,
+                defaultColDef: defaultColDef,
+                // ag-grid sets `user-select: none` on cells by default, which is why
+                // accession / consequence text couldn't be selected and copied.
+                // `enableCellTextSelection` restores native selection; `ensureDomOrder`
+                // keeps DOM order matching visual order so a multi-row copy comes out
+                // as displayed rather than scrambled by row virtualization/sorting.
+                //
+                // NB: ag-grid's isAnimateRows() returns false whenever ensureDomOrder
+                // is set, so `animateRows` was removed rather than left as dead config.
+                // Correct copy order matters more here than row-slide animation; drop
+                // `ensureDomOrder` and restore `animateRows={true}` to trade back.
+                enableCellTextSelection: true,
+                ensureDomOrder: true
             })
         })
     });
@@ -11416,6 +11485,80 @@ var $527ebc19dc92444d$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 
 
 
+// Primers detail: PCR/qPCR primer design, genome specificity and pan-genome
+// coverage checks (gramene-primers <PrimerDesigner>, backed by the
+// gramene-swagger /primers endpoints).
+//
+// Enabled per site by config.details.primers:
+//   true                    use the site's grameneData API
+//   { apiBase, pangenome }  apiBase: a swagger that serves /primers;
+//                           pangenome: false hides the pan-genome check
+//
+// The designer's serializable state ({v: 1, ...}) lives in the uiViewState
+// bundle keyed by geneId (controlled mode), so a saved view restores the
+// inputs, re-runs the design and re-attaches to a submitted check (an expired
+// job shows "Re-run check"). The store keeps a pasted sequence, so switching
+// detail tabs (which unmounts this component) does not lose it; viewSnapshot
+// leaves it out of saved views. Styles are injected at runtime by the
+// component; no CSS import is needed.
+const $88d24ae9beb83d5d$var$MODES = [
+    'gene',
+    'transcript',
+    'region',
+    'sequence'
+];
+const $88d24ae9beb83d5d$var$geneHref = (id)=>`?idList=${encodeURIComponent(id)}`;
+// Plain left clicks on gene links in check results open a new tab, so the
+// design and a running check's job id survive; modified clicks use geneHref.
+const $88d24ae9beb83d5d$var$openGene = (id)=>window.open($88d24ae9beb83d5d$var$geneHref(id), '_blank', 'noopener');
+const $88d24ae9beb83d5d$var$Primers = (props)=>{
+    const geneId = props.searchResult.id;
+    const gene = props.geneDocs[geneId] // Gene.ensureGene() guarantees it is loaded
+    ;
+    const conf = props.config.details.primers // true | { apiBase?, pangenome? }
+    ;
+    const apiBase = conf && typeof conf === 'object' && conf.apiBase || props.grameneAPI;
+    const byGene = props.uiViewState && props.uiViewState.byGene && props.uiViewState.byGene[geneId];
+    const saved = byGene && byGene.primers;
+    const { doSetPrimersState: doSetPrimersState } = props;
+    const onStateChange = (0, $gXNCa$react.useCallback)((state)=>doSetPrimersState({
+            geneId: geneId,
+            state: state
+        }), [
+        geneId,
+        doSetPrimersState
+    ]);
+    if (!conf) // e.g. a saved view opened on a site that does not enable the tab
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("p", {
+        children: "Primer design is not enabled on this site."
+    });
+    if (!gene) return null;
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$grameneprimers.PrimerDesigner), {
+        apiBase: apiBase,
+        gene: gene,
+        systemName: gene.system_name,
+        modes: $88d24ae9beb83d5d$var$MODES,
+        defaultMode: "gene",
+        // an empty slice (never visited, or a snapshot without primers) leaves
+        // the designer uncontrolled until its first change is stored
+        state: saved && Object.keys(saved).length ? saved : undefined,
+        onStateChange: onStateChange,
+        features: {
+            pangenome: !(conf && conf.pangenome === false)
+        },
+        geneHref: $88d24ae9beb83d5d$var$geneHref,
+        onGeneClick: $88d24ae9beb83d5d$var$openGene,
+        geneLabel: gene.name || gene._id,
+        theme: "light"
+    }, geneId);
+};
+var $88d24ae9beb83d5d$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneAPI', 'selectUiViewState', 'doSetPrimersState', $88d24ae9beb83d5d$var$Primers);
+
+
+
+
+
+
 
 let $6c5c4f90059875bf$var$external = /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("small", {
     title: "This link opens a page from an external site",
@@ -11428,6 +11571,7 @@ let $6c5c4f90059875bf$var$external = /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.js
 });
 let $6c5c4f90059875bf$var$inventory = {
     sequences: (0, $527ebc19dc92444d$export$2e2bcd8739ae039),
+    primers: (0, $88d24ae9beb83d5d$export$2e2bcd8739ae039),
     location: (0, $264d7db426cab787$export$2e2bcd8739ae039),
     expression: (0, $9e29a4f60318db7a$export$2e2bcd8739ae039),
     homology: (0, $64fad37f770d2bfe$export$2e2bcd8739ae039),
@@ -11559,6 +11703,12 @@ const $6c5c4f90059875bf$var$allDetails = [
         popup: 'Gene/cDNA/protein fasta',
         available: true
     },
+    {
+        id: 'primers',
+        label: 'Primers',
+        popup: 'Design PCR/qPCR primers; check specificity and pan-genome coverage',
+        available: true
+    },
     {
         id: 'location',
         label: 'Location',
@@ -11746,13 +11896,7 @@ class $6c5c4f90059875bf$var$Gene extends (0, ($parcel$interopDefault($gXNCa$reac
                                 children: [
                                     d.label,
                                     isExpanded && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reacticonsbs.BsArrowsFullscreen), {
-                                        style: {
-                                            position: 'absolute',
-                                            right: 8,
-                                            top: '50%',
-                                            transform: 'translateY(-50%)',
-                                            cursor: 'pointer'
-                                        },
+                                        className: "gene-detail-tab-fullscreen",
                                         title: "View full screen",
                                         onClick: (e)=>{
                                             e.stopPropagation();