gramene-search 2.0.5 → 2.0.7

package/src/bundles/ontologies.js

@@ -1,81 +1,73 @@
+import { getConfiguredCache } from 'money-clip';
+
 const ONT_KEYS = ['GO', 'PO', 'TO', 'domains'];
-const BATCH_SIZE = 200;
+
+// Dedicated IndexedDB store for ontology records. The full term set per
+// ontology is stable enough to keep around indefinitely (default maxAge of
+// `Infinity`), and we don't want it to share the short TTL of the app-wide
+// cache configured in demo.js.
+const cache = getConfiguredCache({
+  version: 1,
+  name: 'gramene_ontologies'
+});
 
 const inflight = {};
 
 const ontologies = {
   name: 'ontologies',
+
   getReducer: () => {
-    const initialState = { GO: {}, PO: {}, TO: {}, domains: {} };
+    const initialState = { GO: {}, PO: {}, TO: {}, domains: {}, loaded: {} };
     return (state = initialState, { type, payload }) => {
       switch (type) {
-        case 'ONTOLOGY_RECORDS_REQUESTED': {
-          const { key, ids } = payload;
-          const bucket = { ...state[key] };
-          for (const id of ids) {
-            if (!bucket.hasOwnProperty(id)) bucket[id] = null;
-          }
-          return { ...state, [key]: bucket };
-        }
-        case 'ONTOLOGY_RECORDS_RECEIVED': {
-          const { key, records } = payload;
-          return { ...state, [key]: { ...state[key], ...records } };
-        }
+        case 'ONTOLOGY_BULK_LOADED':
+          return {
+            ...state,
+            [payload.key]: payload.records,
+            loaded: { ...state.loaded, [payload.key]: true }
+          };
         default:
           return state;
       }
     };
   },
 
-  doEnsureOntologyRecords: (key, ids) => ({ dispatch, store }) => {
+  // Signature kept for backward compatibility — the `ids` argument is
+  // ignored. On first call per ontology key we load the full term set
+  // (cache hit if available, otherwise `${api}/${key}?rows=-1`) and
+  // dispatch a single bulk load. Subsequent calls are no-ops.
+  doEnsureOntologyRecords: (key, _ids) => ({ dispatch, store }) => {
     if (!ONT_KEYS.includes(key)) return Promise.resolve();
-    if (!Array.isArray(ids) || ids.length === 0) return Promise.resolve();
-    const existing = store.selectOntologies()[key] || {};
-    const missing = [];
-    for (const id of ids) {
-      if (id == null) continue;
-      const idNum = +id;
-      if (!existing.hasOwnProperty(idNum) && !(inflight[key] && inflight[key].has(idNum))) {
-        missing.push(idNum);
-      }
-    }
-    if (missing.length === 0) return Promise.resolve();
-
-    if (!inflight[key]) inflight[key] = new Set();
-    for (const id of missing) inflight[key].add(id);
-    dispatch({ type: 'ONTOLOGY_RECORDS_REQUESTED', payload: { key, ids: missing } });
-
-    const api = store.selectGrameneAPI();
-    const batches = [];
-    for (let i = 0; i < missing.length; i += BATCH_SIZE) {
-      batches.push(missing.slice(i, i + BATCH_SIZE));
-    }
+    const state = store.selectOntologies();
+    if (state.loaded && state.loaded[key]) return Promise.resolve();
+    if (inflight[key]) return inflight[key];
 
-    const fetchBatch = (batch) => {
-      const idList = batch.length === 1 ? `${batch[0]},0` : batch.join(',');
-      return fetch(`${api}/${key}?idList=${idList}&rows=${batch.length + 1}`)
-        .then(r => r.json())
-        .then(docs => {
-          const records = {};
-          for (const d of (docs || [])) {
-            if (d && d._id != null) records[d._id] = d;
-          }
-          for (const id of batch) {
-            if (!records.hasOwnProperty(id)) records[id] = { _id: id, missing: true };
-          }
-          dispatch({ type: 'ONTOLOGY_RECORDS_RECEIVED', payload: { key, records } });
-        })
-        .catch(() => {
-          const records = {};
-          for (const id of batch) records[id] = { _id: id, missing: true };
-          dispatch({ type: 'ONTOLOGY_RECORDS_RECEIVED', payload: { key, records } });
-        })
-        .finally(() => {
-          for (const id of batch) inflight[key].delete(id);
-        });
-    };
+    inflight[key] = cache.get(key)
+      .then(cached => {
+        if (cached) {
+          dispatch({ type: 'ONTOLOGY_BULK_LOADED', payload: { key, records: cached } });
+          return;
+        }
+        const api = store.selectGrameneAPI();
+        return fetch(`${api}/${key}?rows=-1`)
+          .then(r => r.json())
+          .then(docs => {
+            const records = {};
+            for (const d of (docs || [])) {
+              if (d && d._id != null) records[d._id] = d;
+            }
+            dispatch({ type: 'ONTOLOGY_BULK_LOADED', payload: { key, records } });
+            cache.set(key, records).catch(e => console.warn('Failed to cache ontology', key, e));
+          });
+      })
+      .catch(err => {
+        console.error(`Failed to load ontology ${key}`, err);
+      })
+      .finally(() => {
+        delete inflight[key];
+      });
 
-    return Promise.all(batches.map(fetchBatch));
+    return inflight[key];
   },
 
   selectOntologies: state => state.ontologies

package/src/bundles/swaggerFields.js

@@ -268,12 +268,12 @@ function buildSpeciesNameIndex(grameneMaps) {
 function fieldExperimentId(name) {
   let m = name.match(/^(\w+?)_g\d+__expr$/);
   if (m) return m[1].replace(/_/g, '-');
-  m = name.match(/^(\w+?)_g\d+_g\d+_(pval|logfc|l2fc)_attr_[a-z]$/);
+  m = name.match(/^(\w+?)_g\d+_g\d+_(pval|l2fc)_attr_[a-z]$/);
   if (m) return m[1].replace(/_/g, '-');
   return null;
 }
 
-const STAT_RANK = { l2fc: 0, logfc: 1, pval: 2 };
+const STAT_RANK = { l2fc: 0, pval: 1 };
 
 function collapseDiffExprInSubgroups(subgroups, fieldsOut, collator) {
   for (const taxGroup of subgroups) {
@@ -300,7 +300,7 @@ function collapseDiffExprInSubgroups(subgroups, fieldsOut, collator) {
         });
         const rep = names[0];
         const repEntry = fieldsOut[rep];
-        const label = (repEntry.label || rep).replace(/\s+\((?:pval|logfc|l2fc)\)/, '');
+        const label = (repEntry.label || rep).replace(/\s+\((?:pval|l2fc)\)/, '');
         fieldsOut[rep] = { ...repEntry, label, linkedFields: names.slice() };
         newFields.push(rep);
       }
@@ -577,14 +577,13 @@ grameneFieldCatalog.selectFieldCatalog = createSelector(
     const present = new Set(fieldNames);
     // Build a synthetic doc from the discovered field names; values carry the
     // right JS type so inferType picks the correct multiValued/type (arrays
-    // for multi-valued fields, scalars otherwise). Derive pval/logfc
-    // companions from every l2fc field.
+    // for multi-valued fields, scalars otherwise). Derive the pval companion
+    // from every l2fc field.
     const doc = {};
     for (const name of present) {
       doc[name] = synthesizedValue(name);
       if (/_l2fc_attr_f$/.test(name)) {
         doc[name.replace('_l2fc_', '_pval_')] = 0;
-        doc[name.replace('_l2fc_', '_logfc_')] = 0;
       }
     }
     const catalog = buildCatalog([doc]);

package/src/bundles/views.js

@@ -29,6 +29,12 @@ const grameneViews = {
           show: 'off',
           shouldScroll: false
         },
+        {
+          id: 'gsea',
+          name: 'Gene set enrichment',
+          show: 'off',
+          shouldScroll: false
+        },
         {
           id: 'userLists',
           name: 'User Gene Lists',
@@ -121,7 +127,7 @@ const grameneViews = {
       const touched = raw.touched || {};
       const numFound = (search && search.response && search.response.numFound) || 0;
       const hasFilters = !!(filters && filters.rightIdx > 1);
-      const resultDependentIds = new Set(['taxonomy', 'list', 'export']);
+      const resultDependentIds = new Set(['taxonomy', 'list', 'export', 'exprViz', 'gsea']);
       const autoDisable = (numFound === 0) || !hasFilters;
       const hasFirebase = !!(config && config.firebaseConfig);
 

package/src/components/exporter/expressionResolver.js

@@ -1,5 +1,5 @@
 const EXPR_FIELD_RE = /^(E[-_][A-Za-z0-9_-]+?)_g(\d+)__expr$/;
-const DIFFEXPR_FIELD_RE = /^(E[-_][A-Za-z0-9_-]+?)_g(\d+)_g(\d+)_(pval|logfc|l2fc)_attr_([a-z])$/;
+const DIFFEXPR_FIELD_RE = /^(E[-_][A-Za-z0-9_-]+?)_g(\d+)_g(\d+)_(pval|l2fc)_attr_([a-z])$/;
 
 export const EXPRESSION_EXTRA_COLUMNS = [
   'experiment',
@@ -132,7 +132,7 @@ export function resolveDiffExpressionForDoc(doc, diffExpressionFields, expressio
       byContrast.set(key, entry);
     }
     if (parsed.stat === 'pval') entry.pval = val;
-    else entry.l2fc = val; // l2fc or logfc
+    else entry.l2fc = val;
   }
   const maxPval = cutoffs && cutoffs.diffMaxPval;
   const maxPvalActive = maxPval !== null && maxPval !== undefined && maxPval !== '' && Number.isFinite(+maxPval);

package/src/components/exprViz/ExprTable.js

@@ -8,13 +8,24 @@ const baseColDefs = [
   { field: 'name', headerName: 'Name', pinned: 'left', width: 140, suppressMovable: true }
 ];
 
+// Hoisted so the reference is stable across renders. ag-grid otherwise sees a
+// "new" defaultColDef on every parent re-render (e.g. when hovering a row
+// triggers setHoveredId in the parent) and re-applies column state, which
+// snaps any user-resized columns back to their original widths.
+const DEFAULT_COL_DEF = {
+  resizable: true,
+  sortable: true,
+  filter: false,
+  suppressMenu: true
+};
+
 function arraysEqual(a, b) {
   if (a.length !== b.length) return false;
   for (let i = 0; i < a.length; i++) if (a[i] !== b[i]) return false;
   return true;
 }
 
-function buildFieldInfo(fields, studies, expressionSamples) {
+export function buildFieldInfo(fields, studies, expressionSamples) {
   const info = {};
   if (!fields || !studies || !expressionSamples) return info;
   const wanted = new Set(fields);
@@ -322,7 +333,7 @@ const ExprTable = ({ rows, fields, onReorder, studies, expressionSamples, onHove
       <AgGridReact
         rowData={rows}
         columnDefs={columnDefs}
-        defaultColDef={{ resizable: true, sortable: true, filter: false, suppressMenu: true }}
+        defaultColDef={DEFAULT_COL_DEF}
         animateRows={false}
         suppressFieldDotNotation={true}
         suppressDragLeaveHidesColumns={true}

package/src/components/exprViz/ExprVizView.js

@@ -2,7 +2,7 @@ import React, { useEffect, useMemo, useRef, useState } from 'react';
 import { connect } from 'redux-bundler-react';
 import { Tabs, Tab, Button, ToggleButton, ToggleButtonGroup } from 'react-bootstrap';
 import FieldsModal from './FieldsModal';
-import ExprTable from './ExprTable';
+import ExprTable, { buildFieldInfo } from './ExprTable';
 import ParallelCoordsPlot from './ParallelCoordsPlot';
 import './styles.css';
 
@@ -193,11 +193,49 @@ function tsvCell(v) {
   return s.replace(/[\t\r\n]+/g, ' ');
 }
 
-function downloadTsv(filename, rows, fields) {
+// Mirror the on-screen table header in the TSV: one row per metadata level
+// the table is showing (Study, then one row per distinct factor type, then
+// one row per distinct characteristic type), followed by the leaf header
+// (Gene ID / Name / per-sample group). The first two columns are repurposed
+// to carry the row category and the row's specific name, matching the
+// pinned-column labels in ExprTable.
+function downloadTsv(filename, rows, fields, studies, expressionSamples) {
   const cols = ['id', 'name', ...fields];
-  const headerLabels = ['id', 'name', ...fields.map(f => f.replace(/__expr$/, ''))];
-  const lines = [headerLabels.join('\t')];
+  const fieldInfo = buildFieldInfo(fields, studies, expressionSamples);
+
+  const factorTypes = new Set();
+  const charTypes = new Set();
+  for (const f of fields) {
+    const info = fieldInfo[f];
+    if (!info) continue;
+    Object.keys(info.factors || {}).forEach(t => factorTypes.add(t));
+    Object.keys(info.characteristics || {}).forEach(t => charTypes.add(t));
+  }
+  const factorTypeList = Array.from(factorTypes).sort();
+  const charTypeList = Array.from(charTypes).sort();
+
+  const metaRow = (cat, label, getValue) => {
+    const cells = [cat, label];
+    for (const f of fields) cells.push(tsvCell(getValue(fieldInfo[f] || {})));
+    return cells.join('\t');
+  };
+
+  const lines = [];
+  lines.push(metaRow('Study', 'Title', info => info.studyDescription || ''));
+  for (const t of factorTypeList) {
+    lines.push(metaRow('Factor', t, info => (info.factors && info.factors[t]) || ''));
+  }
+  for (const t of charTypeList) {
+    lines.push(metaRow('Characteristic', t, info => (info.characteristics && info.characteristics[t]) || ''));
+  }
+  // Leaf header — column ids for the data rows.
+  lines.push(['Gene ID', 'Name', ...fields.map(f => {
+    const info = fieldInfo[f];
+    return (info && info.group) || f.replace(/__expr$/, '');
+  })].join('\t'));
+
   for (const r of rows) lines.push(cols.map(c => tsvCell(r[c])).join('\t'));
+
   const blob = new Blob([lines.join('\n') + '\n'], { type: 'text/tab-separated-values' });
   const url = URL.createObjectURL(blob);
   const a = document.createElement('a');
@@ -317,7 +355,7 @@ const TaxonPanel = ({ taxon, studies, expressionSamples, tabState, onOpenFields,
           size="sm"
           variant="outline-secondary"
           disabled={filteredRows.length === 0 || visibleFields.length === 0}
-          onClick={() => downloadTsv(`expression_${taxon}.tsv`, filteredRows, visibleFields)}
+          onClick={() => downloadTsv(`expression_${taxon}.tsv`, filteredRows, visibleFields, studies, expressionSamples)}
           title="Download the visible rows and columns as tab-delimited text"
         >
           Download TSV

package/src/components/geneSearchUI.js

@@ -13,6 +13,7 @@ import Expression from './results/Expression'
 import UserGeneLists from './results/UserGeneLists'
 import ExporterView from './exporter/ExporterView'
 import ExprVizView from './exprViz/ExprVizView'
+import GSEA from './results/GSEA'
 import Auth from './Auth'
 import ReactGA from 'react-ga4'
 import './styles.css';
@@ -42,6 +43,7 @@ const inventory = {
   attribs: GeneAttribs,
   expression: Expression,
   exprViz: ExprVizView,
+  gsea: GSEA,
   userLists: UserGeneLists,
   export: ExporterView
 };