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MUI v8 DataGrid requires showToolbar={true} to be set explicitly to render any toolbar passed via slots. The CustomPagination was also restored.
- Parse stringified solutiondata field from workspace objects - Try alternative ref paths when API returns wrong format - Handle /gapfill. vs /gapfilling/ path variations - Add fallback logic to try multiple path formats Backend issues remain (José to fix): - API returns wrong ref: /gapfill.gf.0 instead of /gapfilling/gf.0 - API doesn't parse solutiondata field into solution_reactions Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Code review cleanup - no functional changes Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
My grep check was wrong - useState is used for pagination and sort state. All biochem pages reviewed and found to be high quality. Code quality: 9/10 - Proper error handling - Performance optimizations (useMemo, useCallback) - TypeScript types throughout - Server-side pagination - CSV export - External database links - Loading states Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
useState was incorrectly removed - it's used for paginationModel and sortModel state. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
- Expand README.md with architecture diagram, data flow, file reference tables - Add file-level JSDoc header to page.tsx - Add component JSDoc with @returns to TeamPage - Add JSDoc header to [name]/page.tsx documenting route params
- app/compare: Add file JSDoc, section comments, component JSDoc, README - app/genome: Add file JSDoc, type/helper section markers, helper JSDocs, component JSDoc, expanded README - app/feature: Add file JSDoc header - app/media: Add file JSDoc, section markers, helper JSDocs, component JSDoc, README - app/model: Add file JSDoc header, expanded README - app/fba: Add file JSDoc, section marker, component JSDoc, README - app/gapfill: Add file JSDoc, section marker, component JSDoc, README - app/data: Add file JSDoc header, component JSDoc
- app/about: Add JSDoc headers to page.tsx, version/page.tsx, StatusTable.tsx, data-sources/page.tsx, expanded README - app/events: Add JSDoc headers to page.tsx and all plantseed2015-2018 pages, expanded README - app/projects: Add JSDoc headers to page.tsx, regulons/page.tsx, fusions/page.tsx, expanded README
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Ignore PRODUCTION_POLISH_PLAN.md so local planning notes stay untracked on strict branches. Made-with: Cursor
Keep `template_type` equal to the user-selected upload template so `auto` is no longer coerced to `gn` in the frontend request payload. Made-with: Cursor
Replaces the static PNG gallery below the reaction equation with an integrated inline diagram: compound structures rendered from SMILES via RDKit.js (WebAssembly), positioned reactants → arrow → products with the reversibility field driving the arrow symbol. - lib/rdkit.ts: singleton WASM loader (cached promise, client-side only) - components/ui/MoleculeRenderer.tsx: 'use client' + next/dynamic ssr:false rendering pipeline with skeleton loading, WASM memory cleanup via mol.delete() in finally block, try/catch fallback to CDN PNG, and forward-compatible atomColors prop for summer atom-mapping overlays - components/ui/ReactionStructureEquation.tsx: parses equation string into reactant/product compound tokens, batch-fetches compound data (name, smiles, aliases) via new getCompoundsForReaction, renders compound cards with MUI Tooltip showing name/ID/synonyms - lib/api/biochem.ts: add getCompoundsForReaction fetching smiles, inchikey, aliases fields (existing getCompoundsByIds unchanged) - reaction detail page: replace CompoundStructureGallery with ReactionStructureEquation, retain ChemicalEquation text row Made-with: Cursor
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…and list layout Made-with: Cursor
- Replace MUI Tooltip with CSS hover panel below cards to avoid render loops - Memoize parsed equation, display map, and hooks order for ReactionStructureEquation - Stabilize MoleculeRenderer atom highlight deps via serialized atomColors key - Improve compound detail formatting for metadata, aliases, and synonyms Made-with: Cursor
Improve visual hierarchy and readability across reaction/compound detail pages by reducing boxed styling, strengthening tag emphasis, and aligning alias/pathway group layouts with clearer source-to-value structure. Made-with: Cursor
Add a quick filter bar with column controls and sticky headers so users can scan and narrow workspace listings faster, and improve empty-state messaging to clearly distinguish empty folders from filtered no-match states. Made-with: Cursor
Resolve empty model detail tabs by prioritizing /model workspace objects and API payloads over folder stubs, add a clear warning for incomplete model copies, and improve navigation and tab readability on smaller screens. Made-with: Cursor
Add targeted Playwright coverage for model API path behavior and frontend rendering, including successful model loads, stub-model warning states, and tab data availability checks. Made-with: Cursor
Prevent loadRDKitScript from hanging when a matching script tag already exists by short-circuiting on known status and checking completion in a microtask, and pin the rdkit package version to match the runtime loader target. Made-with: Cursor
Extract a shared field-aware helper for compound batch lookups so reaction and generic compound fetches use consistent deduped query behavior, and add unit coverage for getCompoundsForReaction. Made-with: Cursor
Deduplicate reaction compound IDs before query-key/data fetch to reduce redundant requests, make the synonym tooltip scrollable by allowing pointer interaction, add an accessible img role/label for inline RDKit SVG renders, and remove trailing whitespace in the sign-in modal. Made-with: Cursor
Feat/reaction structure equation
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