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Staging sync: biochem/data-control hardening and review fixes #176

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Merged
VibhavSetlur merged 11 commits into from
May 4, 2026
Merged

Staging sync: biochem/data-control hardening and review fixes #176

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6cc9f6c
fix(lint): migrate event pages to next/image for external images
VibhavSetlur May 1, 2026
39091b6
fix(lint): replace manual stylesheet tag with Next.js-compliant import
VibhavSetlur May 1, 2026
6abf205
fix(lint): resolve exhaustive-deps and migrate to next/image in Molec…
VibhavSetlur May 1, 2026
d54d88a
fix(lint): remove unused genomeData variable in genome detail page
VibhavSetlur May 1, 2026
0857b51
Adding deployment script and updating environment variables for repor…
May 1, 2026
0ed36f3
feat(ui): replace search bar with find-in-page style search
VibhavSetlur May 1, 2026
134937f
fix(search): harden dual-backend filtering and trim e2e suite
VibhavSetlur May 1, 2026
9f51610
feat(model): format gene reactions with linked chips
VibhavSetlur May 1, 2026
e748082
fix(biochem): preserve solr-only pages and expand filter coverage
VibhavSetlur May 4, 2026
748bdaf
fix(review): address Copilot feedback on highlight cleanup and tests
VibhavSetlur May 4, 2026
1020067
Merge remote-tracking branch 'upstream/staging' into staging
VibhavSetlur May 4, 2026
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2 changes: 1 addition & 1 deletion app/(reference-data)/genomes/[ref]/page.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ export default function GenomeDetailPage(props: GenomeDetailProps) {
const genomeRef = decodeURIComponent(params.ref);

// Query for genome data - this would need to be implemented in the API
const { data: genomeData, isLoading, error } = useQuery({
const { isLoading, error } = useQuery({
queryKey: ['genome', genomeRef],
queryFn: async () => {
// Placeholder - would need actual API endpoint
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4 changes: 3 additions & 1 deletion app/events/plantseed2015/page.tsx
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Expand Up @@ -42,9 +42,11 @@ export default function PlantSEED2015Page() {

<Box textAlign="center" mb={4}>
<a href="http://press3.mcs.anl.gov/plantseed2015/files/2015/09/2015-Wkshp_participants.jpeg" target="_blank" rel="noopener noreferrer">
<img
<Image
src="http://press3.mcs.anl.gov/plantseed2015/files/2015/09/2015-Wkshp_participants.jpeg"
alt="2015 Workshop Group Photo"
width={800}
height={600}
style={{ maxWidth: '100%', height: 'auto', objectFit: 'contain' }}
Comment on lines 44 to 50
/>
</a>
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4 changes: 3 additions & 1 deletion app/events/plantseed2016/page.tsx
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Expand Up @@ -42,9 +42,11 @@ export default function PlantSEED2016Page() {

<Box textAlign="center" mb={4}>
<a href="http://bioseed.mcs.anl.gov/~seaver/Files/PlantSEED_Workshop_2016/PlantSEED_Workshop_2016.jpg" target="_blank" rel="noopener noreferrer">
<img
<Image
src="http://bioseed.mcs.anl.gov/~seaver/Files/PlantSEED_Workshop_2016/PlantSEED_Workshop_2016.jpg"
alt="2016 Workshop Group Photo"
width={800}
height={600}
style={{ maxWidth: '100%', height: 'auto', objectFit: 'contain' }}
Comment on lines 44 to 50
/>
</a>
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4 changes: 3 additions & 1 deletion app/events/plantseed2017/page.tsx
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Expand Up @@ -42,9 +42,11 @@ export default function PlantSEED2017Page() {

<Box textAlign="center" mb={4}>
<a href="http://bioseed.mcs.anl.gov/~seaver/Files/PlantSEED_Workshop_2017/PlantSEED_Workshop_2017.png" target="_blank" rel="noopener noreferrer">
<img
<Image
src="http://bioseed.mcs.anl.gov/~seaver/Files/PlantSEED_Workshop_2017/PlantSEED_Workshop_2017.png"
alt="2017 Workshop Group Photo"
width={800}
height={600}
style={{ maxWidth: '100%', height: 'auto', objectFit: 'contain' }}
Comment on lines 44 to 50
/>
</a>
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4 changes: 3 additions & 1 deletion app/events/plantseed2018/page.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -54,9 +54,11 @@ export default function PlantSEED2018Page() {

<Box textAlign="center" mb={4}>
<a href="http://bioseed.mcs.anl.gov/~seaver/Files/PlantSEED_Workshop_2018/PlantSEED_Workshop_2018_Participants.png" target="_blank" rel="noopener noreferrer">
<img
<Image
src="http://bioseed.mcs.anl.gov/~seaver/Files/PlantSEED_Workshop_2018/PlantSEED_Workshop_2018_Participants.png"
alt="2018 Workshop Group Photo"
width={800}
height={600}
style={{ maxWidth: '100%', height: 'auto', objectFit: 'contain' }}
/>
Comment on lines 55 to 63
</a>
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2 changes: 1 addition & 1 deletion app/layout.tsx
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Expand Up @@ -8,6 +8,7 @@ import Providers from '@/components/Providers';
import { AuthProvider } from '@/components/auth/AuthProvider';
import type { Metadata } from "next";
import "./globals.css";
import "@/styles/icomoon/style.css";

export const metadata: Metadata = {
title: "ModelSEED",
Expand All @@ -23,7 +24,6 @@ export default function RootLayout({
<html lang="en" suppressHydrationWarning>
<head>
<link rel="shortcut icon" href="/img/ModelSEED-favicon.png" />
<link rel="stylesheet" href="/icomoon/style.css" />
<link
href="https://fonts.googleapis.com/icon?family=Material+Icons"
rel="stylesheet"
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61 changes: 49 additions & 12 deletions app/model/[...path]/page.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -157,6 +157,20 @@ function toSearchableString(value: unknown): string {
return '';
}

function extractReactionIds(value: unknown): string[] {
const raw = toSearchableString(value);
if (!raw.trim()) return [];
const matches = raw.match(/rxn\d{5}/g) ?? [];
const seen = new Set<string>();
const ordered: string[] = [];
for (const match of matches) {
if (seen.has(match)) continue;
seen.add(match);
ordered.push(match);
}
return ordered;
}

function buildReactionRows(model: Record<string, unknown>): Record<string, unknown>[] {
return asArray<Record<string, unknown>>(model.modelreactions ?? model.reactions).map((reaction, index) => ({
id: String((reaction.id ?? extractRefId(reaction.reaction_ref)) || `rxn-${index}`),
Expand Down Expand Up @@ -185,6 +199,7 @@ function buildGeneRows(model: Record<string, unknown>): Record<string, unknown>[
return explicitGenes.map((gene, index) => ({
id: String((gene.id ?? extractRefId(gene.feature_ref)) || `gene-${index}`),
reactions: toSearchableString(gene.reactions ?? []),
reactionIds: extractReactionIds(gene.reactions ?? []),
functions: gene.functions ? toSearchableString(gene.functions) : 'N/A',
}));
}
Expand All @@ -211,6 +226,7 @@ function buildGeneRows(model: Record<string, unknown>): Record<string, unknown>[
return Array.from(geneToReactions.entries()).map(([gene, reactions]) => ({
id: gene,
reactions: Array.from(reactions).join(', '),
reactionIds: Array.from(reactions),
functions: 'View details',
}));
}
Expand Down Expand Up @@ -400,7 +416,36 @@ function buildTableConfig(model: Record<string, unknown>): Record<Exclude<TabKey
rows: buildGeneRows(model),
columns: [
{ field: 'id', headerName: 'Gene', width: 230 },
{ field: 'reactions', headerName: 'Reactions', flex: 1, minWidth: 260 },
{
field: 'reactions',
headerName: 'Reactions',
flex: 1,
minWidth: 320,
renderCell: (params) => {
const row = params.row as Record<string, unknown>;
const reactionIds = Array.isArray(row.reactionIds)
? (row.reactionIds as string[])
: extractReactionIds(params.value);
if (reactionIds.length === 0) {
return <Typography variant="body2" color="text.secondary">N/A</Typography>;
}
return (
<Stack direction="row" spacing={0.5} useFlexGap flexWrap="wrap" sx={{ py: 0.5 }}>
{reactionIds.map((rxnId) => (
<Chip
key={`${String(row.id ?? 'gene')}-${rxnId}`}
label={rxnId}
size="small"
component={Link}
clickable
href={`/biochem/reactions/${rxnId}`}
sx={{ color: '#00acc1' }}
/>
))}
</Stack>
);
},
},
{ field: 'functions', headerName: 'Functions', flex: 1, minWidth: 260 },
],
},
Expand Down Expand Up @@ -1711,7 +1756,8 @@ export default function ModelDetailPage({ params }: { params: Promise<{ path: st
modelName,
);

const genomeRef = String(modelObject.genome_ref ?? modelObject.genome_id ?? '-');
const genomeRefRaw = String(modelObject.genome_ref ?? modelObject.genome_id ?? '-');
const genomeRef = genomeRefRaw.replace(/\|\|+$/, '').trim() || '-';

const visibleTabs = MODEL_TABS.filter((tab) => !(isPlantModel && tab.key === 'edits'));
const activeTabVisible = visibleTabs.some((tab) => tab.key === activeTab);
Expand All @@ -1727,16 +1773,7 @@ export default function ModelDetailPage({ params }: { params: Promise<{ path: st
},
{
label: 'Genome Ref',
value: genomeRef !== '-' ? (
<Link
href={`https://www.bv-brc.org/view/Genome/${genomeRef}`}
target="_blank"
rel="noreferrer"
style={{ color: '#00acc1', textDecoration: 'none' }}
>
{genomeRef}
</Link>
) : '-',
value: genomeRef,
},
Comment on lines 1759 to 1777
{ label: 'Type', value: String(modelObject.type ?? '-') },
{
Expand Down
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