Remove ontology; read participant aliases via cross-core join

app/(reference-data)/biochem/compounds/[id]/page.tsx

@@ -467,9 +467,6 @@ export default function CompoundDetailPage() {
                     <DetailRow label="Synonyms">
                         <SynonymsDisplay synonyms={synonyms} />
                     </DetailRow>
-                    {cpd.ontology && cpd.ontology !== 'class:null|context:null' && (
-                        <DetailRow label="Ontology"><Typography variant="body2">{cpd.ontology}</Typography></DetailRow>
-                    )}
                     <DetailRow label="Source"><Typography variant="body2">{cpd.source ?? 'N/A'}</Typography></DetailRow>
                 </Box>
             </Box>

app/(reference-data)/biochem/reactions/[id]/page.tsx

@@ -426,13 +426,6 @@ export default function ReactionDetailPage() {
                         <PathwaysDisplay pathways={pathways} />
                     </DetailRow>
 
-                    {rxn.ontology && rxn.ontology !== 'class:null|context:null|step:null' && (
-                        <DetailRow label="Ontology">
-                            <Typography variant="body2" sx={{ wordBreak: 'break-word' }}>
-                                {rxn.ontology}
-                            </Typography>
-                        </DetailRow>
-                    )}
 
                 </CardContent>
             </Card>

lib/api/biochem.ts

@@ -12,6 +12,7 @@
 import {
     CPD_IMG_BASE,
     MODELSEED_API_URL,
+    SOLR_COMPOUNDS_COLLECTION,
     solrCorpusEndpoint,
 } from './config';
 import { hasNestedSchema, parentDocTypeFilter } from './solrSchema';
@@ -114,7 +115,6 @@
     ec_numbers: string[];
     is_obsolete: string;
     is_transport: boolean;
-    ontology: string;
     pathways: string[];
     notes: string[];
     abbreviation?: string;
@@ -146,7 +146,6 @@
     deltagerr: number;
     abbreviation: string;
     aliases: string[];
-    ontology: string;
     inchikey?: string;
     smiles?: string;
     is_cofactor?: boolean;
@@ -461,7 +460,13 @@
                 if (nestedStoichiometryQuickSearch) {
                     const wildcard = usePrefixOnly ? `${token}*` : `*${token}*`;
                     fieldClauses.push(
-                        `({!parent which="${parentDocTypeFilter('reactions')}" v="doc_type:stoichiometry AND (compound:${wildcard} OR participant_name:${wildcard} OR participant_aliases:${wildcard} OR aliases:${wildcard})"})`,
+                        // Participant aliases are NOT denormalised onto the stoichiometry children.
+                        // They are read from the compounds core at query time with a cross-core
+                        // join, so editing a compound's aliases takes effect without reposting
+                        // every reaction that uses it. fromIndex must name the compounds core for
+                        // THIS environment -- compounds_staging from reactions_staging -- or the
+                        // clause silently resolves against the wrong dataset instead of erroring.
+                        `({!parent which="${parentDocTypeFilter('reactions')}" v="doc_type:stoichiometry AND (compound:${wildcard} OR participant_name:${wildcard} OR {!join from=id to=compound fromIndex=${SOLR_COMPOUNDS_COLLECTION}}aliases:${wildcard})"})`,
                     );
                 }
                 if (nestedThermoEvidenceQuickSearch) {
@@ -519,11 +524,7 @@
         url += `&fq=${encodeURIComponent(fq)}`;
     }
 
-    // Filter out ontology field for compounds (Solr compounds_staging has no ontology field)
-    const filterItems = (filterModel?.items ?? []).filter(item => {
-        const field = toSolrField(String(item.field ?? ''));
-        return !(collection === 'compounds' && field === 'ontology');
-    });
+    const filterItems = filterModel?.items ?? [];
 
     const filterClauses = filterItems
         .map((item) => buildFilterClause(item))
@@ -793,14 +794,12 @@
 function matchesFilterItem(
     doc: Record<string, unknown>,
     item: GridFilterItem,
     endpoint?: string,
 ): boolean {
     const operator = String(item.operator ?? '');
     const field = toSolrField(String(item.field ?? ''));
     if (!field || !operator) return true;
 
-    /* Solr compounds_staging has no ontology query field — REST payloads typically omit it too. */
-    if (endpoint === 'compounds' && field === 'ontology') return true;
 
     const rawField = doc[field];
     const fieldValue = normalizeFieldValue(rawField);
@@ -1157,23 +1156,19 @@
 const RXN_VISIBLE = [
     'name', 'id', 'definition', 'reversibility', 'thermo_evidence',
     'stoichiometry', 'status', 'aliases', 'ec_numbers', 'is_obsolete',
-    'is_transport', 'ontology', 'pathways', 'notes',
+    'is_transport', 'pathways', 'notes',
 ];
 // Solr child transformers only return fields also present in the parent `fl` list.
 // Include the stored stoichiometry fields needed by Equation highlighting before
 // requesting the matching child documents.
 const RXN_VISIBLE_NESTED = [
     ...RXN_VISIBLE,
     'compound', 'coefficient', 'compartment', 'is_reactant', 'participant_name',
-    'participant_aliases', 'aliases', 'grade', 'doc_type', '_nest_path_',
+    'grade', 'doc_type', '_nest_path_',
     '[child childFilter="doc_type:stoichiometry OR doc_type:thermo_evidence OR doc_type:thermo-evidence" limit=200]',
 ];
 
-/**
- * Compound quick-search fields — must exist on Solr `compounds_staging`.
- * Note: Solr does not expose an `ontology` field on compounds; querying it yields 400
- * ("undefined field ontology") and breaks the whole quick-search clause.
- */
+/** Compound quick-search fields — every entry must exist on the Solr core. */
 const CPD_SEARCH_FIELDS = ['id', 'name', 'formula', 'synonyms', 'aliases'];
 
 /** Compound visible fields matching Solr `compounds_staging` stored fields (see fl=). */

tests/unit/api/biochem-rest-filtering.test.ts

@@ -98,24 +98,6 @@ describe('biochem REST path local filter/sort/pagination', () => {
     expect(String(fetchMock.mock.calls[0]?.[0] ?? '')).toContain('limit=5000');
   });
 
-  it('ignores ontology column filters on compound REST payloads (Solr has no ontology field)', async () => {
-    const fetchMock = vi.fn().mockResolvedValue({
-      ok: true,
-      json: async () => [{ id: 'cpd00001', name: 'ATP', formula: '', aliases: [] }],
-    });
-    vi.stubGlobal('fetch', fetchMock);
-
-    const biochem = await import('@/lib/api/biochem');
-    const res = await biochem.getCompoundsFromModelseedApi({
-      limit: 10,
-      filterModel: {
-        items: [{ field: 'ontology', operator: 'contains', value: 'nope-miss' }],
-        quickFilterValues: [],
-      },
-    });
-    expect(res.docs).toHaveLength(1);
-  });
-
   it('refines quick search across compound fields locally (OR across searchFields)', async () => {
     const fetchMock = vi.fn().mockResolvedValue({
       ok: true,

tests/unit/api/biochem.test.ts

@@ -118,7 +118,7 @@ describe('getCompounds Solr query shape', () => {
     vi.restoreAllMocks();
   });
 
-  it('quick search must not reference ontology (undefined field on compounds_staging)', async () => {
+  it('quick search only references fields that exist on the compounds core', async () => {
     const biochemApi = await loadBiochemApi();
     const fetchMock = vi.spyOn(globalThis, 'fetch').mockImplementation(() =>
       Promise.resolve(
@@ -143,7 +143,14 @@ describe('getCompounds Solr query shape', () => {
     const qRaw = u.searchParams.get('q');
     expect(qRaw).toBeTruthy();
     const q = decodeURIComponent(qRaw ?? '');
-    expect(q).not.toMatch(/\bontology\b/i);
+    // Every field: token in q must be one the core actually defines. Solr answers an
+    // undefined field in q with a hard 400, and a 400 carries no CORS header, so the
+    // browser reports a CORS failure and points at the wrong layer. Three fields have
+    // reached production this way.
+    const COMPOUND_CORE_FIELDS = ['id', 'name', 'formula', 'synonyms', 'aliases'];
+    const queried = [...q.matchAll(/(\w+):/g)].map((mm) => mm[1]);
+    const unknown = [...new Set(queried)].filter((f) => !COMPOUND_CORE_FIELDS.includes(f));
+    expect(unknown).toEqual([]);
     expect(q).toContain('cpd05323');
     expect(q).toMatch(/formula|aliases|name|id/);
   });

tests/unit/api/biochemStoichiometry.test.ts

@@ -124,9 +124,9 @@ describe('Solr stoichiometry support', () => {
         expect(nestedUrl.searchParams.get('fl')).toBe([
             'name', 'id', 'definition', 'reversibility', 'thermo_evidence',
             'stoichiometry', 'status', 'aliases', 'ec_numbers', 'is_obsolete',
-            'is_transport', 'ontology', 'pathways', 'notes',
+            'is_transport', 'pathways', 'notes',
             'compound', 'coefficient', 'compartment', 'is_reactant', 'participant_name',
-            'participant_aliases', 'aliases', 'grade', 'doc_type', '_nest_path_',
+            'grade', 'doc_type', '_nest_path_',
             '[child childFilter="doc_type:stoichiometry OR doc_type:thermo_evidence OR doc_type:thermo-evidence" limit=200]',
         ].join(','));
         expect(nested.docs[0].participants).toEqual([{
@@ -150,7 +150,7 @@ describe('Solr stoichiometry support', () => {
         expect(reaction.participants).toHaveLength(1);
         await api.getReactions({ filterModel: { items: [], quickFilterValues: ['cpd05331'] } });
         const legacyListUrl = new URL(dataUrl(fetchMock));
-        expect(legacyListUrl.searchParams.get('fl')).toBe('name,id,definition,reversibility,thermo_evidence,stoichiometry,status,aliases,ec_numbers,is_obsolete,is_transport,ontology,pathways,notes');
+        expect(legacyListUrl.searchParams.get('fl')).toBe('name,id,definition,reversibility,thermo_evidence,stoichiometry,status,aliases,ec_numbers,is_obsolete,is_transport,pathways,notes');
         expect(legacyListUrl.searchParams.get('q')).toBe('(id:*cpd05331* OR name:*cpd05331* OR definition:*cpd05331* OR reversibility:*cpd05331* OR status:*cpd05331* OR ec_numbers:*cpd05331* OR aliases:*cpd05331* OR pathways:*cpd05331* OR stoichiometry:*cpd05331* OR notes:*cpd05331*)');
         expect(legacyListUrl.searchParams.get('sort')).toBe('id asc');
         await api.getReactions({ filterModel: { items: [], quickFilterValues: ['Glucoraphanin'] } });
@@ -176,8 +176,8 @@ describe('Solr stoichiometry support', () => {
         expect(nestedQuery).toContain('name:*Glucoraphanin*');
         expect(nestedQuery).toContain('definition:*Glucoraphanin*');
         expect(nestedQuery).not.toContain('stoichiometry:*');
-        expect(nestedQuery).toContain('({!parent which="doc_type:reaction" v="doc_type:stoichiometry AND (compound:*Glucoraphanin* OR participant_name:*Glucoraphanin* OR participant_aliases:*Glucoraphanin* OR aliases:*Glucoraphanin*)"})');
-        expect(nestedQuery).toContain('({!parent which="doc_type:reaction" v="doc_type:stoichiometry AND (compound:*cpd05331* OR participant_name:*cpd05331* OR participant_aliases:*cpd05331* OR aliases:*cpd05331*)"})');
+        expect(nestedQuery).toContain('({!parent which="doc_type:reaction" v="doc_type:stoichiometry AND (compound:*Glucoraphanin* OR participant_name:*Glucoraphanin* OR {!join from=id to=compound fromIndex=compounds_staging}aliases:*Glucoraphanin*)"})');
+        expect(nestedQuery).toContain('({!parent which="doc_type:reaction" v="doc_type:stoichiometry AND (compound:*cpd05331* OR participant_name:*cpd05331* OR {!join from=id to=compound fromIndex=compounds_staging}aliases:*cpd05331*)"})');
         expect(nestedQuery).toContain(') AND (');
         await api.findReactionsForCompound('cpd00002');
         expect(new URL(dataUrl(fetchMock)).searchParams.get('q')).toContain('{!parent which="doc_type:reaction" v="doc_type:stoichiometry AND compound:cpd00002"}');
@@ -237,7 +237,6 @@ describe('reaction request regression matrix', () => {
         await api.getReactions({ filterModel: { items: [], quickFilterValues: ['RegistryAlias'] } });
 
         const query = new URL(dataUrl(fetchMock)).searchParams.get('q') ?? '';
-        expect(query).toContain('participant_aliases:*RegistryAlias*');
         expect(query).toContain('aliases:*RegistryAlias*');
         expect(query).toContain('participant_name:*RegistryAlias*');
         expect(query).toContain('compound:*RegistryAlias*');