feat(biochem): Solr 9 compatibility, per-corpus endpoint configuration, and color-blind-safe atom mapping

.env.example

@@ -118,23 +118,52 @@ NEXT_PUBLIC_SOLR_BASE_URL=
 NEXT_PUBLIC_SOLR_BASE_URL_STAGING=https://staging.modelseed.org/solr/
 NEXT_PUBLIC_SOLR_BASE_URL_PRODUCTION=https://modelseed.org/solr/
 
+# Per-corpus base precedence: explicit override → mode default → shared
+# NEXT_PUBLIC_SOLR_BASE_URL resolution. Leave empty to retain shared-base behavior.
+# A relative value such as /solr/ is served through the SOLR_PROXY_UPSTREAM rewrite.
+NEXT_PUBLIC_SOLR_REACTIONS_BASE_URL=
+NEXT_PUBLIC_SOLR_REACTIONS_BASE_URL_STAGING=
+NEXT_PUBLIC_SOLR_REACTIONS_BASE_URL_PRODUCTION=
+NEXT_PUBLIC_SOLR_COMPOUNDS_BASE_URL=
+NEXT_PUBLIC_SOLR_COMPOUNDS_BASE_URL_STAGING=
+NEXT_PUBLIC_SOLR_COMPOUNDS_BASE_URL_PRODUCTION=
+NEXT_PUBLIC_SOLR_STRUCTURES_BASE_URL=
+NEXT_PUBLIC_SOLR_STRUCTURES_BASE_URL_STAGING=
+NEXT_PUBLIC_SOLR_STRUCTURES_BASE_URL_PRODUCTION=
+
+# Server-side only; for dev/internal use. http://poplar:8983/solr is an internal
+# host and must never be used as a public production value.
+SOLR_PROXY_UPSTREAM=
+
 # =============================================================================
 # SOLR COLLECTION / CORE NAMES
 # =============================================================================
-# The Solr core names for the reactions and compounds collections.
+# The Solr core names for the reactions, compounds, and structures collections.
 # These must match the names configured in your Solr instance.
 #
-# Override:       Required in manual mode, otherwise optional (mode default used)
-# Mode default:   staging=reactions_staging / compounds_staging
-#                 production=reactions / compounds
-# Fallback:       staging: "reactions_staging" / "compounds_staging"
-#                 production: "reactions" / "compounds"
+# Override:       reactions/compounds required in manual mode; structures optional (falls back to structures)
+# Mode default:   staging=reactions_staging / compounds_staging / structures_staging
+#                 production=reactions / compounds / structures
+# Fallback:       staging: "reactions_staging" / "compounds_staging" / "structures_staging"
+#                 production: "reactions" / "compounds" / "structures"
 NEXT_PUBLIC_SOLR_REACTIONS_COLLECTION=
 NEXT_PUBLIC_SOLR_COMPOUNDS_COLLECTION=
+NEXT_PUBLIC_SOLR_STRUCTURES_COLLECTION=
 NEXT_PUBLIC_SOLR_REACTIONS_COLLECTION_STAGING=reactions_staging
 NEXT_PUBLIC_SOLR_COMPOUNDS_COLLECTION_STAGING=compounds_staging
+NEXT_PUBLIC_SOLR_STRUCTURES_COLLECTION_STAGING=structures_staging
 NEXT_PUBLIC_SOLR_REACTIONS_COLLECTION_PRODUCTION=reactions
 NEXT_PUBLIC_SOLR_COMPOUNDS_COLLECTION_PRODUCTION=compounds
+NEXT_PUBLIC_SOLR_STRUCTURES_COLLECTION_PRODUCTION=structures
+
+# =============================================================================
+# SOLR NESTED SCHEMA OVERRIDE
+# =============================================================================
+# Whether the Solr reactions/compounds collections use the Solr-9 nested-
+# document schema (parent docs plus [child] rows). Unset = auto-detect via a
+# one-time probe query per collection. true/1 = force nested-schema queries
+# (parent docs only). false/0 = force legacy (flat) behavior.
+NEXT_PUBLIC_SOLR_NESTED_SCHEMA=
 
 # =============================================================================
 # FEATURE FLAGS

CHANGELOG.md

@@ -17,6 +17,63 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ---
 
+## [3.4.0] - 2026-08-21
+
+### Added
+- Solr reaction, compound and structure lookups can now each use their own endpoint and core through separate environment variables, while retaining the shared Solr base when no per-corpus value is set
+- An optional server-side proxy lets a deployment or local checkout serve Solr from its own origin
+
+### Documentation
+- Documented the full Solr environment surface and endpoint switching scenarios for legacy, Solr 9, temporary, and proxied instances
+
+### Fixed
+- Structure-core environment overrides now reach browser lookups instead of silently falling back to the shared endpoint
+
+---
+
+## [3.3.0] - 2026-08-21
+
+### Added
+- Reaction structure equations now resolve atom-mapping colours from raw InChI canonical order through the structures Solr core, rather than treating canonical `#N` references as SMILES or renderer positions
+- Each mapped participant and the legend now disclose whether a highlight is an exact atom, a symmetry-equivalent orbit, a whole-element block, or unresolved, so researchers can see precisely what the mapping supports
+
+### Fixed
+- Atom-mapping highlights no longer assign chemically false colours when InChI canonical order diverges from stored-SMILES order
+
+---
+
+## [3.2.0] - 2026-08-20
+
+### Added
+- Reaction structure equations now use an open, continuous canvas with prominent common names, secondary IDs, formulas and charges; plain `+` and direction operators; and compound-page links
+- Every reaction participant that has a structure is now drawn, including small species such as water, CO2 and ammonium; only heavy-atom-free species such as H+ stay textual, and they keep their name, formula, charge and compound link
+- Reaction atom mappings now colour atoms and bonds by mapped group across reactants and products, with a legend that discloses mappings that cannot safely be coloured
+- Atom mappings in which several compounds contribute the same element to one product are now coloured as one merged group, and the legend states plainly that individual atom pairing is not determined by the data; group members that are only partially covered are named as uncoloured rather than dropped
+- Each participant shows a labelled colour-dot row naming its mapped elements, so colour is never the only carrier of meaning
+- Mapping colours are applied only to fully covered, mutually mapped compound-element blocks, never by treating InChI canonical-order `#N` indices as renderer atom indices
+- Compound and reaction detail pages now list every thermodynamics record returned by the upgraded Solr schema, one row per source with energy, error and (for reactions) direction operator
+- Compound detail page now shows all pKa and pKb values instead of only the first
+- Reaction detail page now shows an atom-mapping summary with per-compound element counts, a confidence indicator and an expandable raw list
+- Reaction atom mappings now disclose symmetry-equivalent groups without claiming a specific atom correspondence
+- All of the above is feature-detected, so pages render exactly as before against the current production Solr
+
+### Fixed
+- Reaction detail pages now read the live Solr `atom_mapping_data` field while retaining legacy `atom_mapping` fallback
+
+### Changed
+- Replaced the flat reaction atom-flow diagram with the structure canvas; the raw mapping list remains available as secondary detail
+- Reaction thermodynamics direction agreement is now derived from the per-source direction operators rather than a single server flag, and reports three states: "Sources agree on direction" (all operators identical), "Sources could agree on direction" (only one angle-bracket direction, optionally mixed with `=`) and "Sources disagree on direction" (both `>` and `<` present)
+
+### Known Issues
+- RAST MS FBA not working
+- PATRIC-only model submission
+- Workspace write operations limited
+
+### Expected Behaviors
+- Models/Media differ between RAST and PATRIC (intentional system design)
+
+---
+
 ## [3.1.1] - 2026-08-26
 
 ### Fixed

README.md

@@ -44,7 +44,7 @@ Key configuration constants live in `lib/api/config.ts`:
 - `MODELSEED_API_URL` – base URL for Poplar (currently `http://poplar.cels.anl.gov:8000` in development).
 - `USE_MODELSEED_API` – when `true`, user data flows (My Models, My Media, jobs) use `modelseed-api`.
 - `USE_NEW_PROXY` – when `true`, workspace calls route through the REST proxy at `${MODELSEED_API_URL}/api/workspace`.
-- `SOLR_BASE` / `SOLR_REACTIONS_COLLECTION` / `SOLR_COMPOUNDS_COLLECTION` – control Solr endpoint and core selection for biochem pages.
+- `NEXT_PUBLIC_SOLR_BASE_URL`, per-corpus `NEXT_PUBLIC_SOLR_*_BASE_URL` overrides, and `NEXT_PUBLIC_SOLR_*_COLLECTION` control Solr endpoints and core selection for biochem pages; see [Solr configuration](docs/DEPLOYMENT.md#solr-configuration).
 
 ## Running the App Locally
 

VERSION.md

@@ -1 +1 @@
-3.1.1
+3.4.0

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

@@ -20,6 +20,7 @@ import {
 } from '@/lib/api/biochem';
 import { formatFormula } from '@/components/utils/formatFormula';
 import { formatEquation } from '@/components/utils/formatEquation';
+import ThermodynamicsTable from '@/components/ui/ThermodynamicsTable';
 
 /* ─── Helpers ────────────────────────────────────────────────── */
 
@@ -365,12 +366,19 @@ export default function CompoundDetailPage() {
         : [];
     const aliasesWithoutName = cpd.aliases?.filter((a) => !a.startsWith('Name:')) ?? [];
 
-    const pkaDisplay = cpd.pka?.[0]?.replace(/"/g, '') ?? null;
-    const pkbDisplay = cpd.pkb?.[0]?.replace(/"/g, '') ?? null;
+    const pkaValues = (Array.isArray(cpd.pka_value) ? cpd.pka_value : Array.isArray(cpd.pka) ? cpd.pka : [])
+        .map((v) => String(v).replace(/"/g, ''));
+    const pkbValues = (Array.isArray(cpd.pkb_value) ? cpd.pkb_value : Array.isArray(cpd.pkb) ? cpd.pkb : [])
+        .map((v) => String(v).replace(/"/g, ''));
 
     const deltaGDisplay = cpd.deltag === 10000000 ? 'unspecified' : String(cpd.deltag);
     const deltaGerrDisplay = cpd.deltagerr === 10000000 ? 'unspecified' : String(cpd.deltagerr);
 
+    const thermoRecords = cpd.thermodynamics ?? [];
+    const thermoLabel = cpd.n_sources_thermodynamics && cpd.n_sources_thermodynamics > 0
+        ? `Thermodynamics (${cpd.n_sources_thermodynamics} sources)`
+        : 'Thermodynamics';
+
     return (
         <Box sx={{ px: 3, py: 2, maxWidth: 1200, mx: 'auto' }}>
             {/* ── Title ── */}
@@ -419,19 +427,33 @@ export default function CompoundDetailPage() {
 
                 {/* Properties */}
                 <Box sx={{ flex: 1, minWidth: 300 }}>
-                    <DetailRow label="ΔG">
-                        <Typography variant="body2">
-                            {deltaGDisplay === 'unspecified' ? 'N/A' : `${deltaGDisplay}${deltaGerrDisplay !== 'unspecified' ? ` ± ${deltaGerrDisplay}` : ''} kcal/mol`}
-                        </Typography>
-                    </DetailRow>
-                    {pkaDisplay && (
+                    {thermoRecords.length > 0 ? (
+                        <DetailRow label={thermoLabel}>
+                            <ThermodynamicsTable records={thermoRecords} />
+                        </DetailRow>
+                    ) : (
+                        <DetailRow label="ΔG">
+                            <Typography variant="body2">
+                                {deltaGDisplay === 'unspecified' ? 'N/A' : `${deltaGDisplay}${deltaGerrDisplay !== 'unspecified' ? ` ± ${deltaGerrDisplay}` : ''} kcal/mol`}
+                            </Typography>
+                        </DetailRow>
+                    )}
+                    {pkaValues.length > 0 && (
                         <DetailRow label="pKa">
-                            <PKaDisplay value={pkaDisplay} />
+                            <Box sx={{ display: 'flex', flexDirection: 'column', gap: 0.3 }}>
+                                {pkaValues.map((v, i) => (
+                                    <PKaDisplay value={v} key={`pka-${i}`} />
+                                ))}
+                            </Box>
                         </DetailRow>
                     )}
-                    {pkbDisplay && (
+                    {pkbValues.length > 0 && (
                         <DetailRow label="pKb">
-                            <PKaDisplay value={pkbDisplay} />
+                            <Box sx={{ display: 'flex', flexDirection: 'column', gap: 0.3 }}>
+                                {pkbValues.map((v, i) => (
+                                    <PKaDisplay value={v} key={`pkb-${i}`} />
+                                ))}
+                            </Box>
                         </DetailRow>
                     )}
                     <DetailRow label="Weight">

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

@@ -1,5 +1,6 @@
 'use client';
 
+import { useMemo } from 'react';
 import { useParams } from 'next/navigation';
 import { useQuery } from '@tanstack/react-query';
 import Box from '@mui/material/Box';
@@ -13,6 +14,13 @@ import Link from 'next/link';
 import { getReactionById, EXTERNAL_DBS } from '@/lib/api/biochem';
 import ChemicalEquation from '@/components/ui/ChemicalEquation';
 import ReactionStructureEquation from '@/components/ui/ReactionStructureEquation';
+import ThermodynamicsTable from '@/components/ui/ThermodynamicsTable';
+import { normalizeAtomMapping, parseAtomMappings } from '@/lib/utils/atomMapping';
+import {
+    directionAgreementFromRecords,
+    DIRECTION_AGREEMENT_COLOR,
+    DIRECTION_AGREEMENT_LABEL,
+} from '@/lib/utils/reactionDirection';
 
 function extractCompoundIds(equation: string): string[] {
     if (!equation) return [];
@@ -308,6 +316,9 @@ export default function ReactionDetailPage() {
         enabled: !!id,
     });
 
+    const atomMapping = useMemo(() => normalizeAtomMapping(rxn), [rxn]);
+    const atomPairs = useMemo(() => parseAtomMappings(atomMapping.entries), [atomMapping.entries]);
+
     if (isLoading) {
         return (
             <Box sx={{ display: 'flex', justifyContent: 'center', py: 8 }}>
@@ -335,6 +346,9 @@ export default function ReactionDetailPage() {
 
     const compoundIds = extractCompoundIds(rxn.equation || rxn.definition);
 
+    const thermoRecords = rxn.thermodynamics ?? [];
+    const agreement = directionAgreementFromRecords(thermoRecords);
+
     const dg = Number(rxn.deltag);
     const err = Number(rxn.deltagerr);
     const deltaGLabel = Number.isNaN(dg)
@@ -364,6 +378,9 @@ export default function ReactionDetailPage() {
                                 <ReactionStructureEquation
                                     equation={rxn.equation ?? rxn.definition}
                                     reversibility={rxn.reversibility}
+                                    atomMappingPairs={atomPairs}
+                                    atomMappingConfidence={atomMapping.confidence}
+                                    atomMappingHasSymmetryGroups={atomMapping.hasSymmetryGroups}
                                 />
                             )}
                         </Box>
@@ -381,11 +398,47 @@ export default function ReactionDetailPage() {
                         <ChemicalEquation equation={rxn.equation} />
                     </DetailRow>
 
-                    <DetailRow label="Gibbs free energy change (ΔG)">
-                        <Typography variant="body2" sx={{ fontWeight: 500 }}>
-                            {deltaGLabel}
-                        </Typography>
-                    </DetailRow>
+                    {thermoRecords.length > 0 ? (
+                        <DetailRow
+                            label={
+                                typeof rxn.n_sources_thermodynamics === 'number' &&
+                                rxn.n_sources_thermodynamics > 0
+                                    ? `Thermodynamics (${rxn.n_sources_thermodynamics} sources)`
+                                    : 'Thermodynamics'
+                            }
+                        >
+                            <Box sx={{ display: 'flex', flexDirection: 'column', gap: 1 }}>
+                                {agreement !== null ? (
+                                    <Chip
+                                        size="small"
+                                        label={DIRECTION_AGREEMENT_LABEL[agreement]}
+                                        color={DIRECTION_AGREEMENT_COLOR[agreement]}
+                                        sx={{ alignSelf: 'flex-start' }}
+                                    />
+                                ) : (
+                                    typeof rxn.sources_agree_direction === 'boolean' && (
+                                        <Chip
+                                            size="small"
+                                            label={
+                                                rxn.sources_agree_direction
+                                                    ? 'Sources agree on direction'
+                                                    : 'Sources disagree on direction'
+                                            }
+                                            color={rxn.sources_agree_direction ? 'success' : 'warning'}
+                                            sx={{ alignSelf: 'flex-start' }}
+                                        />
+                                    )
+                                )}
+                                <ThermodynamicsTable records={thermoRecords} showOperator />
+                            </Box>
+                        </DetailRow>
+                    ) : (
+                        <DetailRow label="Gibbs free energy change (ΔG)">
+                            <Typography variant="body2" sx={{ fontWeight: 500 }}>
+                                {deltaGLabel}
+                            </Typography>
+                        </DetailRow>
+                    )}
 
                     <DetailRow label="EC numbers">
                         {ecNumbers.length ? (
@@ -454,6 +507,7 @@ export default function ReactionDetailPage() {
                             </Typography>
                         </DetailRow>
                     )}
+
                 </CardContent>
             </Card>
         </Box>