Accommodate ORM schema reorg for search/browse queries

[skearnes]

Summary

ord-schema's 0.8.0 release reorganizes the ORM into role-based schemas (open-reaction-database/ord-schema#859) and splits dataset loading into separate ingest and derivation stages (open-reaction-database/ord-schema#860, open-reaction-database/ord-schema#861):

• public.reactions — the served Reaction proto payload, keyed by reaction_id (moved off ord.reaction.proto).
• public.datasets — per-dataset metadata num_reactions / submitted_at (moved off ord.dataset).
• derived.* — generated SMILES + rdkit_*_id links: reaction_smiles, compound_smiles, product_compound_smiles (moved off ord.reaction / ord.compound / ord.product_compound).
• ord.* — now a pure search index (decomposed message tables only).
• Loading is now two stages — add_dataset / add_parquet_dataset ingest ord.* + public.*, and update_derived_data populates the derived.* SMILES / RDKit links / reaction classes.

This PR updates the search/browse queries to read from the new locations and updates the test-fixture loader to the two-stage API.

Changes

• ReactionSmartsQuery / ReactionComponentQuery (queries.py) — join through derived.reaction_smiles / derived.compound_smiles / derived.product_compound_smiles to reach the rdkit_*_id links, replacing the dropped ord.reaction.rdkit_reaction_id / compound.rdkit_mol_id columns.
• fetch_reactions — reads proto from public.reactions.
• _fetch_dataset_most_used_smiles — joins the derived SMILES tables for the smiles column (new smiles_table / smiles_foreign_key params).
• get_datasets / get_dataset (search.py) — join public.datasets for num_reactions / submitted_at.
• setup_test_postgres (testing.py) — the removed add_dataset(..., rdkit_cartridge=...) keyword is gone; ingest with add_dataset(dataset, session) then derive with update_derived_data(dataset.dataset_id, session, rdkit_cartridge=...), mirroring the ord-schema ORM conftest and preserving the rdkit-cartridge gating.
• queries_test.py — the _max_similarities helper mirrors _mols_join, updated to the same derived-table joins.
• pyproject.toml — bump the pin to ord-schema[orm]>=0.8,<0.9.

Reaction classes (ord-schema#854)

No changes needed: ord-interface does not read the reaction class/name fields anywhere (no query, search, or frontend reference), so #854 — and its move to derived.reaction_classes in #859 — is transparent here.

Correctness note

All joins to the derived.* tables are INNER, which preserves the prior NULL-column filtering: update_derived_tables inserts a derived row only when a SMILES can be generated, so un-derivable entities are dropped exactly as the old rdkit_*_id IS NULL / smiles IS NOT NULL paths did. The API response shapes (DatasetInfo, QueryResult) are unchanged, so no frontend changes are needed.

Release status ✅

ord-schema 0.8.0 is published, so this is unblocked:

• main merged in and uv.lock regenerated (uv lock): ord-schema 0.7.1 → 0.8.0, plus the new uuid6 transitive dependency.
• The ty check pre-commit hook — previously skipped because it could not resolve >=0.8 — now passes, along with ruff check, ruff format, and addlicense.
• The DB-backed pytest suite (Postgres + RDKit cartridge) runs in CI.

🤖 Generated with Claude Code

Greptile Summary

Updates the interface for the ord-schema 0.8 ORM reorganization.

• Routes reaction, compound, and product queries through the new derived.* tables.
• Reads served reaction payloads and dataset metadata from public.*.
• Updates test-database setup to run separate ingestion and derivation stages.
• Raises the ord-schema dependency range to 0.8 and refreshes the lockfile.

Confidence Score: 5/5

The PR appears safe to merge because no blocking failures remain within the follow-up review scope.

No blocking failures remain.

Important Files Changed

Filename	Overview
ord_interface/api/queries.py	Migrates reaction payload, structural search, and SMILES-statistics queries to the reorganized public and derived schemas.
ord_interface/api/search.py	Joins public dataset metadata into dataset listing and lookup responses.
ord_interface/api/testing.py	Updates fixture loading to perform ingestion followed by derived-data generation.
ord_interface/api/queries_test.py	Aligns similarity-test joins with the new derived RDKit-link tables.
pyproject.toml	Updates the supported ord-schema ORM release range to 0.8.
uv.lock	Resolves ord-schema 0.8.0 and its new uuid6 transitive dependency.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  API[Search and browse API] --> IDX[ord.* search index]
  IDX --> DER[derived.* SMILES and RDKit links]
  IDX --> PUB[public.reactions and public.datasets]
  LOAD[Fixture loader] --> INGEST[add_dataset]
  INGEST --> DERIVE[update_derived_data]
  DERIVE --> DER

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