Uniformly schema-qualify ord-schema tables in queries (#190)

The reaction queries mixed `ord.`-qualified and bare table names in
their FROM/JOIN clauses (e.g. `FROM reaction` vs `FROM ord.reaction`,
`JOIN percentage` vs `JOIN ord.percentage`). This is cosmetic, not a
correctness issue: the connection sets `search_path=public,ord` (see
search.py and conftest.py), so bare ord-schema tables already resolve.

Make the qualification uniform by prefixing all ord-schema tables with
`ord.` in FROM/JOIN clauses, matching the convention already used by
fetch_reactions and _fetch_dataset_most_used_smiles. The rdkit-cartridge
tables keep their `rdkit.` prefix (rdkit is not in the search_path), and
bare table-alias column references are left as-is (the dominant style).

No behavior change; the 51 queries_test.py / search_test.py cases pass
against the test Postgres.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: skearnes

ord_interface/api/queries.py

@@ -89,7 +89,7 @@ def query_and_parameters(self) -> tuple[str, list]:
         query = """
             SELECT DISTINCT reaction.reaction_id
             FROM ord.reaction
-            JOIN dataset ON dataset.id = reaction.dataset_id
+            JOIN ord.dataset ON dataset.id = reaction.dataset_id
             WHERE dataset.dataset_id = ANY (%s)
         """
         return query, [self._dataset_ids]
@@ -139,7 +139,7 @@ def query_and_parameters(self) -> tuple[str, list]:
         """Returns the query and any query parameters."""
         query = """
             SELECT DISTINCT reaction.reaction_id
-            FROM reaction
+            FROM ord.reaction
             JOIN rdkit.reactions ON rdkit.reactions.id = reaction.rdkit_reaction_id
             WHERE rdkit.reactions.reaction @> reaction_from_smarts(%s)
         """
@@ -172,7 +172,7 @@ def query_and_parameters(self) -> tuple[str, list]:
             SELECT DISTINCT reaction.reaction_id
             FROM ord.reaction
             JOIN ord.reaction_outcome on reaction_outcome.reaction_id = reaction.id
-            JOIN percentage on percentage.reaction_outcome_id = reaction_outcome.id
+            JOIN ord.percentage on percentage.reaction_outcome_id = reaction_outcome.id
         """
         if self._min_conversion is not None and self._max_conversion is not None:
             query += "WHERE percentage.value >= %s AND percentage.value <= %s\n"
@@ -210,7 +210,7 @@ def query_and_parameters(self) -> tuple[str, list]:
             JOIN ord.reaction_outcome on reaction_outcome.reaction_id = reaction.id
             JOIN ord.product_compound on product_compound.reaction_outcome_id = reaction_outcome.id
             JOIN ord.product_measurement on product_measurement.product_compound_id = product_compound.id
-            JOIN percentage on percentage.product_measurement_id = product_measurement.id
+            JOIN ord.percentage on percentage.product_measurement_id = product_measurement.id
             WHERE product_measurement.type = 'YIELD'
         """
         params = []
@@ -250,7 +250,7 @@ def query_and_parameters(self) -> tuple[str, list]:
         query = """
             SELECT DISTINCT reaction.reaction_id
             FROM ord.reaction
-            JOIN reaction_provenance ON reaction_provenance.reaction_id = reaction.id
+            JOIN ord.reaction_provenance ON reaction_provenance.reaction_id = reaction.id
             WHERE reaction_provenance.doi = ANY (%s)
         """
         return query, [self._dois]
@@ -307,14 +307,14 @@ def query_and_parameters(self) -> tuple[str, list]:
         """Returns the query and any query parameters."""
         if self._target == ReactionComponentQuery.Target.INPUT:
             mols_sql = """
-            JOIN reaction_input ON reaction_input.reaction_id = reaction.id
-            JOIN compound ON compound.reaction_input_id = reaction_input.id
+            JOIN ord.reaction_input ON reaction_input.reaction_id = reaction.id
+            JOIN ord.compound ON compound.reaction_input_id = reaction_input.id
             JOIN rdkit.mols ON rdkit.mols.id = compound.rdkit_mol_id
             """
         else:
             mols_sql = """
-            JOIN reaction_outcome ON reaction_outcome.reaction_id = reaction.id
-            JOIN product_compound ON product_compound.reaction_outcome_id = reaction_outcome.id
+            JOIN ord.reaction_outcome ON reaction_outcome.reaction_id = reaction.id
+            JOIN ord.product_compound ON product_compound.reaction_outcome_id = reaction_outcome.id
             JOIN rdkit.mols ON rdkit.mols.id = product_compound.rdkit_mol_id
             """
         if self._match_mode == ReactionComponentQuery.MatchMode.EXACT: