Drug reconciliation: deterministic tie-break for aliases shared by salt-form duplicates

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>

Simon-Pierre Boucher committed 1 mo ago (Sep 11, 2026) parent 3b30d3a Browse files

1 changed file +31 −4

modified packages/connectors/src/connectors/clinicaltrials/drugs.ts +31 −4

				`@@ -187,14 +187,41 @@ export async function reconcileInterventionDrugs(db: Database, opts: { remap?: b`
187	if (opts.remap) {	187	if (opts.remap) {
188	await db.execute(sql`UPDATE trial_interventions SET drug_id = NULL, match_type = 'UNRESOLVED' WHERE intervention_type IN ('DRUG','BIOLOGICAL') AND match_type IN ('ALIAS','PROBABILISTIC')`);	188	await db.execute(sql`UPDATE trial_interventions SET drug_id = NULL, match_type = 'UNRESOLVED' WHERE intervention_type IN ('DRUG','BIOLOGICAL') AND match_type IN ('ALIAS','PROBABILISTIC')`);
189	}	189	}
190	− // Unambiguous alias map: normalized → drug_id (aliases shared by several drugs are excluded).	190	+ // Alias map: normalized → drug_id. An alias shared by several drugs is accepted only when one
		191	+ // candidate is strictly preferred by a deterministic rule (SPEC §97 duplicate resolution):
		192	+ // 0 the alias is the drug's own generic name (alias_type generic AND normalized(drugs.name) = alias)
		193	+ // 1 the alias is a brand of the drug
		194	+ // 2 the drug's name carries no salt/ester token (base molecule rather than "X Hydrochloride")
		195	+ // 3 anything else
		196	+ // Two candidates at the same best priority → ambiguous → skipped (never guessed). Salt-form
		197	+ // duplicates ("Erlotinib" vs "Erlotinib Hydrochloride") are also reported for the merge queue.
191	await db.execute(sql`CREATE TEMP TABLE IF NOT EXISTS _alias_map (normalized text PRIMARY KEY, drug_id varchar(32) NOT NULL)`);	198	await db.execute(sql`CREATE TEMP TABLE IF NOT EXISTS _alias_map (normalized text PRIMARY KEY, drug_id varchar(32) NOT NULL)`);
192	await db.execute(sql`TRUNCATE _alias_map`);	199	await db.execute(sql`TRUNCATE _alias_map`);
193	await db.execute(sql`	200	await db.execute(sql`
194	INSERT INTO _alias_map (normalized, drug_id)	201	INSERT INTO _alias_map (normalized, drug_id)
195	− SELECT normalized, min(drug_id) FROM drug_aliases WHERE length(normalized) >= 3	202	+ WITH cand AS (
196	− GROUP BY normalized HAVING count(DISTINCT drug_id) = 1`);	203	+ SELECT a.normalized, a.drug_id,
197	− const [amb] = await db.execute<{ n: string }>(sql`SELECT count(*)::text AS n FROM (SELECT normalized FROM drug_aliases GROUP BY normalized HAVING count(DISTINCT drug_id) > 1) x`);	204	+ min(CASE
		205	+ WHEN a.alias_type = 'generic' AND lower(regexp_replace(d.name, '[^A-Za-z0-9]+', ' ', 'g')) = a.normalized THEN 0
		206	+ WHEN a.alias_type = 'brand' THEN 1
		207	+ WHEN NOT (lower(d.name) ~ ${sql.raw(`'\\m(${SALT_TOKENS.join('\|')})\\M'`)}) THEN 2
		208	+ ELSE 3 END) AS prio
		209	+ FROM drug_aliases a JOIN drugs d ON d.id = a.drug_id
		210	+ WHERE length(a.normalized) >= 3
		211	+ GROUP BY a.normalized, a.drug_id
		212	+ ),
		213	+ best AS (
		214	+ SELECT normalized, min(prio) AS prio FROM cand GROUP BY normalized
		215	+ ),
		216	+ pick AS (
		217	+ SELECT c.normalized, c.drug_id, count(*) OVER (PARTITION BY c.normalized) AS n_best
		218	+ FROM cand c JOIN best b ON b.normalized = c.normalized AND b.prio = c.prio
		219	+ )
		220	+ SELECT normalized, drug_id FROM pick WHERE n_best = 1`);
		221	+ const [amb] = await db.execute<{ n: string }>(sql`
		222	+ SELECT count(*)::text AS n FROM (
		223	+ SELECT a.normalized FROM drug_aliases a WHERE length(a.normalized) >= 3 GROUP BY a.normalized HAVING count(DISTINCT a.drug_id) > 1
		224	+ EXCEPT SELECT normalized FROM _alias_map) x`);
198		225
199	// Pass 1: exact normalized alias.	226	// Pass 1: exact normalized alias.
200	const p1 = await db.execute<{ n: string }>(sql`	227	const p1 = await db.execute<{ n: string }>(sql`
201		228

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Drug reconciliation: deterministic tie-break for aliases shared by salt-form duplicates

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