discover.py compared the raw OpenAlex cited_id against papers.id (a DOI/arXiv
id), so an ingested paper cited by its OpenAlex id was mis-reported as a
discovery lead. graph.py already resolved this via papers.openalex_id, but the
fix was never propagated — two 'dangling' implementations disagreed.
Extract the resolution into one shared constant RESOLVED_CITATIONS_SQL in
graph.py; build_citation_graph and all four discover.py queries
(discovery_leads / citing_papers / cited_by / cocited_papers) now go through it,
so the 'what counts as ingested' rule cannot drift again.
Live-DB validated: before, 13 ingested papers leaked into discovery_leads;
after, the real discovery_leads() returns 0 ingested papers among its leads.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Fixes preprint/journal duplicate problem: arXiv papers were ingested
under their preprint OpenAlex ID, but corpus citations reference the
published-version OpenAlex ID → those citations were invisible in the
graph (appeared as dangling).
Changes:
- infra/schema.sql: CREATE TABLE paper_identifiers (paper_id, openalex_id)
with UNIQUE index; seeded from papers.openalex_id on migration
- codex/graph.py: build_citation_graph LEFT JOINs paper_identifiers as
a second resolution path: COALESCE(p.id, pi.paper_id, c.cited_id)
- codex/ingest.py: every ingest inserts openalex_id into paper_identifiers
(ON CONFLICT DO NOTHING) — aliases can be added manually alongside
Live DB: 35 rows seeded + 4 published-version aliases added:
math/0503219 → W2163787581 (DCG 2007)
math/0306167 → W2136126748 (Commun Analysis Geom 2004)
math/0203250 → W1567166970 (Trans AMS 2003)
1005.2698 → W1511400044 (Geom & Topol 2015)
Effect: dangling 574→570; Bobenko+Springborn 2007 now IN-KB rank 9.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
build_citation_graph now does:
SELECT c.citing_id, COALESCE(p.id, c.cited_id) AS cited_id
FROM citations c
LEFT JOIN papers p ON p.openalex_id = c.cited_id
Before: cited_id (OpenAlex IDs) never matched papers.id (DOIs) →
13 cross-citations between ingested papers were invisible in graph.
After: in-KB papers use their canonical DOI key; dangling references
keep their raw OpenAlex ID unchanged.
Test: test_cross_citation_uses_doi_when_in_kb (42 passed).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
