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fix(discover): resolve cited_id via shared resolver (audit C-1)

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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>
This commit is contained in:
Tarik Moussa
2026-06-15 11:12:55 +02:00
parent 3092f1814e
commit eee147275a
2 changed files with 45 additions and 19 deletions
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27
codex/graph.py
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@@ -23,6 +23,23 @@ logger = logging.getLogger(__name__)
_MIN_PAGERANK_NODES = 5
# Single source of truth for resolving ``citations.cited_id`` to a canonical
# paper id. ``cited_id`` stores OpenAlex IDs while ``papers.id`` stores DOIs /
# arXiv ids, so an in-KB reference cited by its OpenAlex id does not match
# ``papers.id`` directly. This resolves it to the canonical ``papers.id`` (via
# ``papers.openalex_id``, then the ``paper_identifiers`` alias table); dangling
# references keep their raw id. Both :func:`build_citation_graph` and
# :mod:`codex.discover` query through this so the "what counts as ingested" rule
# cannot drift between them again (audit C-1). Trusted constant — no user input.
RESOLVED_CITATIONS_SQL = """
SELECT c.citing_id,
COALESCE(p.id, pi.paper_id, c.cited_id) AS cited_id
FROM citations c
LEFT JOIN papers p ON p.openalex_id = c.cited_id
LEFT JOIN paper_identifiers pi
ON pi.openalex_id = c.cited_id AND p.id IS NULL
"""
def build_citation_graph(conn: Any) -> nx.DiGraph:
"""Load the ``citations`` table into a directed graph.
@@ -45,15 +62,7 @@ def build_citation_graph(conn: Any) -> nx.DiGraph:
-------
nx.DiGraph with every (citing_id, cited_id) pair as an edge.
"""
rows = conn.execute(
"""
SELECT c.citing_id, COALESCE(p.id, pi.paper_id, c.cited_id) AS cited_id
FROM citations c
LEFT JOIN papers p ON p.openalex_id = c.cited_id
LEFT JOIN paper_identifiers pi
ON pi.openalex_id = c.cited_id AND p.id IS NULL
"""
).fetchall()
rows = conn.execute(RESOLVED_CITATIONS_SQL).fetchall()
g: nx.DiGraph = nx.DiGraph()
for row in rows:
g.add_edge(row["citing_id"], row["cited_id"])