diff --git a/codex/graph.py b/codex/graph.py index c0818d2..981662d 100644 --- a/codex/graph.py +++ b/codex/graph.py @@ -47,9 +47,11 @@ def build_citation_graph(conn: Any) -> nx.DiGraph: """ rows = conn.execute( """ - SELECT c.citing_id, COALESCE(p.id, c.cited_id) AS cited_id + 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() g: nx.DiGraph = nx.DiGraph() diff --git a/codex/ingest.py b/codex/ingest.py index 87c9d73..b63799d 100644 --- a/codex/ingest.py +++ b/codex/ingest.py @@ -147,6 +147,19 @@ def ingest_paper( }, ) + # Register openalex_id in paper_identifiers (alias table). + # Every ingest records the primary openalex_id so the graph JOIN + # resolves it even if papers.openalex_id is later updated. + if paper.openalex_id: + conn.execute( + """ + INSERT INTO paper_identifiers (paper_id, openalex_id) + VALUES (%s, %s) + ON CONFLICT DO NOTHING + """, + (paper.id, paper.openalex_id), + ) + # --------------------------------------------------------------- # 4. Parse + chunk + embed source file (if provided) # DELETE existing chunks for this paper first, then bulk INSERT diff --git a/infra/schema.sql b/infra/schema.sql index 9259506..514ea32 100644 --- a/infra/schema.sql +++ b/infra/schema.sql @@ -125,3 +125,21 @@ CREATE INDEX IF NOT EXISTS figures_paper_idx ON figures (paper_id); -- F-16 Chunk Quality Gate: section classification ALTER TABLE chunks ADD COLUMN IF NOT EXISTS section TEXT; + +-- F-17 Paper identifier aliases: one paper → many OpenAlex IDs +-- (arXiv preprint ID + journal published ID + any future version) +-- Each OpenAlex ID maps to exactly one paper (UNIQUE on openalex_id). +-- Populated automatically by ingest; add extra aliases manually. +CREATE TABLE IF NOT EXISTS paper_identifiers ( + paper_id TEXT NOT NULL REFERENCES papers(id) ON DELETE CASCADE, + openalex_id TEXT NOT NULL, + PRIMARY KEY (paper_id, openalex_id) +); + +CREATE UNIQUE INDEX IF NOT EXISTS paper_identifiers_oa_idx + ON paper_identifiers (openalex_id); + +-- Seed from existing papers.openalex_id +INSERT INTO paper_identifiers (paper_id, openalex_id) +SELECT id, openalex_id FROM papers WHERE openalex_id IS NOT NULL +ON CONFLICT DO NOTHING;