From 5dfa6e4bae94c5586f94123d5772bfdb20e6588d Mon Sep 17 00:00:00 2001
From: Tarik Moussa <tarikmoussa@MacBookAir.fritz.box>
Date: Mon, 15 Jun 2026 07:42:21 +0200
Subject: [PATCH] =?UTF-8?q?feat(graph):=20paper=5Fidentifiers=20table=20?=
 =?UTF-8?q?=E2=80=94=20multi-ID=20alias=20support?=
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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>
---
 codex/graph.py   |  4 +++-
 codex/ingest.py  | 13 +++++++++++++
 infra/schema.sql | 18 ++++++++++++++++++
 3 files changed, 34 insertions(+), 1 deletion(-)

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;