fix(graph): resolve cited_id to papers.id via openalex_id JOIN

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>

codex/graph.py

@@ -31,6 +31,11 @@ def build_citation_graph(conn: Any) -> nx.DiGraph:
     the citing paper references the cited paper.  Both ingested papers
     and dangling targets (cited but not yet ingested) appear as nodes.
 
+    ``cited_id`` in the citations table stores OpenAlex IDs; ``papers.id``
+    stores DOIs.  A LEFT JOIN resolves cited papers that are in the KB to
+    their canonical DOI key via ``papers.openalex_id``.  Dangling references
+    (not in KB) keep their raw OpenAlex ID.
+
     Parameters
     ----------
     conn:
@@ -40,7 +45,13 @@ def build_citation_graph(conn: Any) -> nx.DiGraph:
     -------
     nx.DiGraph with every (citing_id, cited_id) pair as an edge.
     """
-    rows = conn.execute("SELECT citing_id, cited_id FROM citations").fetchall()
+    rows = conn.execute(
+        """
+        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
+        """
+    ).fetchall()
     g: nx.DiGraph = nx.DiGraph()
     for row in rows:
         g.add_edge(row["citing_id"], row["cited_id"])

tests/graph/test_graph.py

@@ -80,6 +80,24 @@ class TestBuildCitationGraph:
         g = build_citation_graph(_make_conn(rows))
         assert "not_in_papers" in g.nodes()
 
+    def test_cross_citation_uses_doi_when_in_kb(self):
+        # Simulate DB COALESCE: cited_id already resolved to papers.id (DOI)
+        # for in-KB papers; dangling references keep their OpenAlex ID.
+        rows = [
+            {
+                "citing_id": "https://doi.org/10.1234/paper-a",
+                "cited_id": "https://doi.org/10.5678/paper-b",
+            },
+            {
+                "citing_id": "https://doi.org/10.5678/paper-b",
+                "cited_id": "https://openalex.org/W999",
+            },
+        ]
+        g = build_citation_graph(_make_conn(rows))
+        assert g.has_edge("https://doi.org/10.1234/paper-a", "https://doi.org/10.5678/paper-b")
+        assert g.has_edge("https://doi.org/10.5678/paper-b", "https://openalex.org/W999")
+        assert g.number_of_nodes() == 3
+
 
 # ---------------------------------------------------------------------------
 # citation_pagerank