fix(ingest): canonicalise papers.id to the caller id (audit C-7, T-3)

openalex.fetch_paper fills paper.id from OpenAlex's URL-form doi/id
(e.g. https://doi.org/10.48550/arxiv.math/0603097), and ingest upserted that as
papers.id. Live DB confirmed 35/36 ids were URL-form — breaking bare-id lookups
(graph related / discover citing / search by id) and leaving cited_id matching
to rely solely on openalex_id.

ingest now sets paper.id to the caller-supplied id (the arXiv id / DOI the CLI
and ingest scripts use); OpenAlex's work id is retained as openalex_id and in
paper_identifiers. Regression test: fetch_paper returns a URL-form id, papers.id
upsert uses the bare caller id.

T-3: the OpenAlex test fixture used a bare 'doi' (not the URL form the API
emits) and never asserted paper.id, which masked this. Fixture now uses the URL
form and the test pins fetch_paper's mapping.

NOTE: existing rows keep their URL-form ids until re-ingested — run ingest_all.sh
to migrate the 36-paper corpus (chosen migration path).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

tests/ingest/test_ingest.py

@@ -106,6 +106,37 @@ def test_ingest_paper_basic() -> None:
     )
 
 
+def test_ingest_canonicalises_paper_id_to_caller_arg() -> None:
+    """papers.id is the caller-supplied id, not OpenAlex's URL-form id (audit C-7).
+
+    Real OpenAlex returns the doi/id as a full URL; ingest must key the paper on
+    the bare id the caller passed (matching ingest scripts and CLI lookups), and
+    keep the OpenAlex work id only as openalex_id.
+    """
+    oa_paper = Paper(
+        id="https://doi.org/10.48550/arxiv.math/0603097",  # URL form, as OpenAlex emits
+        title="A Test Paper",
+        openalex_id="https://openalex.org/W4301005794",
+        authors=["Alice", "Bob"],
+        year=2008,
+        abstract="Test abstract.",
+    )
+    mock_conn = MagicMock()
+
+    with (
+        patch("codex.ingest.openalex.fetch_paper", return_value=oa_paper),
+        patch("codex.ingest.openalex.fetch_citations", return_value=[]),
+        patch("codex.ingest.get_embedder", return_value=_fake_embedder()),
+        patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
+    ):
+        result = ingest_paper("math/0603097")
+
+    papers_params = mock_conn.execute.call_args_list[0][0][1]
+    assert papers_params["id"] == "math/0603097", "papers.id must be the caller's bare id"
+    assert papers_params["openalex_id"] == "https://openalex.org/W4301005794"
+    assert result.paper_id == "math/0603097"
+
+
 # ---------------------------------------------------------------------------
 # 2. test_ingest_paper_source_tex
 # ---------------------------------------------------------------------------

tests/sources/test_openalex.py

@@ -15,7 +15,8 @@ from codex.sources.openalex import _resolve_id
 
 _SAMPLE_WORK = {
     "id": "https://openalex.org/W2741809807",
-    "doi": "10.1145/3592430",
+    # Real OpenAlex returns the DOI as a full URL, not a bare DOI (audit T-3).
+    "doi": "https://doi.org/10.1145/3592430",
     "title": "Conformal Prediction: A Review",
     "publication_year": 2023,
     "authorships": [
@@ -90,6 +91,10 @@ def test_fetch_paper_success(monkeypatch: pytest.MonkeyPatch) -> None:
     assert paper.authors == ["Alice Smith", "Bob Jones"]
     assert paper.abstract == "Conformal prediction is great"
     assert paper.openalex_id == "https://openalex.org/W2741809807"
+    # fetch_paper maps id from the (URL-form) doi; ingest later canonicalises
+    # papers.id to the caller's bare id (audit C-7). Pin the real mapping here so
+    # the fixture cannot silently misrepresent OpenAlex again (audit T-3).
+    assert paper.id == "https://doi.org/10.1145/3592430"
 
 
 def test_fetch_paper_arxiv_id_prefixed(monkeypatch: pytest.MonkeyPatch) -> None: