Add crossref.fetch_references(doi), which parses message.reference[].DOI into Citations (DOI-less book/unstructured refs are skipped — they cannot join the graph). Wire it as the third leg of the ingest citation fallback chain: OpenAlex-empty -> S2 -> Crossref, for DOI papers only (Crossref's works endpoint is DOI-keyed). Cited DOIs are normalized to the canonical bare lower-case form via _norm_cited_id.
As a fallback it fires only when OpenAlex and S2 both return no references, so it adds a forward-looking third source without changing the already-covered corpus.
Tests: fetch_references unit tests (DOI edges / unstructured skipped / no refs / 404) and ingest tests for both fallback directions. Full suite 361 passed; ruff + mypy clean. Live-validated: 33/40/24 refs for Springer/ACM/Wiley DOIs.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
openalex._map_paper set Paper.id from the raw `doi` field, which OpenAlex
returns as a full URL (https://doi.org/10.x). The canonical papers.id (M-1
migration) is the bare, lower-cased DOI, so re-ingesting a DOI paper missed
ON CONFLICT (id) and tripped the separate papers_openalex_id_key constraint
(UniqueViolation).
Fix: _normalize_doi() strips https://doi.org//http://doi.org//doi: and
lower-cases; applied in the DOI branch of _map_paper only (W-id fallback
untouched). Also un-breaks _s2_id_for/Crossref recovery, which the URL form
silently defeated. Corrected the _SAMPLE_WORK fixture to the URL form (the bare
fixture hid the bug) + added _normalize_doi and re-ingest idempotency regression
tests.
Live verification: re-ingest of 10.1007/s00454-019-00132-8 (previously crashed)
now UPDATEs in place — single row, added_at unchanged, no stray row, citations
45->45. Unblocks roadmap R-A/R-C. Full suite 348 green.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Three papers lacked abstracts and 1911.00966 was fully degraded (OpenAlex 404
-> empty `Paper(id, title="")` stub). Recovery sources verified, then wired in:
- arxiv.fetch_metadata: resolve an arXiv id to a Paper via the Atom export API
(authoritative for preprints). Used as an ingest fallback on OpenAlex 404,
replacing the empty stub.
- crossref.py (new): fetch_abstract(doi), JATS-stripped, Crossref Polite Pool.
- semanticscholar.fetch_abstract: fetch just the abstract field.
- ingest.py: _recover_abstract() supplements an empty abstract from S2 then
Crossref *before* embedding, so the paper gets a real (non-zero) vector.
Live DB backfill: 1911.00966 fully recovered from arXiv (bibkey
PinkallSpringborn2019, 384-char abstract, its 10 chunks now visible to chunk
search); 10.1007/s00454-019-00132-8 abstract from S2 (1186 chars). Book chapter
10.1007/978-3-642-17413-1_7 has no abstract in OpenAlex/S2/Crossref -> documented
limit. Corpus now has 1 paper without an abstract.
Also documented DQ-5 (not fixed): ingest_paper is not idempotent for DOI papers
(openalex returns full-URL id vs the bare canonical id) -> re-ingest trips
papers_openalex_id_key. Blocks roadmap R-A/R-C; needs a careful _map_paper fix.
Tests: arxiv/crossref/s2 fetchers + ingest recovery paths (342 passing).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
