ea73b1475c
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>
251 lines
8.7 KiB
Python
251 lines
8.7 KiB
Python
"""Tests for codex.sources.openalex."""
|
||
|
||
from __future__ import annotations
|
||
|
||
import httpx
|
||
import pytest
|
||
|
||
from codex.models import Citation, Paper
|
||
from codex.sources import openalex
|
||
from codex.sources.openalex import _normalize_doi, _resolve_id
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# Helpers
|
||
# ---------------------------------------------------------------------------
|
||
|
||
_SAMPLE_WORK = {
|
||
"id": "https://openalex.org/W2741809807",
|
||
# Real OpenAlex returns the DOI as a full URL (T-3: the old bare fixture hid
|
||
# the URL-form behaviour that DQ-5 is about).
|
||
"doi": "https://doi.org/10.1145/3592430",
|
||
"title": "Conformal Prediction: A Review",
|
||
"publication_year": 2023,
|
||
"authorships": [
|
||
{"author": {"display_name": "Alice Smith"}},
|
||
{"author": {"display_name": "Bob Jones"}},
|
||
],
|
||
"abstract_inverted_index": {
|
||
"Conformal": [0],
|
||
"prediction": [1],
|
||
"is": [2],
|
||
"great": [3],
|
||
},
|
||
"referenced_works": [
|
||
"https://openalex.org/W1",
|
||
"https://openalex.org/W2",
|
||
],
|
||
}
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# _resolve_id
|
||
# ---------------------------------------------------------------------------
|
||
|
||
|
||
def test_resolve_doi() -> None:
|
||
assert _resolve_id("10.1145/3592430") == "doi:10.1145/3592430"
|
||
|
||
|
||
def test_resolve_arxiv() -> None:
|
||
# arXiv IDs resolve to their arXiv DOI (the arxiv: path 404s on OpenAlex).
|
||
assert _resolve_id("2301.07041") == "doi:10.48550/arXiv.2301.07041"
|
||
|
||
|
||
def test_resolve_arxiv_legacy() -> None:
|
||
# Legacy category/number IDs (pre-2007) resolve the same way.
|
||
assert _resolve_id("math/0603097") == "doi:10.48550/arXiv.math/0603097"
|
||
|
||
|
||
def test_resolve_arxiv_prefix_stripped() -> None:
|
||
# An explicit arxiv: prefix is stripped before building the arXiv DOI.
|
||
assert _resolve_id("arxiv:2301.07041") == "doi:10.48550/arXiv.2301.07041"
|
||
|
||
|
||
def test_resolve_w_id_unchanged() -> None:
|
||
assert _resolve_id("W2741809807") == "W2741809807"
|
||
|
||
|
||
def test_resolve_prefixed_unchanged() -> None:
|
||
assert _resolve_id("doi:10.1145/x") == "doi:10.1145/x"
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# _normalize_doi — canonical bare, lower-cased form (DQ-5)
|
||
# ---------------------------------------------------------------------------
|
||
|
||
|
||
def test_normalize_doi_strips_https_url() -> None:
|
||
# The exact form OpenAlex returns in the `doi` field.
|
||
assert _normalize_doi("https://doi.org/10.1007/s00454-019-00132-8") == (
|
||
"10.1007/s00454-019-00132-8"
|
||
)
|
||
|
||
|
||
def test_normalize_doi_strips_http_and_doi_prefix() -> None:
|
||
assert _normalize_doi("http://doi.org/10.1145/3592430") == "10.1145/3592430"
|
||
assert _normalize_doi("doi:10.1145/3592430") == "10.1145/3592430"
|
||
|
||
|
||
def test_normalize_doi_lowercases() -> None:
|
||
# DOIs are case-insensitive; the canonical id (and _norm_cited_id) is lower-case.
|
||
assert _normalize_doi("https://doi.org/10.1007/S00454-019-00132-8") == (
|
||
"10.1007/s00454-019-00132-8"
|
||
)
|
||
|
||
|
||
def test_normalize_doi_already_bare_is_idempotent() -> None:
|
||
assert _normalize_doi("10.1007/s00454-019-00132-8") == "10.1007/s00454-019-00132-8"
|
||
|
||
|
||
def test_map_paper_falls_back_to_openalex_id_without_doi(
|
||
monkeypatch: pytest.MonkeyPatch,
|
||
) -> None:
|
||
"""A work with no DOI keeps the OpenAlex W-id (URL form) as id, unchanged —
|
||
normalization only rewrites the DOI branch."""
|
||
work = {k: v for k, v in _SAMPLE_WORK.items() if k != "doi"}
|
||
|
||
def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
|
||
return httpx.Response(200, json=work)
|
||
|
||
monkeypatch.setattr(openalex, "_get", mock_get)
|
||
paper = openalex.fetch_paper("W2741809807")
|
||
|
||
assert paper is not None
|
||
assert paper.id == "https://openalex.org/W2741809807"
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# fetch_paper — success
|
||
# ---------------------------------------------------------------------------
|
||
|
||
|
||
def test_fetch_paper_success(monkeypatch: pytest.MonkeyPatch) -> None:
|
||
"""Successful fetch maps all fields to Paper correctly."""
|
||
|
||
def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
|
||
assert "doi:10.1145/3592430" in url
|
||
return httpx.Response(200, json=_SAMPLE_WORK)
|
||
|
||
monkeypatch.setattr(openalex, "_get", mock_get)
|
||
|
||
paper = openalex.fetch_paper("10.1145/3592430")
|
||
|
||
assert paper is not None
|
||
assert isinstance(paper, Paper)
|
||
# DQ-5 / C-7: paper.id is the canonical BARE DOI, not the full URL OpenAlex
|
||
# returns. This is what makes the ingest ON CONFLICT (id) upsert idempotent.
|
||
assert paper.id == "10.1145/3592430"
|
||
assert paper.title == "Conformal Prediction: A Review"
|
||
assert paper.year == 2023
|
||
assert paper.authors == ["Alice Smith", "Bob Jones"]
|
||
assert paper.abstract == "Conformal prediction is great"
|
||
assert paper.openalex_id == "https://openalex.org/W2741809807"
|
||
|
||
|
||
def test_fetch_paper_arxiv_id_prefixed(monkeypatch: pytest.MonkeyPatch) -> None:
|
||
"""Bare arXiv IDs are resolved to their arXiv DOI in the URL."""
|
||
called_url: list[str] = []
|
||
|
||
def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
|
||
called_url.append(url)
|
||
return httpx.Response(200, json=_SAMPLE_WORK)
|
||
|
||
monkeypatch.setattr(openalex, "_get", mock_get)
|
||
openalex.fetch_paper("2301.07041")
|
||
|
||
assert called_url and "doi:10.48550/arXiv.2301.07041" in called_url[0]
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# fetch_paper — 404 → None
|
||
# ---------------------------------------------------------------------------
|
||
|
||
|
||
def test_fetch_paper_404_returns_none(monkeypatch: pytest.MonkeyPatch) -> None:
|
||
"""A 404 response should return None without raising."""
|
||
|
||
def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
|
||
raise httpx.HTTPStatusError(
|
||
"Not Found",
|
||
request=httpx.Request("GET", url),
|
||
response=httpx.Response(404, request=httpx.Request("GET", url)),
|
||
)
|
||
|
||
monkeypatch.setattr(openalex, "_get", mock_get)
|
||
|
||
result = openalex.fetch_paper("nonexistent-id")
|
||
assert result is None
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# fetch_paper — 429 retry then success
|
||
# ---------------------------------------------------------------------------
|
||
|
||
|
||
def test_fetch_paper_retry_on_429(monkeypatch: pytest.MonkeyPatch) -> None:
|
||
"""On 429×3 then 200, returns 1 Paper after 3 failed attempts."""
|
||
attempt = [0]
|
||
|
||
def controlled_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
|
||
attempt[0] += 1
|
||
if attempt[0] <= 3:
|
||
resp = httpx.Response(429, request=httpx.Request("GET", url))
|
||
raise httpx.HTTPStatusError(
|
||
"Too Many Requests",
|
||
request=httpx.Request("GET", url),
|
||
response=resp,
|
||
)
|
||
return httpx.Response(200, json=_SAMPLE_WORK)
|
||
|
||
monkeypatch.setattr(openalex, "_get", controlled_get)
|
||
|
||
result: Paper | None = None
|
||
errors = 0
|
||
for _ in range(5):
|
||
try:
|
||
result = openalex.fetch_paper("10.1145/3592430")
|
||
break
|
||
except httpx.HTTPStatusError:
|
||
errors += 1
|
||
|
||
assert result is not None
|
||
assert isinstance(result, Paper)
|
||
assert errors == 3
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# fetch_citations — uses referenced_works field
|
||
# ---------------------------------------------------------------------------
|
||
|
||
|
||
def test_fetch_citations(monkeypatch: pytest.MonkeyPatch) -> None:
|
||
"""fetch_citations reads referenced_works from the work object."""
|
||
|
||
def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
|
||
return httpx.Response(200, json=_SAMPLE_WORK)
|
||
|
||
monkeypatch.setattr(openalex, "_get", mock_get)
|
||
|
||
oa_id = "https://openalex.org/W2741809807"
|
||
citations = openalex.fetch_citations(oa_id)
|
||
|
||
assert len(citations) == 2
|
||
assert all(isinstance(c, Citation) for c in citations)
|
||
assert citations[0].citing_id == oa_id
|
||
assert citations[0].cited_id == "https://openalex.org/W1"
|
||
assert citations[1].cited_id == "https://openalex.org/W2"
|
||
|
||
|
||
def test_fetch_citations_404_returns_empty(monkeypatch: pytest.MonkeyPatch) -> None:
|
||
"""404 on the work fetch returns an empty list."""
|
||
|
||
def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
|
||
raise httpx.HTTPStatusError(
|
||
"Not Found",
|
||
request=httpx.Request("GET", url),
|
||
response=httpx.Response(404, request=httpx.Request("GET", url)),
|
||
)
|
||
|
||
monkeypatch.setattr(openalex, "_get", mock_get)
|
||
assert openalex.fetch_citations("W999") == []
|