9e5184385a
Resolved 4 conflicts: cli.py (R-D citing-coverage warning + main's small-corpus JSON/hub-title changes both kept); ingest.py (C-7 paper.id=caller-id pin first, then DQ-2 abstract recovery); test_ingest.py + test_openalex.py (kept both branches' tests). C-7/DQ-5 overlap (both canonicalise papers.id): kept both layers — openalex._canonical_id normalizes fetch_paper's id (DQ-5); ingest pins papers.id to the caller's bare id (C-7); they converge on the bare canonical id. Fixed the auto-merged test_fetch_paper_success that had contradictory bare/URL assertions. 402 tests pass; ruff + mypy clean. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
290 lines
10 KiB
Python
290 lines
10 KiB
Python
"""Tests for codex.sources.openalex."""
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from __future__ import annotations
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import httpx
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import pytest
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from codex.models import Citation, Paper
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from codex.sources import openalex
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from codex.sources.openalex import _canonical_id, _normalize_doi, _resolve_id
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# ---------------------------------------------------------------------------
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# Helpers
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# ---------------------------------------------------------------------------
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_SAMPLE_WORK = {
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"id": "https://openalex.org/W2741809807",
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# Real OpenAlex returns the DOI as a full URL, not a bare DOI (audit T-3 / DQ-5
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# — the old bare fixture hid the URL-form behaviour both fixes address).
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"doi": "https://doi.org/10.1145/3592430",
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"title": "Conformal Prediction: A Review",
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"publication_year": 2023,
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"authorships": [
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{"author": {"display_name": "Alice Smith"}},
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{"author": {"display_name": "Bob Jones"}},
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],
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"abstract_inverted_index": {
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"Conformal": [0],
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"prediction": [1],
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"is": [2],
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"great": [3],
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},
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"referenced_works": [
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"https://openalex.org/W1",
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"https://openalex.org/W2",
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],
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}
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# ---------------------------------------------------------------------------
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# _resolve_id
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# ---------------------------------------------------------------------------
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def test_resolve_doi() -> None:
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assert _resolve_id("10.1145/3592430") == "doi:10.1145/3592430"
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def test_resolve_arxiv() -> None:
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# arXiv IDs resolve to their arXiv DOI (the arxiv: path 404s on OpenAlex).
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assert _resolve_id("2301.07041") == "doi:10.48550/arXiv.2301.07041"
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def test_resolve_arxiv_legacy() -> None:
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# Legacy category/number IDs (pre-2007) resolve the same way.
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assert _resolve_id("math/0603097") == "doi:10.48550/arXiv.math/0603097"
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def test_resolve_arxiv_prefix_stripped() -> None:
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# An explicit arxiv: prefix is stripped before building the arXiv DOI.
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assert _resolve_id("arxiv:2301.07041") == "doi:10.48550/arXiv.2301.07041"
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def test_resolve_w_id_unchanged() -> None:
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assert _resolve_id("W2741809807") == "W2741809807"
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def test_resolve_prefixed_unchanged() -> None:
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assert _resolve_id("doi:10.1145/x") == "doi:10.1145/x"
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# ---------------------------------------------------------------------------
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# _normalize_doi — canonical bare, lower-cased form (DQ-5)
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# ---------------------------------------------------------------------------
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def test_normalize_doi_strips_https_url() -> None:
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# The exact form OpenAlex returns in the `doi` field.
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assert _normalize_doi("https://doi.org/10.1007/s00454-019-00132-8") == (
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"10.1007/s00454-019-00132-8"
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)
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def test_normalize_doi_strips_http_and_doi_prefix() -> None:
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assert _normalize_doi("http://doi.org/10.1145/3592430") == "10.1145/3592430"
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assert _normalize_doi("doi:10.1145/3592430") == "10.1145/3592430"
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def test_normalize_doi_lowercases() -> None:
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# DOIs are case-insensitive; the canonical id (and _norm_cited_id) is lower-case.
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assert _normalize_doi("https://doi.org/10.1007/S00454-019-00132-8") == (
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"10.1007/s00454-019-00132-8"
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)
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def test_normalize_doi_already_bare_is_idempotent() -> None:
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assert _normalize_doi("10.1007/s00454-019-00132-8") == "10.1007/s00454-019-00132-8"
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# ---------------------------------------------------------------------------
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# _canonical_id — arXiv DOI → bare arXiv id (arXiv half of DQ-5)
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# ---------------------------------------------------------------------------
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def test_canonical_id_strips_arxiv_doi_modern() -> None:
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# arXiv works carry the arXiv DOI; the canonical id is the bare arXiv id.
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assert _canonical_id("https://doi.org/10.48550/arXiv.2305.10988") == "2305.10988"
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def test_canonical_id_strips_arxiv_doi_legacy() -> None:
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assert _canonical_id("https://doi.org/10.48550/arXiv.math/0603097") == "math/0603097"
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def test_canonical_id_leaves_regular_doi_bare() -> None:
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# A normal journal DOI is only normalized (bare + lower-case), not stripped.
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assert _canonical_id("https://doi.org/10.1007/S00454-019-00132-8") == (
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"10.1007/s00454-019-00132-8"
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)
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def test_fetch_paper_arxiv_doi_yields_bare_id(monkeypatch: pytest.MonkeyPatch) -> None:
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"""An arXiv work maps to the BARE arXiv id (not the arXiv DOI), so re-ingesting
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by arXiv id hits ON CONFLICT (id) instead of tripping papers_openalex_id_key."""
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work = {**_SAMPLE_WORK, "doi": "https://doi.org/10.48550/arXiv.2305.10988"}
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def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
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return httpx.Response(200, json=work)
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monkeypatch.setattr(openalex, "_get", mock_get)
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paper = openalex.fetch_paper("2305.10988")
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assert paper is not None
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assert paper.id == "2305.10988"
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def test_map_paper_falls_back_to_openalex_id_without_doi(
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monkeypatch: pytest.MonkeyPatch,
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) -> None:
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"""A work with no DOI keeps the OpenAlex W-id (URL form) as id, unchanged —
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normalization only rewrites the DOI branch."""
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work = {k: v for k, v in _SAMPLE_WORK.items() if k != "doi"}
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def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
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return httpx.Response(200, json=work)
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monkeypatch.setattr(openalex, "_get", mock_get)
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paper = openalex.fetch_paper("W2741809807")
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assert paper is not None
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assert paper.id == "https://openalex.org/W2741809807"
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# ---------------------------------------------------------------------------
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# fetch_paper — success
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# ---------------------------------------------------------------------------
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def test_fetch_paper_success(monkeypatch: pytest.MonkeyPatch) -> None:
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"""Successful fetch maps all fields to Paper correctly."""
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def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
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assert "doi:10.1145/3592430" in url
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return httpx.Response(200, json=_SAMPLE_WORK)
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monkeypatch.setattr(openalex, "_get", mock_get)
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paper = openalex.fetch_paper("10.1145/3592430")
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assert paper is not None
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assert isinstance(paper, Paper)
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# DQ-5: openalex._canonical_id normalizes OpenAlex's URL-form doi to the BARE
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# lower-cased DOI at the source layer; ingest additionally pins papers.id to the
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# caller's id (audit C-7). Both converge on the bare canonical id — which is what
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# makes the ingest ON CONFLICT (id) upsert idempotent. (T-3: the fixture is
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# URL-form so this mapping can't silently regress.)
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assert paper.id == "10.1145/3592430"
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assert paper.title == "Conformal Prediction: A Review"
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assert paper.year == 2023
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assert paper.authors == ["Alice Smith", "Bob Jones"]
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assert paper.abstract == "Conformal prediction is great"
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assert paper.openalex_id == "https://openalex.org/W2741809807"
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def test_fetch_paper_arxiv_id_prefixed(monkeypatch: pytest.MonkeyPatch) -> None:
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"""Bare arXiv IDs are resolved to their arXiv DOI in the URL."""
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called_url: list[str] = []
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def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
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called_url.append(url)
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return httpx.Response(200, json=_SAMPLE_WORK)
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monkeypatch.setattr(openalex, "_get", mock_get)
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openalex.fetch_paper("2301.07041")
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assert called_url and "doi:10.48550/arXiv.2301.07041" in called_url[0]
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# ---------------------------------------------------------------------------
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# fetch_paper — 404 → None
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# ---------------------------------------------------------------------------
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def test_fetch_paper_404_returns_none(monkeypatch: pytest.MonkeyPatch) -> None:
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"""A 404 response should return None without raising."""
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def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
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raise httpx.HTTPStatusError(
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"Not Found",
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request=httpx.Request("GET", url),
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response=httpx.Response(404, request=httpx.Request("GET", url)),
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)
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monkeypatch.setattr(openalex, "_get", mock_get)
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result = openalex.fetch_paper("nonexistent-id")
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assert result is None
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# ---------------------------------------------------------------------------
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# fetch_paper — 429 retry then success
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# ---------------------------------------------------------------------------
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def test_fetch_paper_retry_on_429(monkeypatch: pytest.MonkeyPatch) -> None:
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"""On 429×3 then 200, returns 1 Paper after 3 failed attempts."""
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attempt = [0]
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def controlled_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
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attempt[0] += 1
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if attempt[0] <= 3:
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resp = httpx.Response(429, request=httpx.Request("GET", url))
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raise httpx.HTTPStatusError(
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"Too Many Requests",
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request=httpx.Request("GET", url),
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response=resp,
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)
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return httpx.Response(200, json=_SAMPLE_WORK)
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monkeypatch.setattr(openalex, "_get", controlled_get)
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result: Paper | None = None
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errors = 0
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for _ in range(5):
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try:
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result = openalex.fetch_paper("10.1145/3592430")
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break
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except httpx.HTTPStatusError:
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errors += 1
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assert result is not None
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assert isinstance(result, Paper)
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assert errors == 3
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# ---------------------------------------------------------------------------
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# fetch_citations — uses referenced_works field
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# ---------------------------------------------------------------------------
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def test_fetch_citations(monkeypatch: pytest.MonkeyPatch) -> None:
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"""fetch_citations reads referenced_works from the work object."""
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def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
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return httpx.Response(200, json=_SAMPLE_WORK)
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monkeypatch.setattr(openalex, "_get", mock_get)
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oa_id = "https://openalex.org/W2741809807"
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citations = openalex.fetch_citations(oa_id)
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assert len(citations) == 2
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assert all(isinstance(c, Citation) for c in citations)
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assert citations[0].citing_id == oa_id
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assert citations[0].cited_id == "https://openalex.org/W1"
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assert citations[1].cited_id == "https://openalex.org/W2"
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def test_fetch_citations_404_returns_empty(monkeypatch: pytest.MonkeyPatch) -> None:
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"""404 on the work fetch returns an empty list."""
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def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
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raise httpx.HTTPStatusError(
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"Not Found",
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request=httpx.Request("GET", url),
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response=httpx.Response(404, request=httpx.Request("GET", url)),
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)
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monkeypatch.setattr(openalex, "_get", mock_get)
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assert openalex.fetch_citations("W999") == []
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