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>
201 lines
6.8 KiB
Python
201 lines
6.8 KiB
Python
"""Tests for codex.sources.arxiv."""
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from __future__ import annotations
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import io
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import tarfile
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import httpx
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import pytest
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from codex.sources import arxiv
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# ---------------------------------------------------------------------------
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# Helpers
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# ---------------------------------------------------------------------------
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def _make_tar_gz(files: dict[str, bytes]) -> bytes:
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"""Build an in-memory .tar.gz archive from a dict of {name: content}."""
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buf = io.BytesIO()
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with tarfile.open(fileobj=buf, mode="w:gz") as tf:
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for name, content in files.items():
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info = tarfile.TarInfo(name=name)
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info.size = len(content)
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tf.addfile(info, io.BytesIO(content))
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return buf.getvalue()
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# ---------------------------------------------------------------------------
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# fetch_source — success: in-memory tar.gz with one .tex
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# ---------------------------------------------------------------------------
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def test_fetch_source_returns_latex(monkeypatch: pytest.MonkeyPatch) -> None:
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"""fetch_source extracts and returns the LaTeX content from a .tar.gz."""
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latex_content = b"\\documentclass{article}\n\\begin{document}\nHello world\n\\end{document}"
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tar_bytes = _make_tar_gz({"main.tex": latex_content})
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def mock_get(
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url: str,
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*,
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timeout: int = 60,
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follow_redirects: bool = True,
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) -> httpx.Response:
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return httpx.Response(200, content=tar_bytes)
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monkeypatch.setattr(httpx, "get", mock_get)
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result = arxiv.fetch_source("2301.07041")
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assert result is not None
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assert "\\documentclass" in result
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assert "Hello world" in result
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# ---------------------------------------------------------------------------
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# fetch_source — 404 → None
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# ---------------------------------------------------------------------------
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def test_fetch_source_404_returns_none(monkeypatch: pytest.MonkeyPatch) -> None:
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"""A 404 response should return None."""
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def mock_get(
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url: str,
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*,
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timeout: int = 60,
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follow_redirects: bool = True,
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) -> httpx.Response:
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return httpx.Response(404)
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monkeypatch.setattr(httpx, "get", mock_get)
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result = arxiv.fetch_source("nonexistent-id")
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assert result is None
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# ---------------------------------------------------------------------------
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# fetch_source — no .tex in archive → None
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# ---------------------------------------------------------------------------
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def test_fetch_source_no_tex_returns_none(monkeypatch: pytest.MonkeyPatch) -> None:
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"""If the archive contains no .tex files, return None."""
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tar_bytes = _make_tar_gz({"README.md": b"# Paper\nNo LaTeX here."})
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def mock_get(
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url: str,
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*,
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timeout: int = 60,
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follow_redirects: bool = True,
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) -> httpx.Response:
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return httpx.Response(200, content=tar_bytes)
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monkeypatch.setattr(httpx, "get", mock_get)
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result = arxiv.fetch_source("2301.07041")
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assert result is None
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# ---------------------------------------------------------------------------
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# fetch_source — fallback to largest .tex when no \documentclass
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# ---------------------------------------------------------------------------
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def test_fetch_source_fallback_to_largest_tex(monkeypatch: pytest.MonkeyPatch) -> None:
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"""When no file has \\documentclass, the largest .tex is returned."""
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small_tex = b"% small file\n\\section{Intro}"
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large_tex = b"% large file\n" + b"x" * 500
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tar_bytes = _make_tar_gz({"small.tex": small_tex, "large.tex": large_tex})
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def mock_get(
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url: str,
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*,
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timeout: int = 60,
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follow_redirects: bool = True,
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) -> httpx.Response:
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return httpx.Response(200, content=tar_bytes)
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monkeypatch.setattr(httpx, "get", mock_get)
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result = arxiv.fetch_source("2301.07041")
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assert result is not None
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assert "large file" in result
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# ---------------------------------------------------------------------------
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# fetch_pdf_url — pure computation, no mock needed
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# ---------------------------------------------------------------------------
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def test_fetch_pdf_url_pure_computation() -> None:
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"""fetch_pdf_url returns the correct URL without making any HTTP request."""
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url = arxiv.fetch_pdf_url("2301.07041")
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assert url == "https://arxiv.org/pdf/2301.07041.pdf"
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url2 = arxiv.fetch_pdf_url("1234.56789")
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assert url2 == "https://arxiv.org/pdf/1234.56789.pdf"
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# ---------------------------------------------------------------------------
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# fetch_metadata — parse the Atom feed into a Paper (DQ-2)
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# ---------------------------------------------------------------------------
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_ATOM_FEED = """<?xml version="1.0" encoding="UTF-8"?>
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<feed xmlns="http://www.w3.org/2005/Atom">
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<entry>
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<title>A discrete version of Liouville's theorem on conformal maps</title>
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<summary>Liouville's theorem says that in dimension greater than two,
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all conformal maps are Moebius transformations.</summary>
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<published>2019-11-03T00:00:00Z</published>
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<author><name>Ulrich Pinkall</name></author>
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<author><name>Boris Springborn</name></author>
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</entry>
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</feed>"""
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_ATOM_EMPTY = """<?xml version="1.0" encoding="UTF-8"?>
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<feed xmlns="http://www.w3.org/2005/Atom"><title>ArXiv Query</title></feed>"""
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def test_fetch_metadata_parses_entry(monkeypatch: pytest.MonkeyPatch) -> None:
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"""A valid Atom feed yields a populated Paper."""
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def mock_get(url: str, **kwargs: object) -> httpx.Response:
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return httpx.Response(200, text=_ATOM_FEED, request=httpx.Request("GET", url))
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monkeypatch.setattr(httpx, "get", mock_get)
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paper = arxiv.fetch_metadata("1911.00966")
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assert paper is not None
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assert paper.id == "1911.00966"
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assert paper.title.startswith("A discrete version of Liouville")
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assert paper.authors == ["Ulrich Pinkall", "Boris Springborn"]
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assert paper.year == 2019
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assert paper.abstract and "conformal maps" in paper.abstract
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assert paper.openalex_id is None
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def test_fetch_metadata_no_entry_returns_none(monkeypatch: pytest.MonkeyPatch) -> None:
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"""A feed with no <entry> (id not found) returns None."""
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def mock_get(url: str, **kwargs: object) -> httpx.Response:
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return httpx.Response(200, text=_ATOM_EMPTY, request=httpx.Request("GET", url))
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monkeypatch.setattr(httpx, "get", mock_get)
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assert arxiv.fetch_metadata("0000.00000") is None
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def test_fetch_metadata_strips_arxiv_prefix(monkeypatch: pytest.MonkeyPatch) -> None:
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"""An ``arXiv:`` prefix is stripped so Paper.id is the bare id."""
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def mock_get(url: str, **kwargs: object) -> httpx.Response:
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return httpx.Response(200, text=_ATOM_FEED, request=httpx.Request("GET", url))
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monkeypatch.setattr(httpx, "get", mock_get)
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paper = arxiv.fetch_metadata("arXiv:1911.00966")
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assert paper is not None
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assert paper.id == "1911.00966"
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