241 lines
8.2 KiB
Python
241 lines
8.2 KiB
Python
from __future__ import annotations
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import pytest
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from sqlalchemy import select
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from sqlalchemy.ext.asyncio import AsyncSession
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from app.db.models import Publication, PublicationIdentifier
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from app.services.arxiv import application as arxiv_service
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from app.services.publication_identifiers import application as identifier_service
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from app.services.publication_identifiers.types import IdentifierKind
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from app.services.publications.types import UnreadPublicationItem
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def test_derive_display_identifier_prefers_doi_over_arxiv() -> None:
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display = identifier_service.derive_display_identifier_from_values(
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doi="10.1000/example",
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pub_url="https://arxiv.org/abs/1504.08025",
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pdf_url=None,
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)
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assert display is not None
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assert display.kind == "doi"
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assert display.value == "10.1000/example"
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assert display.url == "https://doi.org/10.1000/example"
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def test_derive_display_identifier_uses_arxiv_when_doi_missing() -> None:
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display = identifier_service.derive_display_identifier_from_values(
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doi=None,
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pub_url="https://arxiv.org/pdf/1504.08025v2",
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pdf_url=None,
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)
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assert display is not None
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assert display.kind == "arxiv"
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assert display.value == "1504.08025v2"
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assert display.label == "arXiv: 1504.08025v2"
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def test_derive_display_identifier_uses_pmcid_when_present() -> None:
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display = identifier_service.derive_display_identifier_from_values(
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doi=None,
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pub_url=None,
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pdf_url="https://pmc.ncbi.nlm.nih.gov/articles/PMC2175868/pdf/file.pdf",
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)
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assert display is not None
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assert display.kind == "pmcid"
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assert display.value == "PMC2175868"
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def test_normalize_arxiv_id_handles_urls() -> None:
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from app.services.publication_identifiers.normalize import normalize_arxiv_id
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assert normalize_arxiv_id("https://arxiv.org/abs/1504.08025") == "1504.08025"
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assert normalize_arxiv_id("http://arxiv.org/pdf/1504.08025v2.pdf") == "1504.08025v2"
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assert normalize_arxiv_id("https://arxiv.org/html/1504.08025v2") == "1504.08025v2"
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# Modern arxiv format
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assert normalize_arxiv_id("https://arxiv.org/abs/2012.00001") == "2012.00001"
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# Old arxiv format
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assert normalize_arxiv_id("https://arxiv.org/abs/math/9901123") == "math/9901123"
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def test_normalize_arxiv_id_handles_raw_text() -> None:
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from app.services.publication_identifiers.normalize import normalize_arxiv_id
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assert normalize_arxiv_id("1504.08025v1") == "1504.08025v1"
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assert normalize_arxiv_id("arXiv:1504.08025") == "1504.08025"
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assert normalize_arxiv_id("arxiv: 1504.08025v1") == "1504.08025v1"
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assert normalize_arxiv_id("Preprint at arXiv:math/9901123v2") == "math/9901123v2"
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assert normalize_arxiv_id("Not an arxiv: 123") is None
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def test_normalize_pmcid_handles_urls_and_text() -> None:
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from app.services.publication_identifiers.normalize import normalize_pmcid
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assert normalize_pmcid("https://pmc.ncbi.nlm.nih.gov/articles/PMC2175868/") == "PMC2175868"
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assert normalize_pmcid("http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234567") == "PMC1234567"
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assert normalize_pmcid("PMCID: PMC1234567") == "PMC1234567"
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assert normalize_pmcid("pmc1234567") == "PMC1234567"
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assert normalize_pmcid("Not a PMCID 1234567") is None
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def test_normalize_pmid_handles_urls() -> None:
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from app.services.publication_identifiers.normalize import normalize_pmid
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assert normalize_pmid("https://pubmed.ncbi.nlm.nih.gov/12345678/") == "12345678"
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assert normalize_pmid("http://pubmed.ncbi.nlm.nih.gov/12345678") == "12345678"
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assert normalize_pmid("https://pubmed.ncbi.nlm.nih.gov/not-a-pmid/") is None
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def _publication(*, title: str, pub_url: str | None = None) -> Publication:
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return Publication(
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cluster_id=None,
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fingerprint_sha256="f" * 64,
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title_raw=title,
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title_normalized=title.lower(),
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year=2024,
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citation_count=0,
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author_text=None,
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venue_text=None,
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pub_url=pub_url,
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pdf_url=None,
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)
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@pytest.mark.asyncio
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async def test_discover_and_sync_skips_arxiv_when_crossref_finds_doi(
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db_session: AsyncSession,
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monkeypatch: pytest.MonkeyPatch,
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) -> None:
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publication = _publication(title="Reliable Paper Title for DOI discovery")
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db_session.add(publication)
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await db_session.flush()
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async def _fake_crossref(*, item):
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return "10.1000/strong-doi"
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async def _fail_arxiv(*, item, request_email=None, timeout_seconds=None):
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raise AssertionError("arXiv should be skipped after strong DOI evidence.")
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monkeypatch.setattr(
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"app.services.crossref.application.discover_doi_for_publication",
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_fake_crossref,
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)
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monkeypatch.setattr(
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"app.services.arxiv.application.discover_arxiv_id_for_publication",
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_fail_arxiv,
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)
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await identifier_service.discover_and_sync_identifiers_for_publication(
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db_session,
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publication=publication,
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scholar_label="Ada Lovelace",
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)
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result = await db_session.execute(
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select(PublicationIdentifier).where(
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PublicationIdentifier.publication_id == int(publication.id),
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PublicationIdentifier.kind == IdentifierKind.DOI.value,
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)
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)
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assert result.scalar_one_or_none() is not None
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@pytest.mark.asyncio
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async def test_discover_and_sync_skips_arxiv_for_low_quality_title(
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db_session: AsyncSession,
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monkeypatch: pytest.MonkeyPatch,
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) -> None:
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publication = _publication(title="AI 2024")
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db_session.add(publication)
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await db_session.flush()
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calls = {"count": 0}
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async def _fake_crossref(*, item):
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return None
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async def _fake_arxiv(*, item, request_email=None, timeout_seconds=None):
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calls["count"] += 1
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return "1234.5678"
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monkeypatch.setattr(
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"app.services.crossref.application.discover_doi_for_publication",
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_fake_crossref,
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)
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monkeypatch.setattr(
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"app.services.arxiv.application.discover_arxiv_id_for_publication",
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_fake_arxiv,
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)
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await identifier_service.discover_and_sync_identifiers_for_publication(
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db_session,
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publication=publication,
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scholar_label="Alan Turing",
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)
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assert calls["count"] == 0
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@pytest.mark.asyncio
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async def test_discover_and_sync_calls_arxiv_when_item_is_eligible(
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db_session: AsyncSession,
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monkeypatch: pytest.MonkeyPatch,
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) -> None:
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publication = _publication(title="Neural Representation Learning for Graph Signals")
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db_session.add(publication)
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await db_session.flush()
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async def _fake_crossref(*, item):
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return None
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async def _fake_arxiv(*, item, request_email=None, timeout_seconds=None):
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return "2501.00001v2"
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monkeypatch.setattr(
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"app.services.crossref.application.discover_doi_for_publication",
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_fake_crossref,
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)
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monkeypatch.setattr(
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"app.services.arxiv.application.discover_arxiv_id_for_publication",
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_fake_arxiv,
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)
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await identifier_service.discover_and_sync_identifiers_for_publication(
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db_session,
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publication=publication,
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scholar_label="Grace Hopper",
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)
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result = await db_session.execute(
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select(PublicationIdentifier).where(
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PublicationIdentifier.publication_id == int(publication.id),
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PublicationIdentifier.kind == IdentifierKind.ARXIV.value,
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)
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)
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identifier = result.scalar_one_or_none()
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assert identifier is not None
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assert identifier.value_normalized == "2501.00001v2"
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@pytest.mark.asyncio
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async def test_discover_arxiv_id_returns_none_if_no_title() -> None:
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item = UnreadPublicationItem(
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publication_id=1,
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scholar_profile_id=1,
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scholar_label="First Last",
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title="",
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year=2023,
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citation_count=0,
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venue_text=None,
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pub_url=None,
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pdf_url=None,
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)
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result = await arxiv_service.discover_arxiv_id_for_publication(item=item)
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assert result is None
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@pytest.mark.asyncio
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async def test_build_arxiv_query() -> None:
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query = arxiv_service._build_arxiv_query("Super AI Model", "Smith")
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assert query == 'ti:"Super AI Model" AND au:"Smith"'
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query2 = arxiv_service._build_arxiv_query("Only Title Here", None)
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assert query2 == 'ti:"Only Title Here"'
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