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Merged
merged 7 commits into from
Sep 9, 2024
Merged

Check if a journal name starts with the #320

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5aa213e
check if a journal name starts with instead
geemi725 Sep 7, 2024
6238225
Added: UNDEFINED_JOURNAL_QUALITY
geemi725 Sep 7, 2024
17e3d72
test updated
geemi725 Sep 8, 2024
c2c7a20
ignore codespell on title
geemi725 Sep 8, 2024
bb537f3
vcr mode: record new_episode
geemi725 Sep 8, 2024
d653d9b
Merge branch 'september-2024-release' into issue-317
geemi725 Sep 8, 2024
f838f7b
asyncio
geemi725 Sep 8, 2024
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7 changes: 6 additions & 1 deletion paperqa/clients/journal_quality.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,12 @@ async def _process(
# remember, if both have docnames (i.e. key) they are
# wiped and re-generated with resultant data
return doc_details + DocDetails( # type: ignore[call-arg]
source_quality=self.data.get(query.journal.casefold(), -1) # type: ignore[union-attr]
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Should we be using casefold?

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I think so? just to be more robust with journal names. @mskarlin thoughts?

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yup that's what we've been using on title comparisons!

source_quality=max(
[
self.data.get(query.journal.casefold(), DocDetails.UNDEFINED_JOURNAL_QUALITY), # type: ignore[union-attr]
self.data.get("the " + query.journal.casefold(), DocDetails.UNDEFINED_JOURNAL_QUALITY), # type: ignore[union-attr]
]
)
)

def query_creator(self, doc_details: DocDetails, **kwargs) -> JournalQuery | None:
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19 changes: 18 additions & 1 deletion tests/test_clients.py
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Expand Up @@ -299,7 +299,7 @@ async def test_s2_only_fields_filtering():
assert not s2_details.source_quality, "No source quality data should exist" # type: ignore[union-attr]


@pytest.mark.vcr
@pytest.mark.vcr(record_mode="new_episodes")
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Don't think you need this - I was wrong

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@pytest.mark.vcr(record_mode="new_episodes")
@pytest.mark.vcr

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I think we should let the VCR config in conftest.py be the one source of truth. So I vote we do actually commit this change

@pytest.mark.asyncio
async def test_crossref_journalquality_fields_filtering():
async with aiohttp.ClientSession() as session:
Expand Down Expand Up @@ -327,6 +327,23 @@ async def test_crossref_journalquality_fields_filtering():
"doi:10.1038/s42256-024-00832-8."
), "Citation should be populated"

async with aiohttp.ClientSession() as session:
crossref_client = DocMetadataClient(
session,
clients=cast(
Collection[
type[MetadataPostProcessor[Any]] | type[MetadataProvider[Any]]
],
[CrossrefProvider, JournalQualityPostProcessor],
),
)
nejm_crossref_details = await crossref_client.query(
title="Beta-Blocker Interruption or Continuation after Myocardial Infarction", # codespell:ignore
fields=["title", "doi", "authors", "journal"],
)

assert nejm_crossref_details.source_quality == 3, "Should have source quality data" # type: ignore[union-attr]


@pytest.mark.vcr
@pytest.mark.asyncio
Expand Down