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import pytest
from grobid_tei_xml import parse_citation_xml
from grobid_tei_xml.types import GrobidBiblio, GrobidAuthor
from fuzzycat.grobid_unstructured import grobid_api_process_citation, grobid_parse_unstructured, grobid_ref_to_release
def test_grobid_ref_to_release():
d = GrobidBiblio(
title="some title",
doi='10.1234/5678',
journal='some journal',
authors=[
GrobidAuthor(
full_name='ahab sailor',
given_name='ahab',
surname='sailor',
),
GrobidAuthor(full_name='mary jane', given_name='mary', surname='jane'),
],
)
r = grobid_ref_to_release(d)
assert r.title == d.title
assert r.ext_ids.doi == d.doi
assert r.extra['container_name'] == d.journal
assert r.contribs[0].surname == d.authors[0].surname
assert r.contribs[1].raw_name == d.authors[1].full_name
def test_transform_grobid_ref_xml():
"""
This used to be a test of the grobid2json file in this repository. Now it
is a backwards compatibility test for grobid_tei_xml
"""
citation_xml = """
<biblStruct >
<analytic>
<title level="a" type="main">Mesh migration following abdominal hernia repair: a comprehensive review</title>
<author>
<persName
xmlns="http://www.tei-c.org/ns/1.0">
<forename type="first">H</forename>
<forename type="middle">B</forename>
<surname>Cunningham</surname>
</persName>
</author>
<author>
<persName
xmlns="http://www.tei-c.org/ns/1.0">
<forename type="first">J</forename>
<forename type="middle">J</forename>
<surname>Weis</surname>
</persName>
</author>
<author>
<persName
xmlns="http://www.tei-c.org/ns/1.0">
<forename type="first">L</forename>
<forename type="middle">R</forename>
<surname>Taveras</surname>
</persName>
</author>
<author>
<persName
xmlns="http://www.tei-c.org/ns/1.0">
<forename type="first">S</forename>
<surname>Huerta</surname>
</persName>
</author>
<idno type="DOI">10.1007/s10029-019-01898-9</idno>
<idno type="PMID">30701369</idno>
</analytic>
<monogr>
<title level="j">Hernia</title>
<imprint>
<biblScope unit="volume">23</biblScope>
<biblScope unit="issue">2</biblScope>
<biblScope unit="page" from="235" to="243" />
<date type="published" when="2019-01-30" />
</imprint>
</monogr>
</biblStruct>"""
citation = parse_citation_xml(citation_xml)
assert citation
d = citation.to_legacy_dict()
assert d['title'] == "Mesh migration following abdominal hernia repair: a comprehensive review"
assert d['authors'][2]['given_name'] == "L"
assert d['authors'][2]['surname'] == "Taveras"
assert d['authors'][2]['name'] == "L R Taveras"
assert d['doi'] == "10.1007/s10029-019-01898-9"
assert d['pmid'] == "30701369"
assert d['date'] == "2019-01-30"
assert d['pages'] == "235-243"
assert d['volume'] == "23"
assert d['issue'] == "2"
assert d['journal'] == "Hernia"
def test_grobid_parse_unstructured():
"""
NOTE: this test makes live network requests to GROBID
"""
r = grobid_parse_unstructured("blah")
assert r is None
r = grobid_parse_unstructured(
"""Cunningham HB, Weis JJ, Taveras LR, Huerta S. Mesh migration following abdominal hernia repair: a comprehensive review. Hernia. 2019 Apr;23(2):235-243. doi: 10.1007/s10029-019-01898-9. Epub 2019 Jan 30. PMID: 30701369."""
)
assert r.title == "Mesh migration following abdominal hernia repair: a comprehensive review"
assert r.contribs[0].surname == "Cunningham"
assert r.contribs[1].surname == "Weis"
assert r.contribs[2].surname == "Taveras"
assert r.contribs[3].surname == "Huerta"
assert r.extra['container_name'] == "Hernia"
assert r.release_year == 2019
assert r.volume == "23"
assert r.issue == "2"
assert r.pages == "235-243"
assert r.ext_ids.doi == "10.1007/s10029-019-01898-9"
assert r.ext_ids.pmid == "30701369"
def test_grobid_parse_unstructured_timeout():
"""
NOTE: this test makes live network requests to GROBID
"""
with pytest.raises(TimeoutError):
grobid_parse_unstructured("blah", timeout=0.000001)
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