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import xml
import json
import pytest
from grobid_tei_xml import teixml2json, parse_document_xml, GrobidDocument, GrobidCitation
from grobid_tei_xml.grobid2json import transform_grobid_ref_xml
def test_small_xml():
with open('tests/files/small.xml', 'r') as f:
tei_xml = f.read()
with open('tests/files/small.json', 'r') as f:
json_form = json.loads(f.read())
assert teixml2json(tei_xml) == json_form
def test_invalid_xml():
with pytest.raises(xml.etree.ElementTree.ParseError):
teixml2json("this is not XML")
with pytest.raises(ValueError):
teixml2json("<xml></xml>")
def test_grobid_teixml2json() -> None:
with open("tests/files/example_grobid.tei.xml", "r") as f:
blob = f.read()
obj = teixml2json(blob, True)
assert (
obj["title"] ==
"Changes of patients' satisfaction with the health care services in Lithuanian Health Promoting Hospitals network"
)
ref = [c for c in obj["citations"] if c["id"] == "b12"][0]
assert ref["authors"][0] == {
"given_name": "K",
"name": "K Tasa",
"surname": "Tasa"
}
assert ref["journal"] == "Quality Management in Health Care"
assert ref["title"] == "Using patient feedback for quality improvement"
assert ref["date"] == "1996"
assert ref["pages"] == "206-225"
assert ref["volume"] == "8"
assert (
ref["unstructured"] ==
"Tasa K, Baker R, Murray M. Using patient feedback for qua- lity improvement. Quality Management in Health Care 1996;8:206-19."
)
def test_transform_grobid_ref_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>"""
d = transform_grobid_ref_xml(citation_xml)
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"
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