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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.types import *
def test_teixml2json_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
assert parse_document_xml(tei_xml).to_dict() == json_form
def test_teixml2json_small_xml():
with open('tests/files/small.xml', 'r') as f:
tei_xml = f.read()
doc = parse_document_xml(tei_xml)
expected = GrobidDocument(
grobid_version='0.5.1-SNAPSHOT',
grobid_timestamp='2018-04-02T00:31+0000',
language_code='en',
header=GrobidHeader(
title="Dummy Example File",
authors=[
GrobidAuthor(
name="Brewster Kahle",
given_name="Brewster",
surname="Kahle",
affiliation=GrobidAffiliation(
department="Faculty ofAgricultrial Engineering",
laboratory="Plant Physiology Laboratory",
institution="Technion-Israel Institute of Technology",
address=GrobidAddress(
post_code="32000",
settlement="Haifa",
country="Israel",
),
)
),
GrobidAuthor(
name="J Doe",
given_name="J",
surname="Doe",
),
],
journal=GrobidJournal(
name="Dummy Example File. Journal of Fake News. pp. 1-2. ISSN 1234-5678",
),
date="2000",
),
abstract="Everything you ever wanted to know about nothing",
body="Introduction \nEverything starts somewhere, as somebody [1] once said. \n\n In Depth \n Meat \nYou know, for kids. \n Potatos \nQED.",
citations=[
GrobidCitation(
index=0,
id="b0",
authors=[
GrobidAuthor(
name="A Seaperson",
given_name="A",
surname="Seaperson"
)
],
date="2001",
journal="Letters in the Alphabet",
title="Everything is Wonderful",
volume="20",
pages="1-11",
),
GrobidCitation(
index=1,
id="b1",
authors=[],
date="2011-03-28",
journal="The Dictionary",
title="All about Facts",
volume="14",
),
],
)
assert doc == expected
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."
)
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