From 2bf52b0622005ed8a7c51e59faa9873600d9cb5f Mon Sep 17 00:00:00 2001
From: Bryan Newbold <bnewbold@archive.org>
Date: Thu, 21 Oct 2021 18:22:12 -0700
Subject: more progress

---
 tests/test_parse.py | 213 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 213 insertions(+)
 create mode 100644 tests/test_parse.py

(limited to 'tests/test_parse.py')

diff --git a/tests/test_parse.py b/tests/test_parse.py
new file mode 100644
index 0000000..e79d41d
--- /dev/null
+++ b/tests/test_parse.py
@@ -0,0 +1,213 @@
+import xml
+import json
+import pytest
+
+from grobid_tei_xml import teixml2json, parse_document_xml, parse_citations_xml, GrobidDocument, GrobidCitation
+from grobid_tei_xml.types import *
+
+
+def test_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_small_xml_json():
+
+    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())
+
+    d = parse_document_xml(tei_xml).to_dict()
+
+    # munge back to the old JSON format
+    d.update(d.pop('header'))
+    addr = d['authors'][0]['affiliation']['address']
+    addr['postCode'] = addr.pop('post_code')
+
+    # remove nulls from old JSON
+    for c in json_form['citations']:
+        for k in list(c.keys()):
+            if c[k] == None:
+                c.pop(k)
+
+    assert d == json_form
+
+
+def test_invalid_xml():
+
+    with pytest.raises(xml.etree.ElementTree.ParseError):
+        parse_document_xml("this is not XML")
+    with pytest.raises(xml.etree.ElementTree.ParseError):
+        parse_citations_xml("this is not XML")
+    with pytest.raises(ValueError):
+        parse_document_xml("<xml></xml>")
+
+
+def test_example_grobid_tei_xml() -> None:
+
+    with open("tests/files/example_grobid.tei.xml", "r") as f:
+        blob = f.read()
+
+    doc = parse_document_xml(blob)
+
+    assert (
+        doc.header.title ==
+        "Changes of patients' satisfaction with the health care services in Lithuanian Health Promoting Hospitals network"
+    )
+
+    ref = [c for c in doc.citations if c.id == "b12"][0]
+    assert ref.authors[0].name == "K Tasa"
+    assert ref.authors[0].given_name == "K"
+    assert ref.authors[0].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_single_citations_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 = parse_citations_xml(citation_xml)[0]
+    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_citation_list_xml():
+
+    with open('tests/files/example_citation_list.xml', 'r') as f:
+        tei_xml = f.read()
+
+    citations = parse_citations_xml(tei_xml)
+    assert len(citations) == 10
+    assert citations[
+        7].title == "Global Hunger Index: The Challenge of Hidden Hunger"
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