def test_drops_extlink_urls():
xml = textwrap.dedent(
'''\
<?xml version="1.1" encoding="utf8" ?>
<article xmlns:ali="http://www.niso.org/schemas/ali/1.0/"
xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:mml="http://www.w3.org/1998/Math/MathML" article-type="research-article">
<p>
Crystal Protein Data Bank (
<ext-link ext-link-type="uri" xlink:href="http://www.pdb.org">www.pdb.org</ext-link>
). Crystal structures of complexes with program PyMOL (
<ext-link ext-link-type="uri" xlink:href="http://www.pymol.org">www.pymol.org</ext-link>
)
<xref rid="pone.0026760-Yun1" ref-type="bibr">[14]</xref>
,
<xref rid="pone.0026760-Yun2" ref-type="bibr">[16]</xref>
,
<xref rid="pone.0026760-Stamos1" ref-type="bibr">[23]</xref>
–
<xref rid="pone.0026760-Qiu1" ref-type="bibr">[25]</xref>
.
</p>
</article>'''
)
chunks = extract_text_chunks([etree.fromstring(xml)])
assert len(chunks) == 1
chunk = chunks[0].text
print(chunk)
assert 'program PyMOL.' in chunk
assert '[14]' not in chunk
assert '//www.' not in chunk
def test_extract_title_with_italics():
xml = '<article><article-title>Activating mutations in <italic>ALK</italic> provide a therapeutic target in neuroblastoma</article-title></article>'
chunks = extract_text_chunks([etree.fromstring(xml)])
assert len(chunks) == 1
assert (
'Activating mutations in ALK provide a therapeutic target in neuroblastoma'
== chunks[0].text
)
def test_extract_figure_label():
xml_input = '<article><fig id="pone-0026760-g003" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0026760.g003</object-id><label>Figure 3</label><caption><title>Anchorage-independent growth of ERBB2 mutants.</title></caption><graphic/></fig></article>'
root_nodes = [etree.fromstring(xml_input)]
annotations_map = {}
chunks = extract_text_chunks(root_nodes, annotations_map=annotations_map)
assert not annotations_map
xml_paths = [c.xml_path for c in chunks]
assert 'article/fig/label' in xml_paths
assert 'Figure 3' in [c.text for c in chunks if c.xml_path == 'article/fig/label']
def test_extract_explicit_table(xml_file, rows, cols):
with open(data_file_path(xml_file), 'r') as fh:
table_xml = fh.read()
chunks = extract_text_chunks([etree.fromstring(table_xml.strip())])
table_header = [c.text for c in chunks if c.xml_path.endswith('thead')]
assert len(table_header) == 1
assert len(table_header[0].split(TABLE_DELIMITER)) == cols
table_body = [c.text for c in chunks if c.xml_path.endswith('tbody')]
assert len(table_body) == 1
assert len(table_body[0].split(TABLE_DELIMITER)) == cols * rows
def test_keep_extlink_supplementary():
xml = textwrap.dedent(
'''\
<?xml version="1.1" encoding="utf8" ?>
<article xmlns:ali="http://www.niso.org/schemas/ali/1.0/"
xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:mml="http://www.w3.org/1998/Math/MathML" article-type="research-article">
<p>
Introduction of the <italic>NTRK3</italic> G623R mutation to the <italic>ETV6-NTRK3</italic> construct (Ba/F3-ETV6-NTRK3 G623R) conferred reduced sensitivity to entrectinib, increasing the IC<sub>50</sub> value in the proliferation assays more than 250-fold (2 to 507 nM) relative to the Ba/F3-ETV6-NTRK3 cells (Figure <xref ref-type="fig" rid="MDW042F3">3</xref>E). The <italic>NTRK3</italic> G623R mutation conferred even greater loss of sensitivity to the other tested Trk inhibitors, TSR-011 (Tesaro) and LOXO-101 (LOXO), eliciting IC<sub>50</sub> proliferation values of >1000 nM (<ext-link ext-link-type="uri" xlink:href="http://annonc.oxfordjournals.org/lookup/suppl/doi:10.1093/annonc/mdw042/-/DC1">supplementary Figure S4C, available at <italic>Annals of Oncology</italic> online</ext-link>).
</p>
</article>'''
)
chunks = extract_text_chunks([etree.fromstring(xml)])
assert len(chunks) == 1
chunk = chunks[0].text
print(chunk)
assert '(supplementary Figure S4C, available at Annals of Oncology online)' in chunk
def test_floating_table():
xml_input = data_file_path('floating_table.xml')
with open(xml_input, 'r') as fh:
xml_data = fh.read()
chunks = extract_text_chunks([etree.fromstring(xml_data)])
expected_columns = 6
expected_rows = 16
table_header = [c.text for c in chunks if c.xml_path.endswith('thead')]
assert len(table_header) == 1
header = table_header[0].split(TABLE_DELIMITER)
assert header == ['Patient sample', 'Exon', 'DNA', 'Protein', 'Domain', 'Germline/ Somatic']
table_body = [c.text for c in chunks if c.xml_path.endswith('tbody')]
assert len(table_body) == 1
assert len(table_body[0].split(TABLE_DELIMITER)) == expected_columns * expected_rows
def test_extract_text_chunks_sibling_xrefs():
siblings_example = """<article><abstract><p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis nec diam sed nisl aliquam scelerisque quis at turpis <xref ref-type="bibr">1</xref>. Vestibulum urna quam, accumsan id efficitur eget, fermentum vel eros. Pellentesque nisi urna, fringilla vitae sapien a, eleifend tempus libero. Nullam eget porta velit. Praesent bibendum dolor enim, ac lobortis<xref ref-type="bibr">2</xref>, <xref ref-type="bibr">3</xref>.</p></abstract></article>"""
expected = """Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis nec diam sed nisl aliquam scelerisque quis at turpis. Vestibulum urna quam, accumsan id efficitur eget, fermentum vel eros. Pellentesque nisi urna, fringilla vitae sapien a, eleifend tempus libero. Nullam eget porta velit. Praesent bibendum dolor enim, ac lobortis."""
root_nodes = [etree.fromstring(siblings_example)]
annotations_map = {}
chunks = extract_text_chunks(root_nodes, annotations_map=annotations_map)
full_text = ' '.join(c.text for c in chunks if c.text.strip())
assert '1' in annotations_map.values()
assert '2,3' in annotations_map.values()
for key in annotations_map:
assert key in full_text
final_text, annotations_result = strip_annotation_markers(full_text, annotations_map)
assert final_text == expected
locations = []
text = []
for ann in annotations_result:
text.append(ann.text)
for loc in ann.locations:
locations.append(loc.offset)
assert text == ['', '']
assert locations == [113, 325]
def test_extract_delimited_table(values: List[str or int or float or None], rows: int, cols: int):
values = [escape(v) for v in values]
rows_xml = []
values_used = set()
for row_index in range(rows):
tr = []
for col_index in range(cols):
value = values[(row_index * col_index + col_index) % len(values)]
tr.append(
f'\n<td rowspan="1" colspan="1" id="cell_{row_index}_{col_index}">{value}</td>'
)
values_used.add(value)
rows_xml.append('\n<tr>' + "".join(tr) + '\n</tr>')
table_body_xml = '<tbody>' + "".join(rows_xml) + '\n</tbody>'
thead = []
for col_index in range(cols):
thead.append(f'<td rowspan="1" colspan="1">Column {col_index}</td>')
table_header_xml = '<thead><tr>' + "".join(thead) + '</tr></thead>'
table_xml = f'''
<?xml version="1.1" encoding="utf8" ?>
<article><table-wrap>
<object-id pub-id-type="doi">some doi url</object-id>
<label>Table 1</label>
<caption>
<title>The title of the table</title>
</caption>
<alternatives>
<graphic />
<table frame="hsides" rules="groups">
{table_header_xml}
{table_body_xml}
</table>
</alternatives>
<table-wrap-foot>
<fn>
<label/>
<p>some long description of the table contents in the table footer
</p>
</fn>
</table-wrap-foot>
</table-wrap></article>
'''
chunks = extract_text_chunks([etree.fromstring(table_xml.strip())])
table_header = [c.text for c in chunks if c.xml_path.endswith('thead')]
assert len(table_header) == 1
assert len(table_header[0].split(TABLE_DELIMITER)) == cols
table_body = [c.text for c in chunks if c.xml_path.endswith('tbody')]
if cols == 1 and rows == 1 and all([cleanup_text(v) == '' for v in values_used]):
# will omit the table body if it is entirely empty
assert not table_body
else:
assert len(table_body) == 1
assert len(table_body[0].split(TABLE_DELIMITER)) == cols * rows