def test_should_replace_affiliation_with_author_if_single_tokens(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
author_text = 'Mary Maison 1, John Smith 1'
affiliation_text = '1 University of Science, Smithonia'
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_header_tei_node([
E.note(author_text),
E.lb(),
E.note(affiliation_text),
E.lb()
])))
test_helper.xml_file_path.write_bytes(
etree.tostring(
get_target_xml_node(author_nodes=[
E.contrib(
E.name(E.surname('Maison'), E('given-names', 'Mary'))),
E.contrib(
E.name(E.surname('Smith'), E('given-names', 'John'))),
E.aff(E.label('1'), E.institution('University of Science'),
E.country('Smithonia'))
])))
main(dict_to_args({
**test_helper.main_args_dict, 'fields':
','.join(['title', 'author', 'author_aff', 'abstract']),
'matcher':
'simple'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
assert get_xpath_text(tei_auto_root,
'//byline/docAuthor') == author_text
assert get_xpath_text(tei_auto_root,
'//byline/affiliation') == affiliation_text
def test_should_auto_annotate_label_containing_dot_within_reference(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
label_with_dot = '1.'
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_reference_segmenter_tei_node(
[E.note(label_with_dot + ' ' + REFERENCE_TEXT_1 + ' ')])))
test_helper.xml_file_path.write_bytes(
etree.tostring(
get_target_xml_node(reference_nodes=[
get_jats_reference_node(label_with_dot, REFERENCE_TEXT_1),
])))
main(dict_to_args({
**test_helper.main_args_dict, 'matcher':
'simple',
'fields':
'reference',
'xml-mapping-overrides':
'reference.use-raw-text=true'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
assert get_xpath_text(tei_auto_root, '//listBibl/bibl[1]') == ' '.join(
[label_with_dot, REFERENCE_TEXT_1])
assert get_xpath_text(tei_auto_root,
'//listBibl/bibl[1]/label') == label_with_dot
def test_should_auto_annotate_affiliation_preceding_number_using_simple_matcher(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
author_text = 'Mary Maison 1, John Smith 1'
affiliation_text_1 = '1'
affiliation_text_2 = 'University of Science, Smithonia'
affiliation_text = ' '.join([affiliation_text_1, affiliation_text_2])
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_header_tei_node([
E.note(TITLE_1),
E.lb(),
E.note(author_text),
E.lb(),
E.note(affiliation_text_1),
E.lb(),
E.note(affiliation_text_2),
E.lb(),
E.note(ABSTRACT_PREFIX_1, E.lb(), ABSTRACT_1)
])))
test_helper.xml_file_path.write_bytes(
etree.tostring(
get_target_xml_node(
title=TITLE_1,
author_nodes=[
E.contrib(
E.name(E.surname('Maison'),
E('given-names', 'Mary'))),
E.contrib(
E.name(E.surname('Smith'),
E('given-names', 'John'))),
E.aff(E.institution('University of Science'),
E.country('Smithonia'))
],
abstract_node=E.abstract(E.p(ABSTRACT_1)))))
main(dict_to_args({
**test_helper.main_args_dict, 'fields':
','.join(['title', 'author', 'author_aff', 'abstract']),
'matcher':
'simple'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
assert get_xpath_text(tei_auto_root, '//docTitle/titlePart') == TITLE_1
assert get_xpath_text(tei_auto_root,
'//byline/docAuthor') == author_text
assert get_xpath_text(tei_auto_root,
'//byline/affiliation') == affiliation_text
assert get_xpath_text(
tei_auto_root,
'//div[@type="abstract"]') == (ABSTRACT_PREFIX_1 + ABSTRACT_1)
def test_should_not_preserve_sub_tags(self, annotator: MagicMock):
structured_document = _structured_document_with_sub_elements(
E.sub1('sub1'), E.sub2('sub2'))
assert get_xpath_text(_get_root(structured_document),
'//sub1') == 'sub1'
assert get_xpath_text(_get_root(structured_document),
'//sub2') == 'sub2'
annotate_structured_document_inplace(structured_document,
annotator=annotator,
preserve_tags=True,
preserve_sub_tags=False,
fields={'title'})
assert get_xpath_text(_get_root(structured_document), '//sub1') == ''
assert get_xpath_text(_get_root(structured_document), '//sub2') == ''
def test_should_not_auto_annotate_other_sub_tags(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
target_reference_content_nodes = [
E('article-title', ARTICLE_TITLE_1),
' ',
E.source(SOURCE_1),
]
reference_text = get_nodes_text(target_reference_content_nodes)
target_jats_xml = etree.tostring(
get_target_xml_node(reference_nodes=[
get_jats_reference_node(LABEL_1, *
target_reference_content_nodes),
]))
LOGGER.debug('target_jats_xml: %s', target_jats_xml)
test_helper.xml_file_path.write_bytes(target_jats_xml)
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_reference_segmenter_tei_node(
[E.note(LABEL_1 + ' ' + reference_text)])))
main(dict_to_args({
**test_helper.main_args_dict, 'matcher': 'simple',
'fields': 'reference'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
assert get_xpath_text(tei_auto_root, '//listBibl/bibl') == ' '.join(
[LABEL_1, reference_text])
def test_should_auto_annotate_title(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(get_header_tei_node([E.note(TEXT_1)])))
test_helper.xml_file_path.write_bytes(
etree.tostring(get_target_xml_node(title=TEXT_1)))
main([*test_helper.main_args], save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
assert get_xpath_text(tei_auto_root, '//docTitle/titlePart') == TEXT_1
def test_should_extend_title_annotation_to_whole_line(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
title_text = 'Chocolate bars for mice'
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_header_tei_node([E.note('Title: ' + title_text)])))
test_helper.xml_file_path.write_bytes(
etree.tostring(get_target_xml_node(title=title_text)))
main([*test_helper.main_args, '--matcher=simple'],
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
assert get_xpath_text(tei_auto_root,
'//docTitle/titlePart') == title_text
def test_should_skip_errors(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
tei_raw_other_file_path = test_helper.tei_raw_path.joinpath(
'document0.header.tei.xml')
tei_raw_other_file_path.write_bytes(
etree.tostring(get_header_tei_node([E.note(TEXT_1)])))
xml_other_file_path = test_helper.xml_path.joinpath('document0.xml')
xml_other_file_path.write_bytes(
etree.tostring(get_target_xml_node(title=TEXT_1)) + b'error')
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(get_header_tei_node([E.note(TEXT_1)])))
test_helper.xml_file_path.write_bytes(
etree.tostring(get_target_xml_node(title=TEXT_1)))
main([*test_helper.main_args, '--matcher=simple', '--skip-errors'],
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
assert get_xpath_text(tei_auto_root, '//docTitle/titlePart') == TEXT_1
def test_should_auto_annotate_single_reference(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_reference_segmenter_tei_node(
[E.note(LABEL_1 + ' ' + REFERENCE_TEXT_1)])))
test_helper.xml_file_path.write_bytes(
etree.tostring(
get_target_xml_node(reference_nodes=[
get_jats_reference_node(LABEL_1, REFERENCE_TEXT_1),
])))
main(dict_to_args({
**test_helper.main_args_dict, 'matcher': 'simple',
'fields': 'reference'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
assert get_xpath_text(tei_auto_root, '//listBibl/bibl') == ' '.join(
[LABEL_1, REFERENCE_TEXT_1])
def get_tei_xpath_text(*args, **kwargs):
return get_xpath_text(*args, namespaces=TEI_NS_MAP, **kwargs)