def test_should_ignore_sub_fields_if_excluded(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper,
segment_affiliation: bool, sub_fields: str, expected_country: str):
target_jats_xml = etree.tostring(
get_target_xml_node(affiliation_nodes=[
E.aff(E.label(LABEL_1), ' ', E.country(COUNTRY_1)),
]))
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_affiliation_tei_node(
[TEI_E.affiliation(TEI_E.other(LABEL_1), ' ',
COUNTRY_1)])))
LOGGER.debug('target_jats_xml: %s', target_jats_xml)
test_helper.xml_file_path.write_bytes(target_jats_xml)
main(dict_to_args({
**test_helper.main_args_dict, 'matcher': 'simple',
'segment-affiliation': segment_affiliation,
'fields': 'author_aff',
'sub-fields': sub_fields,
'preserve-sub-tags': True,
'no-preserve-sub-fields': 'author_aff-label'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
first_aff = get_first_affiliation(tei_auto_root)
assert get_tei_xpath_text(first_aff, './tei:marker') == LABEL_1
assert get_tei_xpath_text(
first_aff, './tei:address/tei:country') == expected_country
def test_should_remove_invalid_affiliation(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
# we only create a single jats affiliation that would usually change the tei affiliation
# with --segment-affiliation, we expect to the affiliation segmentation to be updated
prefix = 'Some affiliation'
jats_text = prefix + '.'
tei_text = prefix + ' .'
invalid_affiliation_text = 'invalid affiliation'
target_jats_xml = etree.tostring(
get_target_xml_node(affiliation_nodes=[E.aff(jats_text)]))
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_affiliation_tei_node([
TEI_E.affiliation(tei_text),
TEI_E.affiliation(invalid_affiliation_text)
])))
LOGGER.debug('target_jats_xml: %s', target_jats_xml)
test_helper.xml_file_path.write_bytes(target_jats_xml)
main(dict_to_args({
**test_helper.main_args_dict, 'matcher': 'simple',
'fields': 'author_aff',
'segment-affiliation': True,
'remove-invalid-affiliations': True
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
assert get_text_content(tei_auto_root) == tei_text
def test_should_not_preserve_existing_sub_tags_if_provided_by_excluded(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper,
segment_affiliation: bool):
target_jats_xml = etree.tostring(
get_target_xml_node(affiliation_nodes=[
E.aff(E.label(LABEL_1), ' ' + LABEL_2 + ' ' + TEXT_1),
]))
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_affiliation_tei_node([
TEI_E.affiliation(TEI_E.other(LABEL_1), ' ',
TEI_E.marker(LABEL_2), ' ',
TEI_E.preserved(TEXT_1))
])))
LOGGER.debug('target_jats_xml: %s', target_jats_xml)
test_helper.xml_file_path.write_bytes(target_jats_xml)
main(dict_to_args({
**test_helper.main_args_dict, 'matcher': 'simple',
'segment-affiliation': segment_affiliation,
'fields': 'author_aff',
'preserve-sub-tags': True,
'no-preserve-sub-fields': 'author_aff-label'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
first_aff = get_first_affiliation(tei_auto_root)
assert get_tei_xpath_text(first_aff, './tei:marker') == LABEL_1
assert get_tei_xpath_text(first_aff, './tei:preserved') == TEXT_1
def test_should_group_preserved_and_auto_annotated_address_fields(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
target_jats_xml = etree.tostring(
get_target_xml_node(affiliation_nodes=[
E.aff(E.label(LABEL_1), TEXT_1 + ' ' + CITY_1 +
', ', E.country(COUNTRY_1)),
]))
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_affiliation_tei_node([
TEI_E.affiliation(
TEI_E.marker(LABEL_1), ' ' + TEXT_1 + ' ',
TEI_E.address(TEI_E.settlement(CITY_1), ', ',
TEI_E.country(COUNTRY_1)))
])))
LOGGER.debug('target_jats_xml: %s', target_jats_xml)
test_helper.xml_file_path.write_bytes(target_jats_xml)
main(dict_to_args({
**test_helper.main_args_dict, 'matcher': 'simple',
'segment-affiliation': True,
'preserve-sub-tags': True,
'no-preserve-sub-fields': 'author_aff-label,author_aff-country',
'fields': 'author_aff'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
tei_auto_aff = get_first_affiliation(tei_auto_root)
assert get_tei_xpath_text(tei_auto_aff, './tei:marker') == LABEL_1
assert get_tei_xpath_text(tei_auto_aff,
'./tei:address/tei:settlement') == CITY_1
assert get_tei_xpath_text(tei_auto_aff,
'./tei:address/tei:country') == COUNTRY_1
assert get_tei_xpath_text(tei_auto_aff, './tei:address',
delimiter='|') == (CITY_1 + ', ' + COUNTRY_1)
def test_should_not_merge_multiple_affiliation_annotations_surrounded_by_line_feeds(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper,
segment_affiliation: bool):
aff1_text = '\nSome affiliation 1\n'
aff2_text = '\nSome affiliation 2\n'
target_jats_xml = etree.tostring(
get_target_xml_node(
affiliation_nodes=[E.aff(aff1_text),
E.aff(aff2_text)]))
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_affiliation_tei_node([
TEI_E.affiliation(aff1_text),
TEI_E.affiliation(aff2_text)
])))
LOGGER.debug('target_jats_xml: %s', target_jats_xml)
test_helper.xml_file_path.write_bytes(target_jats_xml)
main(dict_to_args({
**test_helper.main_args_dict, 'matcher': 'simple',
'segment-affiliation': segment_affiliation,
'fields': 'author_aff'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
assert [
s.strip()
for s in get_text_content_list(get_all_affiliations(tei_auto_root))
] == [aff1_text.strip(), aff2_text.strip()]
def test_should_preserve_original_affiliation_annotation(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
# we only create a single jats affiliation that would usually change the tei affiliation
# without --segment-affiliation, we expect to retain the original affiliation segmentation
prefix = 'Some affiliation'
jats_text = prefix + '.'
tei_text = prefix + ' .'
target_jats_xml = etree.tostring(
get_target_xml_node(affiliation_nodes=[
E.aff(jats_text, jats_text),
]))
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_affiliation_tei_node(
[TEI_E.affiliation(tei_text),
TEI_E.affiliation(tei_text)])))
LOGGER.debug('target_jats_xml: %s', target_jats_xml)
test_helper.xml_file_path.write_bytes(target_jats_xml)
main(dict_to_args({
**test_helper.main_args_dict, 'matcher': 'simple',
'fields': 'author_aff'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
assert get_text_content_list(
get_all_affiliations(tei_auto_root)) == [tei_text, tei_text]
def test_should_auto_annotate_single_affiliation_with_all_supported_fields(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
target_reference_content_nodes = [
E('label', LABEL_1), ' ',
E('addr-line',
E('named-content', {'content-type': 'department'},
DEPARTMENT_1)), ' ',
E.institution(INSTITUTION_1), ' ',
E('addr-line', E('named-content', {'content-type': 'city'},
CITY_1)), ' ',
E('addr-line',
E('named-content', {'content-type': 'postcode'}, POST_CODE_1)),
' ',
E('addr-line',
E('named-content', {'content-type': 'state'}, STATE_1)), ' ',
E.country(COUNTRY_1)
]
target_jats_xml = etree.tostring(
get_target_xml_node(affiliation_nodes=[
E.aff(*target_reference_content_nodes),
]))
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_affiliation_tei_node([
TEI_E.affiliation(
get_nodes_text(target_reference_content_nodes))
])))
LOGGER.debug('target_jats_xml: %s', target_jats_xml)
test_helper.xml_file_path.write_bytes(target_jats_xml)
main(dict_to_args({
**test_helper.main_args_dict, 'matcher': 'simple',
'fields': 'author_aff'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
first_aff = get_first_affiliation(tei_auto_root)
assert get_tei_xpath_text(first_aff, './tei:marker') == LABEL_1
assert get_tei_xpath_text(
first_aff, './tei:orgName[@type="department"]') == (DEPARTMENT_1)
assert get_tei_xpath_text(
first_aff, './tei:orgName[@type="institution"]') == (INSTITUTION_1)
assert get_tei_xpath_text(first_aff,
'./tei:address/tei:settlement') == CITY_1
assert get_tei_xpath_text(first_aff,
'./tei:address/tei:postCode') == POST_CODE_1
assert get_tei_xpath_text(first_aff,
'./tei:address/tei:region') == STATE_1
assert get_tei_xpath_text(first_aff,
'./tei:address/tei:country') == COUNTRY_1
def test_should_include_label_and_omitted_separator_in_affiliation(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
tei_text = LABEL_1 + ' - ' + TEXT_1
target_jats_xml = etree.tostring(
get_target_xml_node(affiliation_nodes=[
E.aff(E.label(LABEL_1), TEXT_1),
]))
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(get_affiliation_tei_node([TEI_E.note(tei_text)])))
LOGGER.debug('target_jats_xml: %s', target_jats_xml)
test_helper.xml_file_path.write_bytes(target_jats_xml)
main(dict_to_args({
**test_helper.main_args_dict, 'matcher': 'simple',
'segment-affiliation': True,
'fields': 'author_aff'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
assert get_text_content_list(
get_all_affiliations(tei_auto_root)) == [tei_text]
def test_should_auto_annotate_single_affiliation_with_single_field(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper):
target_reference_content_nodes = [E('label', LABEL_1), ' Some text']
target_jats_xml = etree.tostring(
get_target_xml_node(affiliation_nodes=[
E.aff(*target_reference_content_nodes),
]))
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_affiliation_tei_node([
TEI_E.affiliation(
get_nodes_text(target_reference_content_nodes))
])))
LOGGER.debug('target_jats_xml: %s', target_jats_xml)
test_helper.xml_file_path.write_bytes(target_jats_xml)
main(dict_to_args({
**test_helper.main_args_dict, 'matcher': 'simple',
'fields': 'author_aff'
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
first_aff = get_first_affiliation(tei_auto_root)
assert get_tei_xpath_text(first_aff, './tei:marker') == (LABEL_1)
def test_should_preserve_existing_sub_tags(
self, test_helper: SingleFileAutoAnnotateEndToEndTestHelper,
segment_affiliation: bool):
untagged_text = ' some affiliation '
other1_sub_tag_text = 'other-sub-tag1'
other2_sub_tag_text = 'other-sub-tag2'
target_jats_xml = etree.tostring(
get_target_xml_node(affiliation_nodes=[
E.aff(other1_sub_tag_text + LABEL_1 + untagged_text +
other2_sub_tag_text),
]))
test_helper.tei_raw_file_path.write_bytes(
etree.tostring(
get_affiliation_tei_node([
TEI_E.affiliation(TEI_E.other1(other1_sub_tag_text),
TEI_E.marker(LABEL_1),
get_nodes_text([untagged_text]),
TEI_E.other2(other2_sub_tag_text))
])))
LOGGER.debug('target_jats_xml: %s', target_jats_xml)
test_helper.xml_file_path.write_bytes(target_jats_xml)
main(dict_to_args({
**test_helper.main_args_dict, 'matcher': 'simple',
'segment-affiliation': segment_affiliation,
'fields': 'author_aff',
'preserve-sub-tags': True
}),
save_main_session=False)
tei_auto_root = test_helper.get_tei_auto_root()
first_aff = get_first_affiliation(tei_auto_root)
assert get_tei_xpath_text(first_aff, './tei:marker') == LABEL_1
assert get_tei_xpath_text(first_aff,
'./tei:other1') == other1_sub_tag_text
assert get_tei_xpath_text(first_aff,
'./tei:other2') == other2_sub_tag_text
