def test_should_add_parsed_references(self):
semantic_document = SemanticDocument()
semantic_ref = SemanticReference([
SemanticTitle(
layout_block=LayoutBlock.for_text('Reference Title 1')),
SemanticRawReferenceText(
layout_block=LayoutBlock.for_text('Reference 1'))
])
semantic_ref.content_id = 'b0'
semantic_document.back_section.add_content(
SemanticReferenceList([
SemanticHeading(
layout_block=LayoutBlock.for_text('References')),
semantic_ref
]))
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
assert tei_document.get_xpath_text_content_list(
'//tei:back/tei:div[@type="references"]/tei:listBibl/tei:head'
) == ['References']
assert tei_document.get_xpath_text_content_list(
'//tei:back/tei:div[@type="references"]/tei:listBibl'
'/tei:biblStruct/tei:analytic/tei:title[@type="main"]') == [
'Reference Title 1'
]
assert tei_document.get_xpath_text_content_list(
'//tei:back/tei:div[@type="references"]/tei:listBibl'
'/tei:biblStruct/tei:note[@type="raw_reference"]') == [
'Reference 1'
]
assert tei_document.get_xpath_text_content_list(
'//tei:back/tei:div[@type="references"]/tei:listBibl'
'/tei:biblStruct/@xml:id') == ['b0']
def test_should_add_section_figures_to_back(self):
semantic_document = SemanticDocument()
semantic_document.back_section.add_content(
SemanticSection([
SemanticFigure([
SemanticLabel(
layout_block=LayoutBlock.for_text('Label 1')),
SemanticCaption(
layout_block=LayoutBlock.for_text('Caption 1'))
],
content_id='fig_0')
]))
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
figure_xpath = (
'//tei:back/tei:div[@type="annex"]/tei:figure[not(contains(@type, "table"))]'
)
assert tei_document.get_xpath_text_content_list(
f'{figure_xpath}/tei:head') == ['Label 1']
assert tei_document.get_xpath_text_content_list(
f'{figure_xpath}/tei:label') == ['Label 1']
assert tei_document.get_xpath_text_content_list(
f'{figure_xpath}/tei:figDesc') == ['Caption 1']
assert tei_document.get_xpath_text_content_list(
f'{figure_xpath}/@xml:id') == ['fig_0']
assert not tei_document.xpath(
'//tei:back/tei:div[@type="annex"]/tei:div')
def test_should_add_single_author(self):
semantic_document = SemanticDocument()
title = SemanticNameTitle(layout_block=LayoutBlock.for_text('Title1'))
given_name = SemanticGivenName(
layout_block=LayoutBlock.for_text('Given1'))
middle_name = SemanticMiddleName(
layout_block=LayoutBlock.for_text('Middle1'))
surname = SemanticSurname(
layout_block=LayoutBlock.for_text('Surname1'))
suffix = SemanticNameSuffix(
layout_block=LayoutBlock.for_text('Suffix1'))
author = SemanticAuthor(
[title, given_name, middle_name, surname, suffix])
semantic_document.front.add_content(author)
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:roleName') == ['Title1']
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:forename[@type="first"]') == ['Given1']
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:forename[@type="middle"]') == ['Middle1']
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:surname') == ['Surname1']
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:genName') == ['Suffix1']
def test_should_add_asset_citation_for_resolved_reference(self):
semantic_document = SemanticDocument()
semantic_document.body_section.add_content(
SemanticSection([
SemanticParagraph([
SemanticTextContentWrapper(
layout_block=LayoutBlock.for_text('See')),
SemanticReferenceCitation(
layout_block=LayoutBlock.for_text('Ref 1'),
target_content_id='b0')
]),
SemanticReferenceList([
SemanticReference([
SemanticLabel(layout_block=LayoutBlock.for_text('1'))
],
content_id='b0')
])
]))
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
assert tei_document.get_xpath_text_content_list(
'//tei:body/tei:div/tei:p') == ['See Ref 1']
assert tei_document.get_xpath_text_content_list(
'//tei:body/tei:div/tei:p/tei:ref[@type="bibr"]') == ['Ref 1']
assert tei_document.get_xpath_text_content_list(
'//tei:body/tei:div/tei:p/tei:ref[@type="bibr"]/@target') == [
'#b0'
]
def test_should_set_abstract(self):
semantic_document = SemanticDocument()
semantic_document.front.add_content(
SemanticAbstract(LayoutBlock.for_text(TOKEN_1)))
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
assert tei_document.get_xpath_text_content_list(
'//tei:abstract/tei:p') == [TOKEN_1]
def test_should_add_notes_to_body(self):
semantic_document = SemanticDocument()
semantic_document.body_section.add_note(LayoutBlock.for_text(TOKEN_1),
'other')
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
assert tei_document.get_xpath_text_content_list(
'//tei:body/tei:note[@type="other"]') == [TOKEN_1]
def test_should_set_manuscript_title(self):
semantic_document = SemanticDocument()
semantic_document.front.add_content(
SemanticTitle(layout_block=LayoutBlock.for_text(TOKEN_1)))
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
assert tei_document.get_xpath_text_content_list(
'//tei:fileDesc/tei:titleStmt/tei:title[@level="a"][@type="main"]'
) == [TOKEN_1]
def get_tei_document_for_layout_document(
self,
layout_document: LayoutDocument
) -> TeiDocument:
return get_tei_for_semantic_document(
self.get_semantic_document_for_layout_document(
layout_document
)
)
def test_should_create_back_section(self):
semantic_document = SemanticDocument()
section = semantic_document.back_section.add_new_section()
section.add_heading_block(LayoutBlock.for_text(TOKEN_1))
paragraph = section.add_new_paragraph()
paragraph.add_block_content(LayoutBlock.for_text(TOKEN_2))
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
assert tei_document.get_xpath_text_content_list(
'//tei:back/tei:div[@type="annex"]/tei:div/tei:head') == [TOKEN_1]
assert tei_document.get_xpath_text_content_list(
'//tei:back/tei:div[@type="annex"]/tei:div/tei:p') == [TOKEN_2]
def test_should_unmatched_graphics_to_back(self):
semantic_document = SemanticDocument()
semantic_document.back_section.add_content(
SemanticMixedNote([
SemanticGraphic(
layout_graphic=LayoutGraphic(coordinates=COORDINATES_1),
relative_path='image1.svg')
],
note_type='unmatched_graphics'))
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
graphics_xpath = '//tei:note[@type="unmatched_graphics"]//tei:graphic'
assert tei_document.xpath_nodes(graphics_xpath)
assert tei_document.get_xpath_text_content_list(
f'{graphics_xpath}/@url') == ['image1.svg']
def test_should_add_orphan_affiliation(self):
semantic_document = SemanticDocument()
aff_marker = SemanticMarker(layout_block=LayoutBlock.for_text('1'))
institution = SemanticInstitution(
layout_block=LayoutBlock.for_text('Institution1'))
aff = SemanticAffiliationAddress([aff_marker, institution],
content_id='aff0')
semantic_document.front.add_content(aff)
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
assert tei_document.get_xpath_text_content_list(
'//tei:author/tei:affiliation/tei:note[@type="raw_affiliation"]'
) == [aff.get_text()]
assert tei_document.get_xpath_text_content_list(
'//tei:author/tei:affiliation/tei:note[@type="raw_affiliation"]/tei:label'
) == [aff_marker.get_text()]
assert tei_document.get_xpath_text_content_list(
'//tei:author/tei:affiliation/@key') == ['aff0']
def test_should_add_single_author_with_affiliation(self):
semantic_document = SemanticDocument()
title = SemanticNameTitle(layout_block=LayoutBlock.for_text('Title1'))
given_name = SemanticGivenName(
layout_block=LayoutBlock.for_text('Given1'))
middle_name = SemanticMiddleName(
layout_block=LayoutBlock.for_text('Middle1'))
surname = SemanticSurname(
layout_block=LayoutBlock.for_text('Surname1'))
suffix = SemanticNameSuffix(
layout_block=LayoutBlock.for_text('Suffix1'))
author_marker = SemanticMarker(layout_block=LayoutBlock.for_text('1'))
author = SemanticAuthor(
[title, given_name, middle_name, surname, suffix, author_marker])
aff_marker = SemanticMarker(layout_block=LayoutBlock.for_text('1'))
institution = SemanticInstitution(
layout_block=LayoutBlock.for_text('Institution1'))
aff = SemanticAffiliationAddress([aff_marker, institution],
content_id='aff0')
semantic_document.front.add_content(author)
semantic_document.front.add_content(aff)
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:roleName') == ['Title1']
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:forename[@type="first"]') == ['Given1']
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:forename[@type="middle"]') == ['Middle1']
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:surname') == ['Surname1']
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:genName') == ['Suffix1']
assert tei_document.get_xpath_text_content_list(
'//tei:author/tei:affiliation/tei:note[@type="raw_affiliation"]'
) == [aff.get_text()]
assert tei_document.get_xpath_text_content_list(
'//tei:author/tei:affiliation/tei:note[@type="raw_affiliation"]/tei:label'
) == [aff_marker.get_text()]
assert tei_document.get_xpath_text_content_list(
'//tei:author/tei:affiliation/@key') == ['aff0']
assert tei_document.get_xpath_text_content_list(
'//tei:author/tei:affiliation/tei:orgName[@type="institution"]'
) == [institution.get_text()]
def test_should_use_author_name_part_values(self):
semantic_document = SemanticDocument()
given_name = SemanticGivenName(
layout_block=LayoutBlock.for_text('GIVEN1'))
given_name.value = 'Given1'
middle_name = SemanticMiddleName(
layout_block=LayoutBlock.for_text('MIDDLE1'))
middle_name.value = 'Middle1'
surname = SemanticSurname(
layout_block=LayoutBlock.for_text('SURNAME1'))
surname.value = 'Surname1'
author = SemanticAuthor([given_name, middle_name, surname])
semantic_document.front.add_content(author)
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:forename[@type="first"]') == ['Given1']
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:forename[@type="middle"]') == ['Middle1']
assert tei_document.get_xpath_text_content_list(
'//tei:author//tei:surname') == ['Surname1']
def get_local_file_for_response_media_type(
self, response_media_type: str) -> str:
if response_media_type not in self.get_supported_response_media_type():
raise UnsupportedResponseMediaTypeScienceBeamParserError()
tei_document = get_tei_for_semantic_document(self.semantic_document)
xml_root = tei_document.root
relative_xml_filename = 'tei.xml'
if response_media_type in JATS_MEDIA_TYPES:
xml_root = self._get_tei_to_jats_xml_root(xml_root)
relative_xml_filename = 'jats.xml'
local_xml_filename = os.path.join(self.temp_dir, relative_xml_filename)
self._serialize_xml_to_file(xml_root, local_xml_filename)
LOGGER.debug('local_xml_filename: %r', local_xml_filename)
if response_media_type in ASSET_ZIP_MEDIA_TYPES:
zip_filename = os.path.join(self.temp_dir, 'results.zip')
create_asset_zip_for_semantic_document(
zip_filename,
semantic_document=self.semantic_document,
local_xml_filename=local_xml_filename,
relative_xml_filename=relative_xml_filename)
return zip_filename
return local_xml_filename
def test_should_add_raw_equation_with_label_to_paragraph(self):
# to be consistent with Java GROBID
semantic_document = SemanticDocument()
semantic_document.body_section.add_content(
SemanticSection([
SemanticParagraph([
SemanticTextContentWrapper(
layout_block=LayoutBlock.for_text('Next')),
SemanticRawEquation([
SemanticRawEquationContent(
layout_block=LayoutBlock.for_text('Equation 1')),
SemanticLabel(layout_block=LayoutBlock.for_text('(1)'))
])
]),
]))
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
assert tei_document.get_xpath_text_content_list(
'//tei:body/tei:div/tei:formula') == ['Equation 1 (1)']
assert tei_document.get_xpath_text_content_list(
'//tei:body/tei:div/tei:formula/tei:label') == ['(1)']
assert tei_document.get_xpath_text_content_list(
'//tei:body/tei:div/tei:p') == ['Next']
def test_should_add_section_tables_to_body(self):
semantic_document = SemanticDocument()
semantic_document.body_section.add_content(
SemanticSection([
SemanticTable([
SemanticLabel(
layout_block=LayoutBlock.for_text('Label 1')),
SemanticCaption(
layout_block=LayoutBlock.for_text('Caption 1'))
],
content_id='tab_0')
]))
tei_document = get_tei_for_semantic_document(semantic_document)
LOGGER.debug('tei xml: %r', etree.tostring(tei_document.root))
table_xpath = '//tei:body/tei:figure[@type="table"]'
assert tei_document.get_xpath_text_content_list(
f'{table_xpath}/tei:head') == ['Label 1']
assert tei_document.get_xpath_text_content_list(
f'{table_xpath}/tei:label') == ['Label 1']
assert tei_document.get_xpath_text_content_list(
f'{table_xpath}/tei:figDesc') == ['Caption 1']
assert tei_document.get_xpath_text_content_list(
f'{table_xpath}/@xml:id') == ['tab_0']
assert not tei_document.xpath('//tei:body/tei:div')
def test_should_return_empty_document(self):
semantic_document = SemanticDocument()
tei_document = get_tei_for_semantic_document(semantic_document)
assert not tei_document.xpath('//tei:div')
