def test_component_subtitle_with_face_markup(self):
"""build an article object and component, generate Crossref XML"""
doi = "10.7554/eLife.00666"
title = "Test article"
article = Article(doi, title)
component = Component()
component.title = "A component"
component.subtitle = (
"A <sc>STRANGE</sc> <italic>subtitle</italic>, " +
"and this tag is <not_allowed>!</not_allowed>")
expected_subtitle = (
"A <sc>STRANGE</sc> <i>subtitle</i>, and this tag " +
"is <not_allowed>!</not_allowed>")
article.component_list = [component]
# load a config and override the value
raw_config_object = raw_config("elife")
face_markup = raw_config_object.get("face_markup")
raw_config_object["face_markup"] = "true"
crossref_config = parse_raw_config(raw_config_object)
# generate the crossrefXML
c_xml = generate.CrossrefXML([article], crossref_config, None, True)
crossref_xml_string = c_xml.output_xml()
self.assertIsNotNone(crossref_xml_string)
# A quick test just look for the expected string to test for tags and escape characters
self.assertTrue(expected_subtitle in crossref_xml_string)
# now set the config back to normal
raw_config_object["face_markup"] = face_markup
def test_set_abstract_jats_abstract_format(self):
"""test the abstract using jats abstract format set to true"""
doi = "10.7554/eLife.00666"
title = "Test article"
article = Article(doi, title)
article.abstract = self.abstract
article.abstract_xml = self.abstract_xml
expected_contains = (
'<jats:abstract xmlns:xlink="http://www.w3.org/1999/xlink">'
'<jats:p xmlns:xlink="http://www.w3.org/1999/xlink">'
"<jats:bold><jats:italic><jats:underline><jats:sub><jats:sup>"
"An abstract. "
'<jats:ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.1601/nm.3602">'
"Desulfocapsa sulfexigens</jats:ext-link>."
"</jats:sup></jats:sub></jats:underline></jats:italic></jats:bold> "
'<jats:xref ref-type="bibr">Stock and Wise (1990)</jats:xref>.'
"</jats:p></jats:abstract>"
)
# generate
raw_config_object = raw_config("elife")
jats_abstract = raw_config_object.get("jats_abstract")
raw_config_object["jats_abstract"] = "true"
crossref_config = parse_raw_config(raw_config_object)
crossref_object = generate.CrossrefXML([article], crossref_config, None, True)
crossref_xml_string = crossref_object.output_xml()
# test assertion
self.assertTrue(expected_contains in crossref_xml_string)
# now set the config back to normal
raw_config_object["jats_abstract"] = jats_abstract
def crossref_xml(
poa_articles,
crossref_config=None,
pub_date=None,
add_comment=True,
submission_type="journal",
pretty=False,
indent="",
):
"""build crossref xml and return output as a string"""
if not crossref_config:
crossref_config = parse_raw_config(raw_config(None))
c_xml = build_crossref_xml(poa_articles, crossref_config, pub_date,
add_comment, submission_type)
return c_xml.output_xml(pretty=pretty, indent=indent)
def build_crossref_xml(
poa_articles,
crossref_config=None,
pub_date=None,
add_comment=True,
submission_type="journal",
):
"""
Given a list of article article objects
generate crossref XML from them
"""
if not crossref_config:
crossref_config = parse_raw_config(raw_config(None))
return CrossrefXML(poa_articles, crossref_config, pub_date, add_comment,
submission_type)
def test_set_titles_face_markup_format(self):
"""test the title using face markup set to true"""
doi = "10.7554/eLife.00666"
article = Article(doi, self.title)
expected_contains = ("<titles><title><b>Test article</b> for"
" Desulfocapsa sulfexigens</title></titles>")
# generate
raw_config_object = raw_config("elife")
face_markup = raw_config_object.get("face_markup")
raw_config_object["face_markup"] = "true"
crossref_config = parse_raw_config(raw_config_object)
crossref_object = generate.CrossrefXML([article], crossref_config,
None, True)
crossref_xml_string = crossref_object.output_xml()
# test assertion
self.assertTrue(expected_contains in crossref_xml_string)
# now set the config back to normal
raw_config_object["face_markup"] = face_markup
def crossref_xml_to_disk(
poa_articles,
crossref_config=None,
pub_date=None,
add_comment=True,
submission_type="journal",
pretty=False,
indent="",
):
"""build crossref xml and write the output to disk"""
if not crossref_config:
crossref_config = parse_raw_config(raw_config(None))
c_xml = build_crossref_xml(poa_articles, crossref_config, pub_date,
add_comment, submission_type)
xml_string = c_xml.output_xml(pretty=pretty, indent=indent)
# Write to file
filename = TMP_DIR + os.sep + c_xml.batch_id + ".xml"
with open(filename, "wb") as open_file:
open_file.write(xml_string.encode("utf-8"))
def test_ref_list_citation_elocation_id(self):
"""for test coverage for schema where elocation_id goes into first_page element"""
# load a config and override the value
raw_config_object = raw_config("elife")
original_schema_version = raw_config_object.get(
"crossref_schema_version")
raw_config_object["crossref_schema_version"] = "4.4.0"
crossref_config = parse_raw_config(raw_config_object)
doi = "10.7554/eLife.00666"
title = "Test article"
article = Article(doi, title)
citation = Citation()
citation.elocation_id = "e00003"
article.ref_list = [citation]
c_xml = generate.CrossrefXML([article], crossref_config, None, True)
crossref_xml_string = c_xml.output_xml()
self.assertTrue(
"<first_page>e00003</first_page>" in crossref_xml_string)
# now set the config back to normal
raw_config_object["crossref_schema_version"] = original_schema_version
def generate_crossref_schema_version(self, crossref_schema_version,
expected_snippet):
"""Test non-default crossref schema version"""
# build an article object and component, generate Crossref XML
doi = "10.7554/eLife.00666"
title = "Test article"
article = Article(doi, title)
# load a config and override the value
raw_config_object = raw_config("elife")
original_schema_version = raw_config_object.get(
"crossref_schema_version")
raw_config_object["crossref_schema_version"] = crossref_schema_version
crossref_config = parse_raw_config(raw_config_object)
# generate the crossrefXML
c_xml = generate.CrossrefXML([article], crossref_config, None, True)
crossref_xml_string = c_xml.output_xml()
self.assertIsNotNone(crossref_xml_string)
# A quick test just look for a string value to test
self.assertTrue(expected_snippet in crossref_xml_string)
# now set the config back to normal
raw_config_object["crossref_schema_version"] = original_schema_version
def create_crossref_config(config_section="elife"):
"""utility to create the crossref object"""
raw_config_object = raw_config(config_section)
return parse_raw_config(raw_config_object)
XML_FILES.append([
"tests/test_data/elife-16988-v1.xml", "elife", DEFAULT_PUB_DATE, False
])
XML_FILES.append([
"tests/test_data/elife-11134-v2.xml", "elife", DEFAULT_PUB_DATE, False
])
XML_FILES.append([
"tests/test_data/elife-00508-v1.xml", "elife", DEFAULT_PUB_DATE, False
])
XML_FILES.append(
["tests/test_data/cstp77-jats.xml", "cstp", DEFAULT_PUB_DATE, False])
XML_FILES.append([
"tests/test_data/bmjopen-4-e003269.xml", "bmjopen", DEFAULT_PUB_DATE,
False
])
XML_FILES.append(
["tests/test_data/up-sta-example.xml", None, DEFAULT_PUB_DATE, False])
for xml_file, config_section, pub_date, add_comment in XML_FILES:
generate.TMP_DIR = "tests/test_data"
articles = generate.build_articles_for_crossref([xml_file])
crossref_config = parse_raw_config(raw_config(config_section))
generate.crossref_xml_to_disk(
articles,
crossref_config,
pub_date,
add_comment,
"journal",
pretty=True,
indent="\t",
)
