def test_ref_list_citation_with_no_id(self):
"""for test coverage an article with a ref_list with a citation that has no id attribute"""
doi = "10.7554/eLife.00666"
title = "Test article"
article = Article(doi, title)
citation = Citation()
citation.article_title = "An article title"
article.ref_list = [citation]
c_xml = generate.build_crossref_xml([article])
crossref_xml_string = c_xml.output_xml()
self.assertTrue('<citation key="1">' in crossref_xml_string)
def test_generate_no_contributors(self):
"""Test when an article has no contributors"""
# build an article object and component, generate Crossref XML
doi = "10.7554/eLife.00666"
title = "Test article"
article = Article(doi, title)
# generate the crossrefXML
c_xml = generate.build_crossref_xml([article])
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("<contributors" not in crossref_xml_string)
def test_set_titles(self):
"""test stripping unwanted tags from title"""
doi = "10.7554/eLife.00666"
article = Article(doi, self.title)
expected_contains = (
"<titles><title>Test article for Desulfocapsa sulfexigens</title></titles>"
)
# generate
crossref_object = generate.build_crossref_xml([article])
crossref_xml_string = crossref_object.output_xml()
# test assertion
self.assertTrue(expected_contains in crossref_xml_string)
def test_set_abstract(self):
"""test stripping unwanted tags from abstract"""
doi = "10.7554/eLife.00666"
title = "Test article"
article = Article(doi, title)
article.abstract = self.abstract
expected_contains = (
"<jats:abstract><jats:p>An abstract. Desulfocapsa sulfexigens." +
" Stock and Wise (1990).</jats:p></jats:abstract>")
# generate
crossref_object = generate.build_crossref_xml([article])
crossref_xml_string = crossref_object.output_xml()
# test assertion
self.assertTrue(expected_contains in crossref_xml_string)
def test_generate_blank_affiliation(self):
"""Test when a contributor has a blank affiliation"""
doi = "10.7554/eLife.00666"
title = "Test article"
article = Article(doi, title)
author = Contributor("author", "Surname", "Given names")
aff = Affiliation()
aff.text = ""
author.set_affiliation(aff)
# generate the crossrefXML
c_xml = generate.build_crossref_xml([article])
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("<affiliation>" not in crossref_xml_string)
def crossref_convert(file_path):
if not file_path:
return None
config_section = 'elife'
try:
articles = generate.build_articles_for_crossref([file_path])
except:
# parsing failed somehow
return None
crossref_config = None
#if config_section:
# crossref_config = parse_raw_config(raw_config(config_section))
crossref_xml_object = generate.build_crossref_xml(articles, crossref_config)
crossref_xml = crossref_xml_object.output_xml(pretty=True, indent="\t")
return crossref_xml
def test_article_preprint(self):
"""test for an article with preprint data"""
doi = "10.7554/eLife.00666"
article = Article(doi, title="Sample article")
article.preprint = Preprint(uri="https://example.org/")
expected_contains = (
"<rel:program>"
"<rel:related_item>"
'<rel:intra_work_relation identifier-type="uri"'
' relationship-type="hasPreprint">https://example.org/'
"</rel:intra_work_relation>"
"</rel:related_item>"
"</rel:program>")
# generate
crossref_object = generate.build_crossref_xml([article])
crossref_xml_string = crossref_object.output_xml()
# test assertion
self.assertTrue(expected_contains in crossref_xml_string)
def test_component_subtitle_no_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 STRANGE subtitle, and this tag is"
" <not_allowed>!</not_allowed>")
article.component_list = [component]
# generate the crossrefXML
c_xml = generate.build_crossref_xml([article])
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)
def test_ref_list_data_citation_with_pmid(self):
"""
for test coverage an article with a ref_list with a
data citation that has a pmid attribute
"""
doi = "10.7554/eLife.00666"
title = "Test article"
article = Article(doi, title)
citation = Citation()
citation.data_title = "An data title"
citation.publication_type = "data"
citation.pmid = "pmid"
article.ref_list = [citation]
expected_contains = (
"<rel:program><rel:related_item><rel:description>An data title</rel:description>"
+
'<rel:inter_work_relation identifier-type="pmid" relationship-type="references">'
+
"pmid</rel:inter_work_relation></rel:related_item></rel:program>")
# generate
c_xml = generate.build_crossref_xml([article])
crossref_xml_string = c_xml.output_xml()
# test assertion
self.assertTrue(expected_contains in crossref_xml_string)
def test_set_datasets(self):
"""a basic non-XML example for set_datasets"""
doi = "10.7554/eLife.00666"
title = "Test article"
article = Article(doi, title)
# dataset_1 example with a uri
dataset_1 = Dataset()
dataset_1.dataset_type = "datasets"
dataset_1.uri = (
"https://github.com/elifesciences/XML-mapping/blob/master/elife-00666.xml"
)
dataset_1.title = "Kitchen sink"
# dataset_2 example with accession_id
dataset_2 = Dataset()
dataset_2.dataset_type = "prev_published_datasets"
dataset_2.accession_id = "EGAS00001000968"
# dataset_3 example with doi
dataset_3 = Dataset()
dataset_3.dataset_type = "prev_published_datasets"
dataset_3.doi = "10.5061/dryad.cv323"
# dataset_4 example with no dataset_type will be treated as a generated dataset by default
dataset_4 = Dataset()
dataset_4.uri = "http://cghub.ucsc.edu"
# dataset_5 example with an unsupported dataset_type
dataset_5 = Dataset()
dataset_5.dataset_type = "foo"
dataset_5.uri = "https://elifesciences.org"
# dataset_6 example with no identifier, not get added to the XML output, for test coverage
dataset_6 = Dataset()
dataset_6.dataset_type = "prev_published_datasets"
# add the datasets to the article object
article.add_dataset(dataset_1)
article.add_dataset(dataset_2)
article.add_dataset(dataset_3)
article.add_dataset(dataset_4)
article.add_dataset(dataset_5)
article.add_dataset(dataset_6)
# expected values
expected_xml_snippet_1 = (
"<rel:program><rel:related_item><rel:description>Kitchen sink</rel:description>"
+ '<rel:inter_work_relation identifier-type="uri" ' +
'relationship-type="isSupplementedBy">' +
"https://github.com/elifesciences/XML-mapping/blob/master/elife-00666.xml"
+ "</rel:inter_work_relation></rel:related_item>")
expected_xml_snippet_2 = (
'<rel:related_item><rel:inter_work_relation identifier-type="accession" '
+
'relationship-type="references">EGAS00001000968</rel:inter_work_relation>'
+ "</rel:related_item>")
expected_xml_snippet_3 = (
'<rel:related_item><rel:inter_work_relation identifier-type="doi" '
+
'relationship-type="references">10.5061/dryad.cv323</rel:inter_work_relation>'
+ "</rel:related_item>")
expected_xml_snippet_4 = (
'<rel:related_item><rel:inter_work_relation identifier-type="uri" '
+ 'relationship-type="isSupplementedBy">http://cghub.ucsc.edu' +
"</rel:inter_work_relation></rel:related_item>")
expected_xml_snippet_5 = (
'<rel:related_item><rel:inter_work_relation identifier-type="uri" '
+
'relationship-type="isSupplementedBy">https://elifesciences.org' +
"</rel:inter_work_relation></rel:related_item>")
# generate output
c_xml = generate.build_crossref_xml([article])
crossref_xml_string = c_xml.output_xml()
self.assertIsNotNone(crossref_xml_string)
# Test for expected strings in the XML output
self.assertTrue(expected_xml_snippet_1 in crossref_xml_string)
self.assertTrue(expected_xml_snippet_2 in crossref_xml_string)
self.assertTrue(expected_xml_snippet_3 in crossref_xml_string)
self.assertTrue(expected_xml_snippet_4 in crossref_xml_string)
self.assertTrue(expected_xml_snippet_5 in crossref_xml_string)