def test_instantiate_article(self):
article_id = 21598
article = parse.instantiate_article(article_id)
self.assertIsNotNone(article, "could not instantiate article object")
self.assertEqual(article.doi, "10.7554/eLife.21598")
# test non-existing data for test coverage
article_id = 99999
self.assertIsNone(parse.instantiate_article(article_id))
def test_set_article_type_by_id(self, fake_get_article_type):
"test allowable and disallowable article_type_id values"
article_id = 21598
article = parse.instantiate_article(article_id)
# test id 1
fake_get_article_type.return_value = "1"
return_value = parse.set_article_type(article, article_id)
self.assertTrue(return_value)
self.assertEqual(article.article_type, "research-article")
self.assertEqual(article.display_channel, "Research Article")
# test id 8
fake_get_article_type.return_value = "8"
return_value = parse.set_article_type(article, article_id)
self.assertTrue(return_value)
self.assertEqual(article.article_type, "discussion")
self.assertEqual(article.display_channel, "Feature Article")
# test id 10
fake_get_article_type.return_value = "10"
return_value = parse.set_article_type(article, article_id)
self.assertTrue(return_value)
self.assertEqual(article.article_type, "research-article")
self.assertEqual(article.display_channel, "Feature Article")
# test id 14
fake_get_article_type.return_value = "14"
return_value = parse.set_article_type(article, article_id)
self.assertTrue(return_value)
self.assertEqual(article.article_type, "research-article")
self.assertEqual(article.display_channel, "Short Report")
# test id 15
fake_get_article_type.return_value = "15"
return_value = parse.set_article_type(article, article_id)
self.assertTrue(return_value)
self.assertEqual(article.article_type, "research-article")
self.assertEqual(article.display_channel, "Research Advance")
# test id 19
fake_get_article_type.return_value = "19"
return_value = parse.set_article_type(article, article_id)
self.assertTrue(return_value)
self.assertEqual(article.article_type, "research-article")
self.assertEqual(article.display_channel, "Tools and Resources")
# test id 21
fake_get_article_type.return_value = "21"
return_value = parse.set_article_type(article, article_id)
self.assertTrue(return_value)
self.assertEqual(article.article_type, "research-article")
self.assertEqual(article.display_channel, "Scientific Correspondence")
# test id that does not exist, recreate the object first
article_id = 21598
article = parse.instantiate_article(article_id)
fake_get_article_type.return_value = "99999"
return_value = parse.set_article_type(article, article_id)
self.assertFalse(return_value)
self.assertEqual(
article.article_type, "research-article"
) # object default value
self.assertEqual(article.display_channel, None)
def test_set_license(self):
article = parse.instantiate_article("12")
return_value = parse.set_license(article, "12")
self.assertTrue(return_value)
self.assertIsNotNone(article.license, "did not create a license")
self.assertEqual(article.license.license_id, "1")
self.assertEqual(article.license.license_type, "open-access")
self.assertEqual(article.license.copyright, True)
self.assertEqual(
article.license.href, "http://creativecommons.org/licenses/by/4.0/"
)
self.assertEqual(article.license.name, "Creative Commons Attribution License")
self.assertEqual(
article.license.paragraph1,
"This article is distributed under the terms of the ",
)
self.assertEqual(
article.license.paragraph2,
(
" permitting unrestricted use and redistribution provided that the original "
+ "author and source are credited."
),
)
# test license_id 2
article = parse.instantiate_article("2935")
return_value = parse.set_license(article, "2935")
self.assertTrue(return_value)
self.assertIsNotNone(article.license, "did not create a license")
self.assertEqual(article.license.license_id, "2")
self.assertEqual(article.license.license_type, "open-access")
self.assertEqual(article.license.copyright, False)
self.assertEqual(
article.license.href, "http://creativecommons.org/publicdomain/zero/1.0/"
)
self.assertEqual(article.license.name, "Creative Commons CC0")
self.assertEqual(
article.license.paragraph1,
(
"This is an open-access article, free of all copyright, and may be freely "
+ "reproduced, distributed, transmitted, modified, built upon, or otherwise "
+ "used by anyone for any lawful purpose. The work is made available under the "
),
)
self.assertEqual(article.license.paragraph2, " public domain dedication.")
# test not finding a value
article = Article()
return_value = parse.set_license(article, "99999")
self.assertFalse(return_value)
def test_set_datasets_bad_data(self, fake_get_datasets):
"test bad ethics data that cannot be parsed"
fake_get_datasets.return_value = "LTLTbad_datasetsGTGTLTLT</omg>GTGT"
article = parse.instantiate_article("12")
return_value = parse.set_datasets(article, "12")
self.assertFalse(return_value)
self.assertEqual(article.datasets, [])
def test_set_author_info(self):
"test settings some authors"
# article 7 has an author with a competing interest
article = parse.instantiate_article("7")
return_value = parse.set_author_info(article, "7")
self.assertTrue(return_value)
self.assertEqual(len(article.contributors), 3)
# article 7 contributor 3
contrib = article.contributors[2]
self.assertEqual(contrib.contrib_type, "author")
self.assertEqual(contrib.surname, "Baldwin")
self.assertEqual(contrib.given_name, "Ian T")
self.assertEqual(contrib.corresp, True)
self.assertEqual(contrib.equal_contrib, False)
self.assertEqual(contrib.auth_id, "1013")
self.assertEqual(contrib.orcid, None)
self.assertEqual(contrib.suffix, None)
self.assertEqual(contrib.collab, None)
self.assertEqual(contrib.conflict, ["Senior Editor, <italic>eLife</italic>"])
self.assertEqual(contrib.group_author_key, None)
# count affiliations
self.assertEqual(len(article.contributors[2].affiliations), 1)
aff = article.contributors[2].affiliations[0]
self.assertEqual(aff.phone, None)
self.assertEqual(aff.fax, None)
self.assertEqual(aff.department, "Department of Molecular Ecology")
self.assertEqual(aff.institution, "Max Planck Institute for Chemical Ecology")
self.assertEqual(aff.city, "Jena")
self.assertEqual(aff.country, "Germany")
self.assertEqual(aff.text, None)
# article 2935 has some group authors
article = parse.instantiate_article("2935")
return_value = parse.set_author_info(article, "2935")
self.assertTrue(return_value)
self.assertEqual(len(article.contributors), 53)
# article 2935 contributor 34 is a group author
contrib = article.contributors[33]
self.assertEqual(contrib.contrib_type, "author")
self.assertEqual(contrib.surname, None)
self.assertEqual(contrib.given_name, None)
self.assertEqual(contrib.collab, "ICGC Breast Cancer Group")
# test not finding a value
article = Article()
return_value = parse.set_author_info(article, "99999")
self.assertFalse(return_value)
def test_set_dates_no_received_or_receipt_date(
self, fake_get_received_date, fake_get_receipt_date
):
fake_get_received_date.return_value = " "
fake_get_receipt_date.return_value = " "
article = parse.instantiate_article("12")
return_value = parse.set_dates(article, "12")
self.assertFalse(return_value)
def test_set_categories(self):
article = parse.instantiate_article("12")
return_value = parse.set_categories(article, "12")
self.assertTrue(return_value)
self.assertEqual(article.article_categories, ["Neuroscience"])
# test not finding a value, currently still returns True
article = Article()
return_value = parse.set_categories(article, "99999")
self.assertTrue(return_value)
def test_set_article_type(self):
article = parse.instantiate_article("12")
return_value = parse.set_article_type(article, "12")
self.assertTrue(return_value)
self.assertEqual(article.article_type, "research-article")
self.assertEqual(article.display_channel, "Short Report")
# test not finding a value
article = Article()
return_value = parse.set_article_type(article, "99999")
self.assertFalse(return_value)
def test_set_dates(self):
article = parse.instantiate_article("12")
return_value = parse.set_dates(article, "12")
self.assertTrue(return_value)
self.assertEqual(article.get_date("received").date, generate_date("2012-05-04"))
self.assertEqual(article.get_date("accepted").date, generate_date("2012-11-29"))
self.assertEqual(article.get_date("license").date, generate_date("2012-11-29"))
# test not finding a value
article = Article()
return_value = parse.set_dates(article, "99999")
self.assertFalse(return_value)
def test_set_title(self):
article = parse.instantiate_article("12")
return_value = parse.set_title(article, "12")
self.assertTrue(return_value)
self.assertEqual(
article.title,
(
"A title with Y<sup>1</sup>S<sup>2</sup>P<sup>3</sup>T<sup>4</sup>S<sup>5</sup>"
+ 'P<sup>6</sup>S<sup>7</sup> repeats, <italic>Drosophila</italic> and "quotations".'
),
)
# test not finding a value
article = Article()
return_value = parse.set_title(article, "99999")
self.assertFalse(return_value)
def test_set_abstract(self):
article = parse.instantiate_article("12")
return_value = parse.set_abstract(article, "12")
self.assertTrue(return_value)
self.assertEqual(
article.abstract,
(
"In this abstract are consensus Y<sup>1</sup>S<sup>2</sup>P<sup>3</sup>"
+ "T<sup>4</sup>S<sup>5</sup>P<sup>6</sup>S<sup>7</sup> repeats, "
+ '<italic>Drosophila</italic> and "quotations".'
),
)
# test not finding a value
article = Article()
return_value = parse.set_abstract(article, "99999")
self.assertFalse(return_value)
def test_set_datasets(self):
article = parse.instantiate_article("14997")
return_value = parse.set_datasets(article, "14997")
self.assertTrue(return_value)
self.assertEqual(len(article.datasets), 2)
# check dataset 1
self.assertEqual(article.datasets[0].dataset_type, "datasets")
self.assertEqual(article.datasets[0].authors, ["Cembrowski M", "Spruston N"])
self.assertEqual(
article.datasets[0].source_id,
"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=adsveykeprejbej&acc=GSE74985",
)
self.assertEqual(article.datasets[0].year, "2016")
self.assertEqual(
article.datasets[0].title,
"Hipposeq: an RNA-seq based atlas of gene expression in excitatory hippocampal neurons",
)
self.assertEqual(article.datasets[0].license_info, "GSE74985")
# check dataset 2
self.assertEqual(article.datasets[1].dataset_type, "prev_published_datasets")
self.assertEqual(article.datasets[1].authors, ["Cembrowski M", "Spruston N"])
self.assertEqual(
article.datasets[1].source_id,
"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67403",
)
self.assertEqual(article.datasets[1].year, "2016")
self.assertEqual(
article.datasets[1].title,
(
"Spatial gene expression gradients underlie prominent heterogeneity "
+ "of CA1 pyramidal neurons"
),
)
self.assertEqual(article.datasets[1].license_info, "GSE67403")
# check data availability
self.assertEqual(
article.data_availability,
u'\u2022Data Availability text <italic>"here"</italic> & such',
)
# test not finding a value, currently still returns True
article = Article()
return_value = parse.set_datasets(article, "99999")
self.assertTrue(return_value)
self.assertEqual(article.datasets, [])
self.assertEqual(article.data_availability, None)
def test_set_organsims(self):
article = parse.instantiate_article("3")
return_value = parse.set_organsims(article, "3")
self.assertTrue(return_value)
self.assertEqual(
article.research_organisms,
[
u"<italic>B. subtilis</italic>",
u"<italic>D. melanogaster</italic>",
u"<italic>E. coli</italic>",
u"Mouse",
],
)
# test not finding a value, currently still returns True
article = Article()
return_value = parse.set_organsims(article, "99999")
self.assertTrue(return_value)
def test_set_funding(self):
article = parse.instantiate_article("12717")
# set the authors in order to populate teh principal_award_recipients correctly
parse.set_author_info(article, "12717")
return_value = parse.set_funding(article, "12717")
self.assertTrue(return_value)
self.assertEqual(len(article.funding_awards), 2)
award = article.funding_awards[0]
self.assertEqual(award.award_group_id, None)
self.assertEqual(award.award_ids, ["1R01NS066936"])
self.assertEqual(
award.institution_name,
"National Institute of Neurological Disorders and Stroke",
)
self.assertEqual(award.institution_id, "100000065")
self.assertEqual(len(award.principal_award_recipients), 1)
self.assertEqual(award.principal_award_recipients[0].surname, "Solecki")
self.assertEqual(award.principal_award_recipients[0].given_name, "David J")
def test_set_keywords(self):
article = parse.instantiate_article("12")
return_value = parse.set_keywords(article, "12")
self.assertTrue(return_value)
self.assertEqual(
article.author_keywords,
[
"circuits",
"in vivo",
"spiking patterns",
"STDP",
"synaptic plasticity",
"visual cortex",
],
)
# test not finding a value, currently still returns True
article = Article()
return_value = parse.set_keywords(article, "99999")
self.assertTrue(return_value)
def test_set_ethics(self):
article = parse.instantiate_article("12")
return_value = parse.set_ethics(article, "12")
self.assertTrue(return_value)
self.assertEqual(
article.ethics,
[
u"Animal experimentation: All surgical procedures and experiments were conducted "
+ u"according to the German federal animal welfare guidelines and were approved by the "
+ u"animal ethics committee responsible for T\xfcbingen, Germany (Regierungspraesidium "
+ u"T\xfcbingen) under protocol numbers 3/07 and 5/09. Animals were deeply "
+ u"anaesthetized with Urethane (1.6-2 mg/kg), with the depth of anesthesia maintained "
+ u"throughout the course of the experiment with supplementary doses as required. "
+ u"Every attempt was made to ensure minimum discomfort to the animals at all times."
],
)
# test not finding a value, currently still returns True
article = Article()
return_value = parse.set_ethics(article, "99999")
self.assertTrue(return_value)
self.assertEqual(article.ethics, [])
def test_set_editor_info(self):
article = parse.instantiate_article("12717")
return_value = parse.set_editor_info(article, "12717")
self.assertTrue(return_value)
self.assertEqual(len(article.contributors), 1)
self.assertEqual(
len(
[
contrib
for contrib in article.contributors
if contrib.contrib_type == "editor"
]
),
1,
)
editor = article.contributors[0]
self.assertEqual(editor.contrib_type, "editor")
self.assertEqual(editor.surname, "Cooper")
self.assertEqual(editor.given_name, "Jonathan A")
self.assertEqual(editor.suffix, "Jnr")
aff = article.contributors[0].affiliations[0]
self.assertEqual(aff.department, "Division of Basic Sciences")
self.assertEqual(aff.institution, "Fred Hutchinson Cancer Research Center")
self.assertEqual(aff.country, "United States")
def test_set_categories_empty_data(self, fake_get_subjects):
fake_get_subjects.return_value = None
article = parse.instantiate_article("12")
return_value = parse.set_categories(article, "12")
self.assertTrue(return_value)
def test_set_dates_no_received_date(self, fake_get_received_date):
fake_get_received_date.return_value = " "
article = parse.instantiate_article("12")
return_value = parse.set_dates(article, "12")
self.assertTrue(return_value)
self.assertEqual(article.get_date("received").date, generate_date("2012-05-28"))
def test_set_funding_empty_data(self, fake_get_funding_ids):
fake_get_funding_ids.return_value = None
article = parse.instantiate_article("12")
return_value = parse.set_funding(article, "12")
self.assertTrue(return_value)
def test_instantiate_article_no_doi(self, fake_get_doi):
fake_get_doi.return_value = ""
article_id = 21598
article = parse.instantiate_article(article_id)
self.assertIsNotNone(article, "could not instantiate article object")
self.assertEqual(article.doi, "10.7554/eLife.21598")
def test_set_editor_info_bad_data(self, fake_get_me_first_nm):
fake_get_me_first_nm.return_value = None
article = parse.instantiate_article("12")
return_value = parse.set_editor_info(article, "12")
self.assertFalse(return_value)
def test_set_organisms_empty_data(self, fake_get_organisms):
fake_get_organisms.return_value = None
article = parse.instantiate_article("12")
return_value = parse.set_organsims(article, "12")
self.assertTrue(return_value)
