def test_wormbase_year(self):
""" Just make sure we can extract something without crashing """
for i in range(600, 610):
wbid = 'WBPaper00044' + str(i)
doc = Document(wormbase=wbid)
doc.update_from_wormbase()
doc.year()
def test_pmid_init1(self):
"""
A pubmed uri doesn't work
"""
uri = 'http://www.ncbi.nlm.nih.gov/pubmed/24098140?dopt=abstract'
doc = Document(pmid=uri)
doc.update_from_pubmed()
self.assertEqual([], list(doc.author()))
def test_pmid_init2(self):
"""
A pubmed id
"""
pmid = "24098140"
doc = Document(pmid=pmid)
doc.update_from_pubmed()
self.assertIn(u'Frédéric MY', list(doc.author()))
def test_pmid_init2(self):
"""
A pubmed id
"""
pmid = "24098140"
doc = Document(pmid=pmid)
doc.update_from_pubmed()
self.assertIn(u'Frédéric MY', list(doc.author()))
def test_pubmed_init1(self):
"""
A pubmed uri
"""
uri = 'http://www.ncbi.nlm.nih.gov/pubmed/24098140?dopt=abstract'
doc = Document(pubmed=uri)
doc.update_from_pubmed()
self.assertIn(u'Frédéric MY', list(doc.author()))
def test_pmid_init1(self):
"""
A pubmed uri doesn't work
"""
uri = 'http://www.ncbi.nlm.nih.gov/pubmed/24098140?dopt=abstract'
doc = Document(pmid=uri)
doc.update_from_pubmed()
self.assertEqual([], list(doc.author()))
def test_pubmed_init1(self):
"""
A pubmed uri
"""
uri = 'http://www.ncbi.nlm.nih.gov/pubmed/24098140?dopt=abstract'
doc = Document(pubmed=uri)
doc.update_from_pubmed()
self.assertIn(u'Frédéric MY', list(doc.author()))
def test_pubmed_multiple_authors_list(self):
"""
When multiple authors are on a paper, all of their names should be
returned in an iterator. Publication order not necessarily preserved
"""
pmid = "24098140"
alist = [
u"Frédéric MY", "Lundin VF", "Whiteside MD", "Cueva JG", "Tu DK",
"Kang SY", "Singh H", "Baillie DL", "Hutter H", "Goodman MB",
"Brinkman FS", "Leroux MR"
]
doc = Document(pmid=pmid)
doc.update_from_pubmed()
self.assertEqual(set(alist), set(doc.author()))
def bibtex_to_document(bibtex_entry, context=None):
""" Takes a single BibTeX entry and translates it into a Document object """
from PyOpenWorm.document import Document
res = Document.contextualize(context)()
update_document_with_bibtex(res, bibtex_entry)
return res
def bibtex_to_document(bibtex_entry, context=None):
""" Takes a single BibTeX entry and translates it into a Document object """
from PyOpenWorm.document import Document
res = Document.contextualize(context)()
update_document_with_bibtex(res, bibtex_entry)
return res
def test_wormbase_year(self):
""" Just make sure we can extract something without crashing """
for i in range(600, 610):
wbid = 'WBPaper00044' + str(i)
doc = Document(wormbase=wbid)
doc.update_from_wormbase()
doc.year()
def test_pubmed_multiple_authors_list(self):
"""
When multiple authors are on a paper, all of their names should be
returned in an iterator. Publication order not necessarily preserved
"""
pmid = "24098140"
alist = [
u"Frédéric MY",
"Lundin VF",
"Whiteside MD",
"Cueva JG",
"Tu DK",
"Kang SY",
"Singh H",
"Baillie DL",
"Hutter H",
"Goodman MB",
"Brinkman FS",
"Leroux MR"]
doc = Document(pmid=pmid)
doc.update_from_pubmed()
self.assertEqual(set(alist), set(doc.author()))
def test_bibtex_init(self):
bibtex = u"""@ARTICLE{Cesar2013,
author = {Jean César},
title = {An amazing title},
year = {2013},
month = jan,
volume = {12},
pages = {12--23},
journal = {Nice Journal},
abstract = {This is an abstract. This line should be long enough to test
multilines...},
comments = {A comment},
keywords = {keyword1, keyword2},
}
"""
self.assertIn(u'Jean César', Document(bibtex=bibtex).author())
def test_wormbase_init(self):
""" Initialize with wormbase source """
doc = Document(wormbase="WBPaper00044287")
doc.update_from_wormbase()
self.assertIn(u'Frederic, M. Y.', list(doc.author()))
def test_wormbase_init(self):
""" Initialize with wormbase source """
doc = Document(wormbase="WBPaper00044287")
doc.update_from_wormbase()
self.assertIn(u'Frederic, M. Y.', list(doc.author()))
def test_data_user_reference(self):
do = Experiment(reference=Document(conf=self.config), conf=self.config)
self.assertIsNotNone(do.reference())