def setup_items(self):
self.table = ReferenceTable()
self.author1 = Author(lastname="FirstLast",
firstname="FirstFirst",
initials="FirstInitials")
self.author2 = Author(lastname="SecondLast",
firstname="SecondFirst",
initials="SecondInitials")
self.pmid = "123456"
self.pmc = "PMC12345"
self.url = "http://www.google.com"
self.journal = "Test journal"
self.year = "1987"
self.title = "Test title"
self.doi = "Test doi"
self.reference = Reference(pmid=self.pmid,
pmc=self.pmc,
doi=self.doi,
url=self.url,
year=self.year,
title=self.title,
journal=self.journal,
authors=[self.author1, self.author2])
def setup_items(self):
self.first_author = Author(lastname="FirstLastname",
firstname="FirstFirstname",
initials="FirstInitials")
self.second_author = Author(lastname="SecondLastname",
firstname="SecondFirstname",
initials="SecondInitials")
self.authors = [self.first_author, self.second_author]
self.test_pmid = "123456"
self.test_pmc = "PMC12345"
self.test_doi = "10.1016/j.chemosphere.2016.03.102"
self.test_url = "http://google.com"
self.test_year = "1999"
self.test_title = "Test title"
self.test_journal = "Test journal"
self.test_ref_id = "Test_id"
self.reference = Reference(id=self.test_ref_id,
pmid=self.test_pmid,
pmc=self.test_pmc,
doi=self.test_doi,
url=self.test_url,
year=self.test_year,
title=self.test_title,
journal=self.test_journal,
authors=self.authors)
self.model = Model("Test")
self.model.references[self.reference.id] = self.reference
def test_author_string4(self):
""" Test correct string for 3 authors """
self.empty_reference.authors = [
Author("Family1", "", "Initials1"),
Author("Family2", "", "Initials2"),
Author("Family3", "", "Initials3")
]
self.empty_reference.year = "2015"
expected = "Family1 Initials1 et al., 2015"
assert self.empty_reference.reference_string() == expected
def test_author_string3(self):
""" Test correct string for two authors """
self.empty_reference.authors = [
Author("FamilyFirst", "", "InitialsFirst"),
Author("FamilySecond", "", "InitialsSecond")
]
self.empty_reference.year = "2015"
expected = "FamilyFirst InitialsFirst and FamilySecond InitialsSecond, 2015"
assert self.empty_reference.reference_string() == expected
def parse_author_node(node):
""" Parse author node of pubmed xml response
Parameters
----------
node : XML node or None
Returns
-------
result: list or None
"""
if node is None:
return
result = []
for element in node.getchildren():
lastname, forename, initials = "", "", ""
lastname_node = element.find("LastName")
if lastname_node is not None:
lastname = lastname_node.text
forename_node = element.find("ForeName")
if forename_node is not None:
forename = forename_node.text
initials_node = element.find("Initials")
if initials_node is not None:
initials = initials_node.text
result.append(Author(lastname, forename, initials))
return result
def parse_references(model_node, model=None, progress=None):
reference_list_node = model_node.find(ge_listOfReferences)
if reference_list_node is None:
return
elif progress is None:
pass
elif not progress.wasCanceled():
progress.setLabelText("Reading references...")
progress.setRange(0, len(reference_list_node))
elif progress.wasCanceled():
return
references = []
for i, reference_node in enumerate(
reference_list_node.iterfind(ge_reference)):
if progress is None:
pass
elif not progress.wasCanceled():
progress.setValue(i)
QApplication.processEvents()
else:
return
new_reference = Reference(id=reference_node.get("id"),
year=reference_node.get("year"),
title=reference_node.get("title"),
journal=reference_node.get("journal"),
url=reference_node.get("url"))
author_list_node = reference_node.find(ge_listOfAuthors)
if author_list_node is not None:
authors = []
for child in author_list_node.iterfind(ge_author):
authors.append(
Author(firstname=child.get("firstname"),
lastname=child.get("lastname"),
initials=child.get("initials")))
new_reference.authors = authors
annotation = annotate_element_from_xml(reference_node)
if annotation:
for x in annotation:
if x.collection == "pubmed":
new_reference.pmid = x.identifier
elif x.collection == "pmc":
new_reference.pmc = x.identifier
elif x.collection == "doi":
new_reference.doi = x.identifier
if model is None:
references.append(new_reference)
else:
model.add_reference(new_reference)
return references
def setup_items(self):
self.table = AuthorTable()
self.firstname = "test firstname"
self.lastname = "test lastname"
self.initials = "test initials"
self.author = Author(lastname=self.lastname,
firstname=self.firstname,
initials=self.initials)
def author(self):
return Author(self.lastnameLineEdit.text(),
self.firstnameLineEdit.text(),
self.initialsLineEdit.text())
def test_author_str(self):
""" Check author_str property returns the proper value"""
assert Author(lastname="Last", initials="P",
firstname="").display_str == "Last P"
assert Author("Last", "", "").display_str == "Last"
def test_setup(self):
author = Author("lastname", "firstname", "initials")
assert author.lastname == "lastname"
assert author.firstname == "firstname"
assert author.initials == "initials"
assert Author() == ("", "", "")
def test_author_string2(self):
""" Test correct string for single author """
self.empty_reference.authors = [Author("Family", "First", "Initials")]
self.empty_reference.year = "2015"
assert self.empty_reference.reference_string(
) == "Family Initials, 2015"