class TestReferenceTable:
@pytest.fixture(autouse=True)
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 test_setup(self):
assert issubclass(ReferenceTable, ElementTable)
assert self.table.rowCount() == 0
assert self.reference.pmid == self.pmid
assert self.reference.pmc == self.pmc
assert self.reference.doi == self.doi
assert self.reference.url == self.url
assert self.reference.year == self.year
assert self.reference.title == self.title
assert self.reference.journal == self.journal
assert self.reference.authors[0] is self.author1
assert self.reference.authors[1] is self.author2
def test_row_from_item(self):
return_value = self.table.row_from_item(self.reference)
assert len(return_value) == len(self.table.header)
for x in return_value:
assert isinstance(x, LinkedItem)
assert x.link is self.reference
assert return_value[0].text() == self.reference.reference_string()
assert return_value[1].text() == self.title
assert return_value[2].text() == self.journal
assert return_value[3].text() == self.year
assert return_value[4].text() == self.pmid
assert return_value[5].text() == self.pmc
assert return_value[6].text() == self.doi
assert return_value[7].text() == self.url
def test_update_row_from_item(self):
assert self.table.rowCount() == 0
self.table.update_row_from_item(self.reference)
assert self.table.rowCount() == 1
assert self.table.item(0,
0).text() == self.reference.reference_string()
assert self.table.item(0, 1).text() == self.title
assert self.table.item(0, 2).text() == self.journal
assert self.table.item(0, 3).text() == self.year
assert self.table.item(0, 4).text() == self.pmid
assert self.table.item(0, 5).text() == self.pmc
assert self.table.item(0, 6).text() == self.doi
assert self.table.item(0, 7).text() == self.url
def test_get_item_from_row(self):
self.table.update_row_from_item(self.reference)
assert self.table.item_from_row(0) is self.reference
def test_get_items(self):
self.table.update_row_from_item(self.reference)
assert self.table.get_items() == [self.reference]
class TestReference:
@pytest.fixture(autouse=True)
def init_objects(self):
self.reference1 = Reference("test_abbrev", "name")
self.reference2 = Reference("test_abbrev", "name")
self.empty_reference = Reference()
def test___init__(self):
""" Test the default values of empty reference """
assert self.empty_reference.authors == []
assert self.empty_reference.pmid == ""
assert self.empty_reference.pmc == ""
assert self.empty_reference.abstract == ""
assert self.empty_reference.doi == ""
assert self.empty_reference.title == ""
assert self.empty_reference.year == ""
assert self.empty_reference.url == ""
assert self.empty_reference.journal == ""
def test_author_string1(self):
""" Check that empty string is returned if no author is set """
assert self.empty_reference.reference_string() == ""
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"
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 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_annotation_property(self):
reference = Reference()
reference.pmc = "1234"
reference.pmid = "54321"
reference.doi = "5555"
assert Annotation("pubmed", reference.pmid) in reference.annotation
assert Annotation("pmc", reference.pmc) in reference.annotation
assert Annotation("doi", reference.doi) in reference.annotation