def test_111(self):
statement = '''SET Evidence = "1.1.1 Easy case"'''
expect = '''SET Evidence = "1.1.1 Easy case'''
lines = list(sanitize_file_lines(statement.split('\n')))
self.assertEqual(1, len(lines))
line = lines[0]
self.assertTrue(expect, line)
def test_e(self):
path = os.path.join(dir_path, 'bel', 'test_bel.bel')
with open(path) as f:
lines = list(sanitize_file_lines(f))
self.assertEqual(26, len(lines))
def test_c(self):
s = ['SET Evidence = "yada yada yada" //this is a comment']
result = list(sanitize_file_lines(s))
expect = [(1, 'SET Evidence = "yada yada yada"')]
self.assertEqual(expect, result)
def test_d(self):
"""Test forgotten delimiters"""
s = ['SET Evidence = "Something', 'or other', 'or other"']
result = list(sanitize_file_lines(s))
expect = [(1, 'SET Evidence = "Something or other or other"')]
self.assertEqual(expect, result)
def test_141(self):
statement = '''SET Evidence = "4.1 Malformed line breakcase
second line"'''
expect = '''SET Evidence = "4.1 Malformed line breakcase second line"'''
lines = [
line for i, line in sanitize_file_lines(statement.split('\n'))
]
self.assertEqual(1, len(lines))
line = lines[0]
self.assertEqual(expect, line)
def test_132(self):
statement = '''SET Evidence = "3.2 Backward slash break test with whitespace \\
second line"'''
expect = '''SET Evidence = "3.2 Backward slash break test with whitespace second line"'''
lines = [
line for i, line in sanitize_file_lines(statement.split('\n'))
]
self.assertEqual(1, len(lines))
line = lines[0]
self.assertEqual(expect, line)
def test_a(self):
s = '''SET Evidence = "The phosphorylation of S6K at Thr389, which is the TORC1-mediated site, was not inhibited
in the SIN1-/- cells (Figure 5A)."'''.split('\n')
expect = [(
1,
'SET Evidence = "The phosphorylation of S6K at Thr389, which is the TORC1-mediated site, was not inhibited '
'in the SIN1-/- cells (Figure 5A)."')]
result = list(sanitize_file_lines(s))
self.assertEqual(expect, result)
def test_b(self):
s = [
'# Set document-defined annotation values\n', 'SET Species = 9606',
'SET Tissue = "t-cells"',
'# Create an Evidence Line for a block of BEL Statements',
'SET Evidence = "Here we show that interfereon-alpha (IFNalpha) is a potent producer \\',
'of SOCS expression in human T cells, as high expression of CIS, SOCS-1, SOCS-2, \\',
'and SOCS-3 was detectable after IFNalpha stimulation. After 4 h of stimulation \\',
'CIS, SOCS-1, and SOCS-3 had ret'
]
result = list(sanitize_file_lines(s))
expect = [
(2, 'SET Species = 9606'), (3, 'SET Tissue = "t-cells"'),
(5,
'SET Evidence = "Here we show that interfereon-alpha (IFNalpha) is a potent producer of SOCS expression in '
'human T cells, as high expression of CIS, SOCS-1, SOCS-2, and SOCS-3 was detectable after IFNalpha '
'stimulation. After 4 h of stimulation CIS, SOCS-1, and SOCS-3 had ret'
)
]
self.assertEqual(expect, result)
def test_f(self):
s = '''SET Evidence = "Arterial cells are highly susceptible to oxidative stress, which can induce both necrosis
and apoptosis (programmed cell death) [1,2]"'''.split('\n')
lines = list(sanitize_file_lines(s))
self.assertEqual(1, len(lines))
def test_e(self):
with open(test_bel_simple) as f:
lines = list(sanitize_file_lines(f))
self.assertEqual(26, len(lines))
