class ItolTest(unittest.TestCase):
def setUp(self):
self.itol = Itol()
def test_initializes(self):
self.assertEqual(type(self.itol.params), dict)
self.assertEqual(self.itol.files, [])
self.assertIsNotNone(self.itol.comm)
def test_add_file(self):
with tempfile.NamedTemporaryFile() as temp:
self.itol.add_file(temp.name)
with self.assertRaises(IOError):
self.itol.add_file(' ')
def test_good_upload(self):
with patch('itolapi.Comm.upload_tree') as mock_upload:
mock_upload.return_value = True
self.itol.comm.tree_id = 1234
self.assertEqual(self.itol.upload(), 1234)
def test_bad_upload(self):
with patch('itolapi.Comm.upload_tree') as mock_upload:
mock_upload.return_value = False
self.itol.comm.tree_id = 1234
self.assertEqual(self.itol.upload(), 0)
def test_get_webpage(self):
self.itol.comm.tree_id = 'asdf'
webpage = self.itol.get_webpage()
self.assertIn('itol.embl.de', webpage)
self.assertIn('asdf', webpage)
def test_get_itol_export(self):
self.itol.comm.tree_id = 1234
export = self.itol.get_itol_export()
self.assertEqual(export.params['tree'], 1234)
@patch('itolapi.itol.pprint.pprint')
def test_print_variables(self, mock_print):
self.itol.params['treeName'] = 'test'
with tempfile.NamedTemporaryFile() as temp:
self.itol.add_file(temp.name)
self.itol.print_variables()
self.assertEqual(mock_print.call_args_list[0][0][0], self.itol.files)
self.assertEqual(mock_print.call_args_list[1][0][0], self.itol.params)
class ItolTest(unittest.TestCase):
def setUp(self):
self.itol = Itol()
def test_initializes(self):
self.assertEqual(type(self.itol.params), dict)
self.assertEqual(self.itol.files, [])
self.assertIsNotNone(self.itol.comm)
def test_add_file(self):
with tempfile.NamedTemporaryFile() as temp:
self.itol.add_file(temp.name)
with self.assertRaises(IOError):
self.itol.add_file(' ')
def test_good_upload(self):
with patch('itolapi.Comm.upload_tree') as mock_upload:
mock_upload.return_value = True
self.itol.comm.tree_id = 1234
self.assertEqual(self.itol.upload(), 1234)
def test_bad_upload(self):
with patch('itolapi.Comm.upload_tree') as mock_upload:
mock_upload.return_value = False
self.itol.comm.tree_id = 1234
self.assertEqual(self.itol.upload(), 0)
def test_get_webpage(self):
self.itol.comm.tree_id = 'asdf'
webpage = self.itol.get_webpage()
self.assertIn('itol.embl.de', webpage)
self.assertIn('asdf', webpage)
def test_get_itol_export(self):
self.itol.comm.tree_id = 1234
export = self.itol.get_itol_export()
self.assertEqual(export.params['tree'], 1234)
@patch('itolapi.itol.pprint.pprint')
def test_print_variables(self, mock_print):
self.itol.params['treeName'] = 'test'
with tempfile.NamedTemporaryFile() as temp:
self.itol.add_file(temp.name)
self.itol.print_variables()
self.assertEqual(mock_print.call_args_list[0][0][0], self.itol.files)
self.assertEqual(mock_print.call_args_list[1][0][0], self.itol.params)
print('')
print('Creating the upload params')
# Create the Itol class
test = Itol()
# Set the tree file
tree = os.path.join(current_dir, 'tree_of_life.tree.txt')
test.add_file(tree)
test.add_file(os.path.join(current_dir, 'colors_tol.txt'))
test.add_file(os.path.join(current_dir, 'labels.txt'))
test.add_file(os.path.join(current_dir, 'ranges.txt'))
# Add parameters
test.params['treeName'] = 'Tree of Life Example'
# Check parameters
test.print_variables()
# Submit the tree
print('')
print((
'Uploading the tree. This may take some time depending on how large the '
'tree is and how much load there is on the itol server'
))
good_upload = test.upload()
if not good_upload:
print('There was an error:' + test.comm.upload_output)
sys.exit(1)
# Read the tree ID
print('Tree ID: ' + str(test.comm.tree_id))
# Read the iTOL API return statement
print('')
print('Creating the upload params')
# Create the Itol class
test = Itol()
# Set the tree file
tree = os.path.join(current_dir, args.tree)
test.add_file(tree)
test.add_file(os.path.join(current_dir, args.colour))
#test.add_file(os.path.join(current_dir, 'labels.txt'))
#test.add_file(os.path.join(current_dir, 'ranges.txt'))
# Add parameters
test.params['treeName'] = 'Tree File'
# Check parameters
test.print_variables()
# Submit the tree
print('')
print(
('Uploading the tree. This may take some time depending on how large the '
'tree is and how much load there is on the itol server'))
good_upload = test.upload()
if not good_upload:
print('There was an error:' + test.comm.upload_output)
sys.exit(1)
# Read the tree ID
print('Tree ID: ' + str(test.comm.tree_id))
# Read the iTOL API return statement
print('iTOL output: ' + str(test.comm.upload_output))
root_path = os.path.join(current_dir, '..')
sys.path.append(root_path)
boom = Itol()
# Set the tree file
tree = os.path.join(current_dir, 'MERS_CoV.tree.txt')
boom.add_file(tree)
# Add parameters
boom.params['treeName'] = 'MERS_CoV'
boom.params['display_mode'] = '2'
boom.params['ignore_branch_length'] = '1'
boom.params['current_font_size'] = '28'
# Check parameters
boom.print_variables()
# Submit the tree
print('')
print(
('Uploading the tree. This may take some time depending on how large the '
'tree is and how much load there is on the itol server'))
good_upload = boom.upload()
if not good_upload:
print('There was an error:' + boom.comm.upload_output)
sys.exit(1)
# Read the tree ID
print('Tree ID: ' + str(boom.comm.tree_id))
# Read the iTOL API return statement