def test_delete_tree_XML_and_remove_source(self):
XML = etree.tostring(etree.parse('data/input/clean_data.phyml',
parser),
pretty_print=True)
names = ["Hill_2012_1", "Hill_2012_2"]
names.sort(reverse=True)
trees = obtain_trees(XML)
old_len = len(trees)
new_xml = XML
for name in names:
new_xml = _swap_tree_in_XML(new_xml, None, name, delete=True)
trees = obtain_trees(new_xml)
self.assert_(len(trees) == old_len - 2)
# check only one source remains
names = get_all_source_names(new_xml)
self.assert_(len(names) == 1)
self.assert_(names[0] == "Hill_2011")
def test_clean_data(self):
XML = etree.tostring(etree.parse('data/input/clean_data.phyml',
parser),
pretty_print=True)
XML = clean_data(XML)
trees = obtain_trees(XML)
self.assert_(len(trees) == 2)
expected_trees = {
'Hill_2011_2': '(A,B,(C,D,E));',
'Hill_2011_1': '(A, B, C, (D, E, F));'
}
for t in trees:
self.assert_(_trees_equal(trees[t], expected_trees[t]))
# check only one source remains
names = get_all_source_names(XML)
self.assert_(len(names) == 1)
self.assert_(names[0] == "Hill_2011")
def test_get_all_source_names(self):
input_data = etree.tostring(xml_full_c)
names = get_all_source_names(input_data)
expected_names = ['Hill_1996', 'Hill_etal_1996', 'Hill_Davis_1996']
self.assert_(expected_names.sort() == names.sort())
def test_all_unique_names_altered(self):
new_xml = all_sourcenames(etree.tostring(non_unique_names))
names = get_all_source_names(new_xml)
expected_names = ['Hill_1996b', 'Hill_1996a', 'Hill_etal_1996', 'Hill_Davis_1996']
self.assert_(expected_names.sort() == names.sort())
def test_full_sourcenames(self):
new_xml = all_sourcenames(etree.tostring(xml_full))
names = get_all_source_names(new_xml)
expected_names = get_all_source_names(etree.tostring(xml_full_c))
self.assertListEqual(names,expected_names)