def test_aux_top(self):
"""elements can have name of top-level term"""
plain = build_obo_dataset_dict(int_file, root_id="int:0")
self.assertFalse("negative" in str(plain["int:6"]["data_pos"]))
result = build_obo_dataset_dict(int_file, root_id="int:0", aux="top")
self.assertTrue("negative" in str(result["int:6"]["data_pos"]))
def test_build_subset(self):
"""create a dataset using a branch of the ontology"""
num_ids = len(self.obo.ids())
result = build_obo_dataset_dict(int_file, "int:2")
self.assertLess(len(result), num_ids)
self.assertTrue("int:2" in result)
def test_aux_parents_only(self):
"""elements can have positive auxiliary data fields from parents"""
result = build_obo_dataset_dict(int_file, aux="parents")
self.assertTrue("integer" in str(result["int:1"]["data_pos"]))
self.assertFalse("comment" in str(result["int:1"]["data_pos"]))
r4 = result["int:4"]
self.assertTrue("zero" in str(r4["data_pos"]))
def test_aux_both_intermediate(self):
"""elements can have both positive and negative aux fields"""
result = build_obo_dataset_dict(int_file,
aux="parents,children,siblings")
# int:4 is a node with both parent and siblings
r4 = result["int:4"]
self.assertTrue("prime" in str(r4["data_neg"]))
self.assertTrue("greater" in str(r4["data_pos"]))
def test_aux_both_nosib(self):
"""elements can have both positive and negative aux fields"""
result = build_obo_dataset_dict(int_file,
aux="parents,children,siblings")
# check that some negative data are provided in the result
r4 = result["int:4"]
self.assertTrue("prime" in str(r4["data_neg"]))
# although negative aux are allowed, r6 node does not have any siblings
r6 = result["int:6"]
self.assertTrue("less" in str(r6["data_pos"]))
def test_aux_children(self):
"""elements can have negative auxiliary data fields from children"""
result = build_obo_dataset_dict(int_file, aux="children")
r2 = result["int:2"]
self.assertTrue("prime" in str(r2["data_neg"]))
def test_aux_siblings(self):
"""elements can have negative auxiliary data fields from siblings"""
result = build_obo_dataset_dict(int_file, aux="siblings")
r4 = result["int:4"]
self.assertTrue("prime" in str(r4["data_neg"]))
def test_aux_parents_comments(self):
"""elements can have auxiliary fields from comments of parents"""
result = build_obo_dataset_dict(int_file, aux="parents,comments")
self.assertTrue("integer" in str(result["int:1"]["data_pos"]))
self.assertTrue("comment" in str(result["int:1"]["data_pos"]))
def test_aux_comment_only(self):
"""elements can have auxiliary data fields from comments"""
result = build_obo_dataset_dict(int_file, aux="comments")
self.assertTrue("comment" in str(result["int:0"]["data_pos"]))
def test_aux_ancestors(self):
"""elements can have all ancestors listed"""
result = build_obo_dataset_dict(int_file, aux="ancestors")
self.assertTrue("integer" in str(result["int:5"]["data_pos"]))
self.assertTrue("root" in str(result["int:5"]["data_pos"]))
def test_aux_synonyms(self):
"""elements can include synonyms"""
result = build_obo_dataset_dict(int_file, aux="parents,synonyms")
self.assertTrue("unity" in str(result["int:6"]["data_pos"]))
self.assertFalse("EXACT" in str(result["int:6"]))