def test_new_term(self):
"""New terms are blank."""
term = OboTerm()
self.assertEqual(term.id, None, "id is None by default")
self.assertEqual(term.name, None, "name is None by default")
self.assertFalse(term.valid(), "not valid when empty")
def test_parse_alt_id(self):
"""alternative id are recorded in a set"""
term = OboTerm()
term.parse("id: ABC:002")
term.parse("name: abc")
self.assertEqual(len(term.alts), 0)
term.parse("alt_id: ABC:2")
term.parse("alt_id: ABC:02")
self.assertEqual(len(term.alts), 2)
self.assertTrue("ABC:2" in term.alts)
def test_parse_obsolete(self):
"""identifies obsolete."""
term = OboTerm()
term.parse("id: ABC:002")
term.parse("name: abc")
term.parse("is_obsolete: true")
self.assertTrue(term.valid(), "valid because non-empty")
self.assertTrue(term.obsolete, "is obsolete")
def test_parse_obsolete_strict(self):
"""is strict about values in is_obsolete line"""
term = OboTerm()
term.parse("id: ABC:002")
term.parse("name: abc")
with self.assertRaises(Exception) as e1:
term.parse("is_obsolete: True")
self.assertTrue("obsolete" in str(e1.exception))
with self.assertRaises(Exception) as e2:
term.parse("is_obsolete: false")
self.assertTrue("obsolete" in str(e1.exception))
def test_parse_obsolete_replaced(self):
"""obsolete terms can record an alternative id"""
term = OboTerm()
term.parse("id: ABC:002")
term.parse("name: abc")
self.assertEqual(len(term.relations), 0, "no relations at start")
term.parse("is_obsolete: true")
self.assertTrue(term.obsolete, "is obsolete")
self.assertEqual(len(term.relations), 0, "still not replaced")
term.parse("replaced_by: ABC:003")
relations = term.relations
self.assertEqual(len(term.relations), 1, "now has one relation")
self.assertEqual(relations[0], ("replaced_by", "ABC:003"))
def test_parse_emptylines(self):
"""can skip over parsing empty lines."""
term = OboTerm()
term.parse("id: ABC:002")
term.parse("")
term.parse("name: child_A")
self.assertTrue("child_A" in str(term))
def test_parse_synonyms_avoid_self_pointers(self):
"""a synonym cannot be the same as the name"""
term = OboTerm()
term.parse("id: ABC:002")
term.parse("name: abc")
term.parse("synonym: abc")
self.assertEqual(term.synonyms, set())
def test_parse_synonyms(self):
"""Parsing a synonym."""
term = OboTerm()
term.parse("id: ABC:002")
term.parse("name: child A")
term.parse("synonym: child a")
self.assertEqual(term.synonyms, set(["child a"]))
def test_parse_extrafield(self):
"""Parsing an arbitrary field."""
term = OboTerm()
term.parse("id: ABC:002")
term.parse("name: child A")
self.assertEqual(term.data, None, "data should have nothing")
term.parse("somefield: somevalue")
self.assertEqual(len(term.data), 1, "data should have one field")
def test_parse_replaced_nonobsolete(self):
"""replaced_by relation cannot be used on non-obsolete terms"""
term = OboTerm()
term.parse("id: ABC:002")
term.parse("name: abc")
with self.assertRaises(Exception) as e1:
term.parse("replaced_by: ABC:003")
self.assertTrue("obsolete" in str(e1.exception))
def test_parse_idterm(self):
"""Parsing id and name."""
term = OboTerm()
term.parse("id: ABC:001")
term.parse("name: root node")
self.assertEqual(term.id, "ABC:001", "id is set")
self.assertEqual(term.name, "root node", "name is set")
self.assertTrue(term.valid(), "valid because non-empty")
self.assertFalse(term.obsolete, "not obsolete is default")
def test_parse_synonyms_requires_name(self):
"""a synonym cannot be assigned before a name"""
term = OboTerm()
term.parse("id: ABC:002")
with self.assertRaises(Exception) as e:
term.parse("synonym: abc")
self.assertTrue("name" in str(e.exception))
def test_str(self):
"""str summarizes content of object"""
term = OboTerm()
term.parse("id: ABC:002")
term.parse("name: child_A")
result = str(term)
self.assertTrue("child_A" in result)
self.assertTrue("ABC" in result)