def test_get_omim(self):
d1 = Omim(diseaseid=1, name='Gaucher')
d2 = Omim(diseaseid=2, name='Fabry')
self.assertEqual(Omim.get(1), d1)
self.assertEqual(Omim.get(2), d2)
self.assertEqual(Omim.get('1'), d1)
self.assertRaises(ValueError, lambda: Omim.get('Fabry'))
self.assertRaises(KeyError, lambda: Omim.get(12))
def test_indexing(self):
def subindex_length(x):
return (
len(x.keys()),
len(x._indicies.keys()),
)
self.assertEqual(subindex_length(Omim), (0, 0))
_ = Omim(diseaseid=1, name='Gaucher')
self.assertEqual(subindex_length(Omim), (1, 1))
_ = Omim(diseaseid=2, name='Fabry')
self.assertEqual(subindex_length(Omim), (2, 2))
Omim.clear()
self.assertEqual(subindex_length(Omim), (0, 0))
def compare_set(diseases):
gaucher = Omim([None, 230800, None])
set1 = BasicHPOSet.from_queries(gaucher.hpo)
for x in diseases:
set2 = BasicHPOSet.from_queries(x.hpo)
_ = set1.similarity(set2)
return None
def test_singleton_handling(self):
d1a = Omim(diseaseid=1, name='Gaucher')
# ID present, will be used
d1b = Omim(diseaseid=1, name='Fabry')
# No name present, ID will be used as well
d1c = Omim(diseaseid=1, name=None)
# New ID, new Name => New Disease
d2a = Omim(diseaseid=2, name='Fabry')
# ID present, Matching by ID
d2b = Omim(diseaseid=2, name='Gaucher')
# ID present, Matching by ID
d2c = Omim(diseaseid=2, name=None)
# New ID but existing name => New disease
d3a = Omim(diseaseid=3, name='Gaucher')
self.assertIs(d1a, d1b)
self.assertIs(d1a, d1c)
self.assertIsNot(d1a, d2a)
self.assertIs(d2a, d2b)
self.assertIs(d2a, d2c)
self.assertIsNot(d1a, d3a)
self.assertIsNot(d2a, d3a)
def test_json(self):
g = Omim(diseaseid=1, name='Foo')
self.assertEqual(g.toJSON(), {'id': 1, 'name': 'Foo'})
self.assertEqual(g.toJSON(verbose=True), {
'id': 1,
'name': 'Foo',
'hpo': set()
})
def make_omim(n) -> List[pyhpo.annotations.DiseaseSingleton]:
Omim.clear()
return [Omim(diseaseid=i, name='Omim{}'.format(i)) for i in range(n)]
def test_string_representation(self):
d = Omim(diseaseid=1, name='Foo')
self.assertEqual(str(d), 'Foo')
def test_equality(self):
g = Omim(diseaseid=1, name='Foo')
self.assertEqual(g, 1)
self.assertEqual(g, 'Foo')
def test_omim_disease_building(self):
a = Omim(diseaseid=1, name='Gaucher type I')
self.assertEqual(a.name, 'Gaucher type I')
self.assertEqual(a.id, 1)
self.assertEqual(a.hpo, set())