def test_append_sample(self):
seeding = Seeding()
seeding.append_sample()
self.assertEqual(1, len(seeding))
s = seeding.dumps()
self.assertIsInstance(s, str)
def test_no_seeding(self):
graph = egf_graph.copy()
seeding = Seeding()
result = seeding.run(graph)
self.assertEqual(graph.number_of_nodes(), result.number_of_nodes())
self.assertEqual(graph.number_of_edges(), result.number_of_edges())
def test_random_sample(self):
graph = generate_random_graph(50, 1000)
seeding = Seeding()
seeding.append_sample(number_edges=10)
seeding.append_sample(number_edges=10)
result = seeding.run(graph)
# TODO this will fail randomly some times lol, so make allowed to be sort of wrong
self.assertIn(result.number_of_edges(), {18, 19, 20})
def add_seed_neighbors(
self, nodes: Union[BaseEntity, Iterable[BaseEntity]]) -> Query:
"""Add a seed by neighbors and return a new query."""
seeding = self.get_seeding() or Seeding()
seeding.append_neighbors(nodes)
return Query(
parent_id=self.id,
assembly=self.assembly,
seeding=seeding.dumps(),
pipeline=self.pipeline,
)
def test_seed_by_neighbor(self):
graph = BELGraph()
a, b, c, d = (Protein(namespace=n(), name=str(i)) for i in range(4))
graph.add_increases(a, b, n(), n())
graph.add_increases(b, c, n(), n())
graph.add_increases(c, d, n(), n())
seeding = Seeding()
seeding.append_neighbors(b)
result = seeding.run(graph)
self.assertIsInstance(result, BELGraph)
# test nodes
self.assertIn(a, result)
self.assertIn(b, result)
self.assertIn(c, result)
self.assertNotIn(d, result)
# test edges
self.assertIn(b, result[a])
self.assertIn(c, result[b])
self.assertNotIn(d, result[c])
def get_seeding(self) -> Optional[Seeding]:
"""Get the seeding container, if it has any entries."""
if self.seeding:
seeding_json = [({
SEED_METHOD:
entry[SEED_METHOD],
SEED_DATA: [
parse_result_to_dsl(node_dict)
for node_dict in entry[SEED_DATA]
],
} if entry[SEED_METHOD] in NODE_SEED_TYPES else entry)
for entry in json.loads(self.seeding)]
return Seeding.from_json(seeding_json)
def test_seeding(self):
query = Query(seeding=Seeding())
self.assertEqual(0, len(query.seeding))
def test_none(self):
"""Test construction of a seeding container."""
seeding = Seeding()
self.assertEqual(0, len(seeding))
self.assertEqual('[]', seeding.dumps())
def test_none(self):
seeding = Seeding()
self.assertEqual(0, len(seeding))
self.assertEqual('[]', seeding.dumps())