def test_batch_size(self):
expected = 10000
rv = get_query_batch_size('blastp')
self.assertEqual(rv, expected)
rv = get_query_batch_size('BLASTP')
self.assertEqual(rv, expected)
def test_batch_size_invalid_input(self):
expected = -1
rv = get_query_batch_size('junk')
self.assertEqual(rv, expected)
rv = get_query_batch_size(12334)
self.assertEqual(rv, expected)
def test_get_batch_length():
"""Test computing batch length"""
PROGRAM = 'blastp'
NUM_CPUS = 16
assert get_batch_length(program='blastp',
mt_mode=MTMode.ZERO,
num_cpus=NUM_CPUS) == get_query_batch_size(PROGRAM)
assert get_batch_length(
program='blastp', mt_mode=MTMode.ONE,
num_cpus=NUM_CPUS) == get_query_batch_size(PROGRAM) * NUM_CPUS
def test_blastconfig():
"""Test BlastConfig defaults"""
PROGRAM = 'blastn'
DB = 'test-db'
QUERIES = 'test-queries'
cloud_provider = GCPConfig(project='test-project',
region='test-region',
zone='test-zone')
machine_type = 'n1-standard-32'
cfg = BlastConfig(program=PROGRAM,
db=DB,
queries_arg=QUERIES,
cloud_provider=cloud_provider,
machine_type=machine_type)
assert cfg.program == PROGRAM
assert cfg.db == DB
assert cfg.queries_arg == QUERIES
assert cfg.db_source.name == cloud_provider.cloud.name
assert cfg.batch_len == get_query_batch_size(cfg.program)
assert not cfg.queries
assert cfg.options == f'-outfmt {ELB_DFLT_OUTFMT}'
assert cfg.mem_request
assert cfg.mem_limit
assert not cfg.taxidlist
assert cfg.db_mem_margin == ELB_BLASTDB_MEMORY_MARGIN
def test_batch_size_env_var(self):
expected = 10
original = os.getenv('ELB_BATCH_LEN')
try:
os.environ['ELB_BATCH_LEN'] = str(expected)
rv = get_query_batch_size('blastn')
self.assertEqual(rv, expected)
finally:
del os.environ['ELB_BATCH_LEN']
if original is not None:
os.environ['ELB_BATCH_LEN'] = original