def check_space_for_hashtable(args, hashtype, force,
_testhook_free_space=None):
"""Check we have enough size to write a hash table."""
hash_size = khmer_args._calculate_tablesize(args, hashtype)
cwd = os.getcwd()
dir_path = os.path.dirname(os.path.realpath(cwd))
target = os.statvfs(dir_path)
if _testhook_free_space is None:
free_space = target.f_frsize * target.f_bavail
else:
free_space = _testhook_free_space # allow us to test this code...
size_diff = hash_size - free_space
if size_diff > 0:
print("ERROR: Not enough free space on disk "
"for saved table files;"
" Need at least %s GB more."
% (float(size_diff) / 1e9,), file=sys.stderr)
print(" Table size: %.1f GB"
% (float(hash_size) / 1e9,), file=sys.stderr)
print(" Free space: %.1f GB"
% (float(free_space) / 1e9,), file=sys.stderr)
if not force:
sys.exit(1)
def check_space_for_hashtable(args, hashtype, force,
_testhook_free_space=None):
"""Check we have enough size to write a hash table."""
hash_size = khmer_args._calculate_tablesize(args, hashtype)
cwd = os.getcwd()
dir_path = os.path.dirname(os.path.realpath(cwd))
target = os.statvfs(dir_path)
if _testhook_free_space is None:
free_space = target.f_frsize * target.f_bavail
else:
free_space = _testhook_free_space # allow us to test this code...
size_diff = hash_size - free_space
if size_diff > 0:
print("ERROR: Not enough free space on disk "
"for saved table files;"
" Need at least %s GB more."
% (float(size_diff) / 1e9,), file=sys.stderr)
print(" Table size: %.1f GB"
% (float(hash_size) / 1e9,), file=sys.stderr)
print(" Free space: %.1f GB"
% (float(free_space) / 1e9,), file=sys.stderr)
if not force:
sys.exit(1)
def test_fail_calculate_foograph_size():
# tests unknown graph type
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem)
try:
nodegraph = khmer_args._calculate_tablesize(args, 'foograph')
assert 0, "previous statement should fail"
except AssertionError:
raise
except Exception as err:
assert "unknown graph type: foograph" in str(err), str(err)
def test_fail_calculate_foograph_size():
# tests unknown graph type
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem)
try:
nodegraph = khmer_args._calculate_tablesize(args, 'foograph')
assert 0, "previous statement should fail"
except AssertionError:
raise
except Exception as err:
assert "unknown graph type: foograph" in str(err), str(err)