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import time
import warnings
import numpy as np
import pytest
from hypothesis import given, settings
from hypothesis import strategies as st
from hypothesis.extra import numpy as st_np
import tiledb
from tiledb.main import metadata_test_aux
from .common import DiskTestCase, assert_captured, rand_utf8
MIN_INT = np.iinfo(np.int64).min
MAX_INT = np.iinfo(np.int64).max
st_int = st.integers(min_value=MIN_INT, max_value=MAX_INT)
st_float = st.floats(allow_nan=False)
st_metadata = st.fixed_dictionaries(
{
"int": st_int,
"double": st_float,
"bytes": st.binary(),
"str": st.text(),
"list_int": st.lists(st_int),
"tuple_int": st.lists(st_int).map(tuple),
"list_float": st.lists(st_float),
"tuple_float": st.lists(st_float).map(tuple),
}
)
st_ndarray = st_np.arrays(
dtype=st.one_of(
st_np.integer_dtypes(endianness="<"),
st_np.unsigned_integer_dtypes(endianness="<"),
st_np.floating_dtypes(endianness="<", sizes=(32, 64)),
st_np.byte_string_dtypes(max_len=1),
st_np.unicode_string_dtypes(endianness="<", max_len=1),
st_np.datetime64_dtypes(endianness="<"),
),
shape=st_np.array_shapes(min_dims=0, max_dims=3, min_side=0, max_side=10),
)
class MetadataTest(DiskTestCase):
def assert_equal_md_values(self, written_value, read_value):
if isinstance(written_value, np.ndarray):
self.assertIsInstance(read_value, np.ndarray)
self.assertEqual(read_value.dtype, written_value.dtype)
np.testing.assert_array_equal(read_value, written_value)
elif not isinstance(written_value, (list, tuple)):
self.assertEqual(read_value, written_value)
# we don't round-trip perfectly sequences
elif len(written_value) == 1:
# sequences of length 1 are read as a single scalar element
self.assertEqual(read_value, written_value[0])
else:
# sequences of length != 1 are read as tuples
self.assertEqual(read_value, tuple(written_value))
def assert_metadata_roundtrip(self, tdb_meta, dict_meta):
for k, v in dict_meta.items():
# test __contains__
self.assertTrue(k in tdb_meta)
# test __getitem__
self.assert_equal_md_values(v, tdb_meta[k])
# test get
self.assert_equal_md_values(v, tdb_meta.get(k))
# test __contains__, __getitem__, get for non-key
non_key = str(object())
self.assertFalse(non_key in tdb_meta)
with self.assertRaises(KeyError):
tdb_meta[non_key]
self.assertIsNone(tdb_meta.get(non_key))
self.assertEqual(tdb_meta.get(non_key, 42), 42)
# test __len__
self.assertEqual(len(tdb_meta), len(dict_meta))
# test __iter__() is consistent with keys()
self.assertEqual(list(tdb_meta), tdb_meta.keys())
# test keys()
self.assertSetEqual(set(tdb_meta.keys()), set(dict_meta.keys()))
# test values() and items()
read_values = tdb_meta.values()
read_items = tdb_meta.items()
self.assertEqual(len(read_values), len(read_items))
for (item_key, item_value), value in zip(read_items, read_values):
self.assertTrue(item_key in dict_meta)
self.assert_equal_md_values(dict_meta[item_key], item_value)
self.assert_equal_md_values(dict_meta[item_key], value)
def assert_not_implemented_methods(self, tdb_meta):
with self.assertRaises(NotImplementedError):
tdb_meta.setdefault("nokey", "hello!")
with self.assertRaises(NotImplementedError):
tdb_meta.pop("nokey", "hello!")
with self.assertRaises(NotImplementedError):
tdb_meta.popitem()
with self.assertRaises(NotImplementedError):
tdb_meta.clear()
def test_errors(self):
path = self.path("test_md_errors")
with tiledb.from_numpy(path, np.ones((5,), np.float64)):
pass
# can't read from a closed array
A = tiledb.open(path)
A.close()
with self.assertRaises(tiledb.TileDBError):
A.meta["x"]
with tiledb.Array(path) as A:
# can't write to a mode='r' array
with self.assertRaises(tiledb.TileDBError):
A.meta["invalid_write"] = 1
# missing key raises KeyError
with self.assertRaises(KeyError):
A.meta["xyz123nokey"]
self.assert_not_implemented_methods(A.meta)
# test invalid input
with tiledb.Array(path, "w") as A:
# keys must be strings
with self.assertRaises(TypeError):
A.meta[123] = 1
# can't write an int > typemax(Int64)
with self.assertRaises(OverflowError):
A.meta["bigint"] = MAX_INT + 1
# can't write mixed-type list
with self.assertRaises(TypeError):
A.meta["mixed_list"] = [1, 2.1]
# can't write mixed-type tuple
with self.assertRaises(TypeError):
A.meta["mixed_list"] = (0, 3.1)
# can't write objects
with self.assertRaises(TypeError):
A.meta["object"] = object()
self.assert_not_implemented_methods(A.meta)
@given(st_metadata)
@settings(deadline=None)
def test_basic(self, test_vals):
path = self.path()
with tiledb.from_numpy(path, np.ones((5,), np.float64)):
pass
with tiledb.Array(path, mode="w") as A:
A.meta.update(test_vals)
with tiledb.Array(path) as A:
self.assert_metadata_roundtrip(A.meta, test_vals)
# test a 1 MB blob
blob = np.random.rand(int((1024**2) / 8)).tobytes()
with tiledb.Array(path, "w") as A:
test_vals["bigblob"] = blob
A.meta["bigblob"] = blob
with tiledb.Array(path) as A:
self.assert_metadata_roundtrip(A.meta, test_vals)
# test del key
with tiledb.Array(path, "w") as A:
del test_vals["bigblob"]
del A.meta["bigblob"]
with tiledb.Array(path) as A:
self.assert_metadata_roundtrip(A.meta, test_vals)
# test update
with tiledb.Array(path, mode="w") as A:
test_vals.update(foo="bar", double=3.14)
A.meta.update(foo="bar", double=3.14)
with tiledb.Array(path) as A:
self.assert_metadata_roundtrip(A.meta, test_vals)
@given(st_metadata, st_ndarray)
@settings(deadline=None)
@pytest.mark.parametrize("use_timestamps", [True, False])
def test_numpy(self, use_timestamps, test_vals, ndarray):
test_vals["ndarray"] = ndarray
path = self.path()
with tiledb.from_numpy(path, np.ones((5,), np.float64)):
pass
with tiledb.Array(path, mode="w") as A:
A.meta.update(test_vals)
with tiledb.Array(path) as A:
self.assert_metadata_roundtrip(A.meta, test_vals)
if use_timestamps:
# test resetting a key with a ndarray value to a non-ndarray value
time.sleep(0.001)
with tiledb.Array(path, "w") as A:
A.meta["ndarray"] = 42
test_vals["ndarray"] = 42
with tiledb.Array(path) as A:
self.assert_metadata_roundtrip(A.meta, test_vals)
# test resetting a key with a non-ndarray value to a ndarray value
with tiledb.Array(path, "w") as A:
A.meta["bytes"] = ndarray
test_vals["bytes"] = ndarray
with tiledb.Array(path) as A:
self.assert_metadata_roundtrip(A.meta, test_vals)
if use_timestamps:
# test del ndarray key
time.sleep(0.001)
with tiledb.Array(path, "w") as A:
del A.meta["ndarray"]
del test_vals["ndarray"]
with tiledb.Array(path) as A:
self.assert_metadata_roundtrip(A.meta, test_vals)
if use_timestamps:
# test update
time.sleep(0.001)
with tiledb.Array(path, mode="w") as A:
test_vals.update(ndarray=np.stack([ndarray, ndarray]), transp=ndarray.T)
A.meta.update(ndarray=np.stack([ndarray, ndarray]), transp=ndarray.T)
with tiledb.Array(path) as A:
self.assert_metadata_roundtrip(A.meta, test_vals)
@pytest.mark.filterwarnings("ignore::UserWarning")
@tiledb.scope_ctx(
{"sm.vacuum.mode": "array_meta", "sm.consolidation.mode": "array_meta"}
)
@pytest.mark.parametrize("use_timestamps", [True, False])
def test_consecutive(self, use_timestamps):
vfs = tiledb.VFS()
path = self.path("test_md_consecutive")
write_count = 100
with tiledb.from_numpy(path, np.ones((5,), np.float64)):
pass
randints = np.random.randint(0, MAX_INT - 1, size=write_count, dtype=np.int64)
randutf8s = [rand_utf8(i) for i in np.random.randint(1, 30, size=write_count)]
# write 100 times, then consolidate
if use_timestamps:
for i in range(write_count):
with tiledb.Array(path, mode="w") as A:
A.meta["randint"] = int(randints[i])
A.meta["randutf8"] = randutf8s[i]
time.sleep(0.001)
else:
for i in range(write_count):
with tiledb.Array(path, mode="w") as A:
A.meta["randint"] = int(randints[i])
A.meta["randutf8"] = randutf8s[i]
self.assertEqual(len(vfs.ls(os.path.join(path, "__meta"))), 100)
with tiledb.Array(path) as A:
self.assertEqual(A.meta["randint"], randints[-1])
self.assertEqual(A.meta["randutf8"], randutf8s[-1])
with tiledb.Array(path, mode="w") as aw:
aw.meta.consolidate()
try:
self.assertEqual(len(vfs.ls(os.path.join(path, "__meta"))), 102)
except AssertionError:
# this test is broken under libtiledb 2.3, see ch 7449
if tiledb.libtiledb.version() >= (2, 3):
warnings.warn(
"Suppressed assertion error with libtiledb 2.3! see ch 7449"
)
else:
raise
with tiledb.Array(path) as A:
self.assertEqual(A.meta["randint"], randints[-1])
self.assertEqual(A.meta["randutf8"], randutf8s[-1])
# use randutf8s as keys, then consolidate
if use_timestamps:
for _ in range(2):
for i in range(write_count):
with tiledb.Array(path, mode="w") as A:
A.meta[randutf8s[i] + "{}".format(randints[i])] = int(
randints[i]
)
A.meta[randutf8s[i]] = randutf8s[i]
time.sleep(0.001)
else:
for _ in range(2):
for i in range(write_count):
with tiledb.Array(path, mode="w") as A:
A.meta[randutf8s[i] + "{}".format(randints[i])] = int(
randints[i]
)
A.meta[randutf8s[i]] = randutf8s[i]
# test data
with tiledb.Array(path) as A:
for i in range(write_count):
key_int = randutf8s[i] + "{}".format(randints[i])
self.assertEqual(A.meta[key_int], randints[i])
self.assertEqual(A.meta[randutf8s[i]], randutf8s[i])
# test expected number of fragments before consolidating
try:
self.assertEqual(len(vfs.ls(os.path.join(path, "__meta"))), 302)
except AssertionError:
# this test is broken under libtiledb 2.3, see ch 7449
if tiledb.libtiledb.version() >= (2, 3):
warnings.warn(
"Suppressed assertion error with libtiledb 2.3! see ch 7449"
)
else:
raise
with tiledb.Array(path, mode="w") as A:
A.meta.consolidate()
# test expected number of fragments before vacuuming
try:
self.assertEqual(len(vfs.ls(os.path.join(path, "__meta"))), 304)
except AssertionError:
# this test is broken under libtiledb 2.3, see ch 7449
if tiledb.libtiledb.version() >= (2, 3):
warnings.warn(
"Suppressed assertion error with libtiledb 2.3! see ch 7449"
)
else:
raise
tiledb.vacuum(path)
# should only have one fragment+'.ok' after vacuuming
try:
self.assertEqual(len(vfs.ls(os.path.join(path, "__meta"))), 1)
except AssertionError:
# this test is broken under libtiledb 2.3, see ch 7449
if tiledb.libtiledb.version() >= (2, 3):
warnings.warn(
"Suppressed assertion error with libtiledb 2.3! see ch 7449"
)
else:
raise
# test data again after consolidation
with tiledb.Array(path) as A:
for i in range(write_count):
key_int = randutf8s[i] + "{}".format(randints[i])
self.assertEqual(A.meta[key_int], randints[i])
self.assertEqual(A.meta[randutf8s[i]], randutf8s[i])
def test_ascii_metadata(self, capfd):
uri = self.path("test_ascii_metadata")
dom = tiledb.Domain(tiledb.Dim(domain=(0, 2), tile=1, dtype=np.int64))
att = tiledb.Attr(dtype=np.int64)
schema = tiledb.ArraySchema(sparse=True, domain=dom, attrs=(att,))
tiledb.Array.create(uri, schema)
metadata_test_aux.write_ascii(uri)
with tiledb.open(uri) as A:
assert A.meta["abc"] == b"xyz"
A.meta.dump()
assert_captured(capfd, "Type: STRING_ASCII")
def test_bytes_metadata(self, capfd):
path = self.path()
with tiledb.from_numpy(path, np.ones((5,), np.float64)):
pass
with tiledb.Array(path, mode="w") as A:
A.meta["bytes"] = b"blob"
with tiledb.Array(path, mode="r") as A:
assert A.meta["bytes"] == b"blob"
A.meta.dump()
assert_captured(capfd, "Type: BLOB")
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