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import sys
import xml.etree.ElementTree
import numpy as np
import pytest
from numpy.testing import assert_array_equal
import tiledb
from tiledb.main import PyFragmentInfo
from .common import DiskTestCase
class FragmentInfoTest(DiskTestCase):
def setUp(self):
super().setUp()
if not tiledb.libtiledb.version() >= (2, 2):
pytest.skip("Only run FragmentInfo test with TileDB>=2.2")
def test_uri_dne(self):
with self.assertRaises(tiledb.TileDBError):
tiledb.array_fragments("does_not_exist")
@pytest.mark.parametrize("use_timestamps", [True, False])
def test_array_fragments(self, use_timestamps):
fragments = 3
A = np.zeros(fragments)
uri = self.path("test_dense_fragments")
dom = tiledb.Domain(tiledb.Dim(domain=(0, 2), tile=fragments, dtype=np.int64))
att = tiledb.Attr(dtype=A.dtype)
schema = tiledb.ArraySchema(domain=dom, attrs=(att,))
tiledb.DenseArray.create(uri, schema)
if use_timestamps:
for fragment_idx in range(fragments):
timestamp = fragment_idx + 1
with tiledb.DenseArray(uri, mode="w", timestamp=timestamp) as T:
T[fragment_idx : fragment_idx + 1] = fragment_idx
else:
for fragment_idx in range(fragments):
with tiledb.DenseArray(uri, mode="w") as T:
T[fragment_idx : fragment_idx + 1] = fragment_idx
fi = tiledb.array_fragments(uri)
assert len(fi) == 3
assert fi.unconsolidated_metadata_num == 3
assert fi.cell_num == (3, 3, 3)
assert fi.has_consolidated_metadata == (False, False, False)
assert fi.nonempty_domain == (((0, 0),), ((1, 1),), ((2, 2),))
assert fi.sparse == (False, False, False)
if use_timestamps: # timestamps cannot be predicted if not used on write
assert fi.timestamp_range == ((1, 1), (2, 2), (3, 3))
assert fi.to_vacuum == ()
assert hasattr(fi, "version") # don't pin to a specific version
for idx, frag in enumerate(fi):
assert frag.cell_num == 3
assert frag.has_consolidated_metadata is False
assert frag.nonempty_domain == ((idx, idx),)
assert frag.sparse is False
if use_timestamps: # timestamps cannot be predicted if not used on write
assert frag.timestamp_range == (idx + 1, idx + 1)
assert hasattr(frag, "version") # don't pin to a specific version
try:
assert xml.etree.ElementTree.fromstring(frag._repr_html_()) is not None
except:
pytest.fail(
f"Could not parse frag._repr_html_(). Saw {frag._repr_html_()}"
)
try:
assert xml.etree.ElementTree.fromstring(fi._repr_html_()) is not None
except:
pytest.fail(f"Could not parse fi._repr_html_(). Saw {fi._repr_html_()}")
@pytest.mark.parametrize("use_timestamps", [True, False])
def test_array_fragments_var(self, use_timestamps):
fragments = 3
uri = self.path("test_array_fragments_var")
dom = tiledb.Domain(
tiledb.Dim(name="dim", domain=(None, None), tile=None, dtype=np.bytes_)
)
schema = tiledb.ArraySchema(
domain=dom,
sparse=True,
attrs=[tiledb.Attr(name="1s", dtype=np.int32, var=True)],
)
tiledb.SparseArray.create(uri, schema)
for fragment_idx in range(fragments):
data = np.array(
[
np.array(
[fragment_idx + 1] * 1,
dtype=np.int32,
),
np.array(
[fragment_idx + 1] * 2,
dtype=np.int32,
),
np.array(
[fragment_idx + 1] * 3,
dtype=np.int32,
),
],
dtype="O",
)
with tiledb.SparseArray(
uri, mode="w", timestamp=fragment_idx + 1 if use_timestamps else None
) as T:
T[["zero", "one", "two"]] = data
fragments_info = tiledb.array_fragments(uri)
self.assertEqual(
fragments_info.nonempty_domain,
((("one", "zero"),), (("one", "zero"),), (("one", "zero"),)),
)
for frag in fragments_info:
self.assertEqual(frag.nonempty_domain, (("one", "zero"),))
@pytest.mark.parametrize("use_timestamps", [True, False])
def test_dense_fragments(self, use_timestamps):
fragments = 3
A = np.zeros(fragments)
uri = self.path("test_dense_fragments")
dom = tiledb.Domain(tiledb.Dim(domain=(0, 2), tile=fragments, dtype=np.int64))
att = tiledb.Attr(dtype=A.dtype)
schema = tiledb.ArraySchema(domain=dom, attrs=(att,))
tiledb.DenseArray.create(uri, schema)
for fragment_idx in range(fragments):
timestamp = fragment_idx + 1 if use_timestamps else None
with tiledb.DenseArray(uri, mode="w", timestamp=timestamp) as T:
T[fragment_idx : fragment_idx + 1] = fragment_idx
fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())
self.assertEqual(fragment_info.get_num_fragments(), fragment_idx + 1)
if use_timestamps: # asserts are not predictable without timestamps
all_expected_uris = []
for fragment_idx in range(fragments):
timestamp = fragment_idx + 1
self.assertEqual(
fragment_info.get_timestamp_range()[fragment_idx],
(timestamp, timestamp),
)
expected_uri = f"__{timestamp}_{timestamp}"
actual_uri = fragment_info.get_uri()[fragment_idx]
all_expected_uris.append(expected_uri)
self.assertTrue(expected_uri in actual_uri)
self.assertTrue(
actual_uri.endswith(str(fragment_info.get_version()[fragment_idx]))
)
self.assertFalse(fragment_info.get_sparse()[fragment_idx])
all_actual_uris = fragment_info.get_uri()
for actual_uri, expected_uri in zip(all_actual_uris, all_expected_uris):
self.assertTrue(expected_uri in actual_uri)
self.assertTrue(
actual_uri.endswith(str(fragment_info.get_version()[fragment_idx]))
)
self.assertEqual(
fragment_info.get_timestamp_range(), ((1, 1), (2, 2), (3, 3))
)
self.assertEqual(fragment_info.get_sparse(), (False, False, False))
@pytest.mark.parametrize("use_timestamps", [True, False])
def test_sparse_fragments(self, use_timestamps):
fragments = 3
A = np.zeros(fragments)
uri = self.path("test_sparse_fragments")
dom = tiledb.Domain(tiledb.Dim(domain=(0, 2), tile=fragments, dtype=np.int64))
att = tiledb.Attr(dtype=A.dtype)
schema = tiledb.ArraySchema(sparse=True, domain=dom, attrs=(att,))
tiledb.SparseArray.create(uri, schema)
for fragment_idx in range(fragments):
timestamp = fragment_idx + 1 if use_timestamps else None
with tiledb.SparseArray(uri, mode="w", timestamp=timestamp) as T:
T[fragment_idx] = fragment_idx
fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())
self.assertEqual(fragment_info.get_num_fragments(), fragment_idx + 1)
if use_timestamps: # asserts are not predictable without timestamps
all_expected_uris = []
for fragment_idx in range(fragments):
timestamp = fragment_idx + 1
self.assertEqual(
fragment_info.get_timestamp_range()[fragment_idx],
(timestamp, timestamp),
)
if uri[0] != "/":
uri = "/" + uri.replace("\\", "/")
expected_uri = f"/__{timestamp}_{timestamp}"
actual_uri = fragment_info.get_uri()[fragment_idx]
all_expected_uris.append(expected_uri)
self.assertTrue(expected_uri in actual_uri)
self.assertTrue(
actual_uri.endswith(str(fragment_info.get_version()[fragment_idx]))
)
self.assertTrue(fragment_info.get_sparse()[fragment_idx])
all_actual_uris = fragment_info.get_uri()
for actual_uri, expected_uri in zip(all_actual_uris, all_expected_uris):
self.assertTrue(expected_uri in actual_uri)
self.assertTrue(
actual_uri.endswith(str(fragment_info.get_version()[fragment_idx]))
)
self.assertEqual(
fragment_info.get_timestamp_range(), ((1, 1), (2, 2), (3, 3))
)
self.assertEqual(fragment_info.get_sparse(), (True, True, True))
def test_nonempty_domain(self):
uri = self.path("test_nonempty_domain")
dom = tiledb.Domain(
tiledb.Dim(name="x", domain=(1, 4)),
tiledb.Dim(name="y", domain=(-2.0, 2.0), dtype=np.float32),
)
att = tiledb.Attr()
schema = tiledb.ArraySchema(sparse=True, domain=dom, attrs=(att,))
tiledb.SparseArray.create(uri, schema)
with tiledb.SparseArray(uri, mode="w") as T:
coords = np.array(
list(itertools.product(np.arange(1, 5), np.arange(-1, 3)))
)
x = coords[:, 0]
y = coords[:, 1]
T[x, y] = np.array(range(16))
with tiledb.SparseArray(uri, mode="w") as T:
x = [1, 3]
y = [-1.5, -1.25]
T[x, y] = np.array(range(2))
fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())
self.assertEqual(
fragment_info.get_nonempty_domain(),
(((1, 4), (-1.0, 2.0)), ((1, 3), (-1.5, -1.25))),
)
def test_nonempty_domain_date(self):
uri = self.path("test_nonempty_domain")
dom = tiledb.Domain(
tiledb.Dim(
name="day",
domain=(np.datetime64("2010-01-01"), np.datetime64("2020")),
dtype="datetime64[D]",
)
)
att = tiledb.Attr()
schema = tiledb.ArraySchema(sparse=True, domain=dom, attrs=(att,))
tiledb.SparseArray.create(uri, schema)
with tiledb.SparseArray(uri, mode="w") as T:
dates = np.array(
["2017-04-01", "2019-10-02", "2019-10-03", "2019-12-04"],
dtype="datetime64[D]",
)
T[dates] = np.array(range(4))
with tiledb.SparseArray(uri, mode="w") as T:
dates = np.array(
["2010-01-01", "2013-10-02", "2014-10-03"], dtype="datetime64[D]"
)
T[dates] = np.array(range(3))
fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())
self.assertEqual(
fragment_info.get_nonempty_domain(),
(
((np.datetime64("2017-04-01"), np.datetime64("2019-12-04")),),
((np.datetime64("2010-01-01"), np.datetime64("2014-10-03")),),
),
)
def test_nonempty_domain_strings(self):
uri = self.path("test_nonempty_domain_strings")
dom = tiledb.Domain(
tiledb.Dim(name="x", domain=(None, None), dtype=np.bytes_),
tiledb.Dim(name="y", domain=(None, None), dtype=np.bytes_),
)
att = tiledb.Attr()
schema = tiledb.ArraySchema(sparse=True, domain=dom, attrs=(att,))
tiledb.SparseArray.create(uri, schema)
with tiledb.SparseArray(uri, mode="w") as T:
x_dims = [b"a", b"b", b"c", b"d"]
y_dims = [b"e", b"f", b"g", b"h"]
T[x_dims, y_dims] = np.array([1, 2, 3, 4])
with tiledb.SparseArray(uri, mode="w") as T:
x_dims = [b"a", b"b"]
y_dims = [b"e", b"f"]
T[x_dims, y_dims] = np.array([1, 2])
fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())
self.assertEqual(
fragment_info.get_nonempty_domain(),
((("a", "d"), ("e", "h")), (("a", "b"), ("e", "f"))),
)
def test_cell_num(self):
uri = self.path("test_cell_num")
dom = tiledb.Domain(tiledb.Dim(domain=(1, 4)))
att = tiledb.Attr()
schema = tiledb.ArraySchema(sparse=True, domain=dom, attrs=(att,))
tiledb.SparseArray.create(uri, schema)
fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())
with tiledb.SparseArray(uri, mode="w") as T:
a = np.array([1, 2, 3, 4])
T[a] = a
with tiledb.SparseArray(uri, mode="w") as T:
b = np.array([1, 2])
T[b] = b
fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())
self.assertEqual(fragment_info.get_cell_num(), (len(a), len(b)))
def test_consolidated_fragment_metadata(self):
fragments = 3
A = np.zeros(fragments)
uri = self.path("test_consolidated_fragment_metadata")
dom = tiledb.Domain(tiledb.Dim(domain=(0, 2), dtype=np.int64))
att = tiledb.Attr(dtype=A.dtype)
schema = tiledb.ArraySchema(domain=dom, attrs=(att,))
tiledb.DenseArray.create(uri, schema)
for fragment_idx in range(fragments):
with tiledb.DenseArray(uri, mode="w") as T:
T[fragment_idx : fragment_idx + 1] = fragment_idx
fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())
self.assertEqual(fragment_info.get_unconsolidated_metadata_num(), 3)
self.assertEqual(
fragment_info.get_has_consolidated_metadata(), (False, False, False)
)
tiledb.consolidate(
uri, config=tiledb.Config(params={"sm.consolidation.mode": "fragment_meta"})
)
fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())
self.assertEqual(fragment_info.get_unconsolidated_metadata_num(), 0)
self.assertEqual(
fragment_info.get_has_consolidated_metadata(), (True, True, True)
)
def test_fragments_to_vacuum(self):
fragments = 3
A = np.zeros(fragments)
uri = self.path("test_fragments_to_vacuum")
dom = tiledb.Domain(tiledb.Dim(domain=(0, 2), dtype=np.int64))
att = tiledb.Attr(dtype=A.dtype)
schema = tiledb.ArraySchema(domain=dom, attrs=(att,))
tiledb.DenseArray.create(uri, schema)
for fragment_idx in range(fragments):
with tiledb.DenseArray(uri, mode="w") as T:
T[fragment_idx : fragment_idx + 1] = fragment_idx
fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())
expected_vacuum_uri = fragment_info.get_uri()[0]
tiledb.consolidate(
uri, config=tiledb.Config(params={"sm.vacuum.mode": "fragments"})
)
fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())
assert len(fragment_info.get_to_vacuum()) == 3
assert fragment_info.get_to_vacuum()[0] == expected_vacuum_uri
tiledb.vacuum(uri)
fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())
assert len(fragment_info.get_to_vacuum()) == 0
@pytest.mark.skipif(
tiledb.libtiledb.version() < (2, 5, 0),
reason=(
"MBRs in FragmentInfo only available in "
"tiledb.libtiledb.version() < (2, 5, 0)"
),
)
@pytest.mark.parametrize("use_timestamps", [True, False])
def test_get_mbr(self, use_timestamps):
fragments = 3
uri = self.path("test_get_mbr")
dom = tiledb.Domain(tiledb.Dim(domain=(0, 2), tile=fragments, dtype=np.int64))
att = tiledb.Attr(dtype=np.uint64)
schema = tiledb.ArraySchema(domain=dom, attrs=(att,), sparse=True)
tiledb.Array.create(uri, schema)
for fragi in range(fragments):
timestamp = fragi + 1
with tiledb.open(
uri, mode="w", timestamp=timestamp if use_timestamps else None
) as T:
T[np.array(range(0, fragi + 1))] = [fragi] * (fragi + 1)
expected_mbrs = ((((0, 0),),), (((0, 1),),), (((0, 2),),))
py_fragment_info = PyFragmentInfo(uri, schema, True, tiledb.default_ctx())
assert py_fragment_info.get_mbrs() == expected_mbrs
array_fragments = tiledb.array_fragments(uri)
with pytest.raises(AttributeError) as excinfo:
array_fragments.mbrs
assert "retrieving minimum bounding rectangles is disabled" in str(
excinfo.value
)
with self.assertRaises(AttributeError):
array_fragments[0].mbrs
assert "retrieving minimum bounding rectangles is disabled" in str(
excinfo.value
)
array_fragments = tiledb.array_fragments(uri, include_mbrs=True)
assert array_fragments.mbrs == expected_mbrs
assert array_fragments[0].mbrs == expected_mbrs[0]
assert array_fragments[1].mbrs == expected_mbrs[1]
assert array_fragments[2].mbrs == expected_mbrs[2]
@pytest.mark.skipif(
tiledb.libtiledb.version() < (2, 5, 0),
reason=(
"MBRs in FragmentInfo only available in "
"tiledb.libtiledb.version() < (2, 5, 0)"
),
)
@pytest.mark.parametrize("use_timestamps", [True, False])
def test_get_var_sized_dim_mbrs(self, use_timestamps):
fragments = 3
uri = self.path("test_get_var_sized_dim_mbrs")
dom = tiledb.Domain(tiledb.Dim(dtype="ascii"))
att = tiledb.Attr(dtype=np.uint64)
schema = tiledb.ArraySchema(domain=dom, attrs=(att,), sparse=True)
tiledb.Array.create(uri, schema)
for fragi in range(fragments):
timestamp = fragi + 1
with tiledb.open(
uri, mode="w", timestamp=timestamp if use_timestamps else None
) as T:
coords = [chr(i) * (fragi + 1) for i in range(97, fragi + 98)]
T[np.array(coords)] = [fragi] * (fragi + 1)
expected_mbrs = (((("a", "a"),),), ((("aa", "bb"),),), ((("aaa", "ccc"),),))
py_fragment_info = PyFragmentInfo(uri, schema, True, tiledb.default_ctx())
assert py_fragment_info.get_mbrs() == expected_mbrs
array_fragments = tiledb.array_fragments(uri)
with pytest.raises(AttributeError) as excinfo:
array_fragments.mbrs
assert "retrieving minimum bounding rectangles is disabled" in str(
excinfo.value
)
with self.assertRaises(AttributeError):
array_fragments[0].mbrs
assert "retrieving minimum bounding rectangles is disabled" in str(
excinfo.value
)
array_fragments = tiledb.array_fragments(uri, include_mbrs=True)
assert array_fragments.mbrs == expected_mbrs
assert array_fragments[0].mbrs == expected_mbrs[0]
assert array_fragments[1].mbrs == expected_mbrs[1]
assert array_fragments[2].mbrs == expected_mbrs[2]
class CreateArrayFromFragmentsTest(DiskTestCase):
@pytest.mark.skipif(
sys.platform == "win32", reason="VFS.copy() does not run on windows"
)
@pytest.mark.parametrize("use_timestamps", [True, False])
def test_create_array_from_fragments(self, use_timestamps):
dshape = (1, 3)
num_frags = 10
def create_array(target_path, dshape):
dom = tiledb.Domain(tiledb.Dim(domain=dshape, tile=len(dshape)))
att = tiledb.Attr(dtype="int64")
schema = tiledb.ArraySchema(domain=dom, attrs=(att,), sparse=True)
tiledb.libtiledb.Array.create(target_path, schema)
def write_fragments(target_path, dshape, num_frags):
for i in range(1, num_frags + 1):
with tiledb.open(
target_path, "w", timestamp=i if use_timestamps else None
) as A:
A[[1, 2, 3]] = np.random.rand(dshape[1])
src_path = self.path("test_create_array_from_fragments_src")
dst_path = self.path("test_create_array_from_fragments_dst")
ts = tuple((t, t) for t in range(1, 11))
create_array(src_path, dshape)
write_fragments(src_path, dshape, num_frags)
frags = tiledb.FragmentInfoList(src_path)
assert len(frags) == 10
if use_timestamps:
assert frags.timestamp_range == ts
if use_timestamps:
tiledb.create_array_from_fragments(src_path, dst_path, (3, 6))
else:
tiledb.create_array_from_fragments(
src_path,
dst_path,
(frags.timestamp_range[2][0], frags.timestamp_range[5][1]),
)
frags = tiledb.FragmentInfoList(dst_path)
assert len(frags) == 4
if use_timestamps:
assert frags.timestamp_range == ts[2:6]
class CopyFragmentsToExistingArrayTest(DiskTestCase):
@pytest.mark.skipif(
sys.platform == "win32", reason="VFS.copy() does not run on windows"
)
def test_copy_fragments_to_existing_array(self):
def create_array(target_path, dshape):
dom = tiledb.Domain(tiledb.Dim(domain=dshape, tile=len(dshape)))
att = tiledb.Attr(dtype="int64")
schema = tiledb.ArraySchema(domain=dom, attrs=(att,), sparse=True)
tiledb.libtiledb.Array.create(target_path, schema)
def write_fragments(target_path, dshape, num_frags, ts_start=1):
for i in range(ts_start, ts_start + num_frags):
with tiledb.open(target_path, "w", timestamp=i) as A:
A[[1, 2, 3]] = np.random.rand(dshape[1])
tiledb.VFS()
src_dshape = (1, 3)
src_num_frags = 10
src_path = self.path("test_copy_fragments_to_existing_array_src")
create_array(src_path, src_dshape)
write_fragments(src_path, src_dshape, src_num_frags)
dst_dshape = (1, 3)
dst_num_frags = 10
dst_path = self.path("test_copy_fragments_to_existing_array_dst")
create_array(dst_path, dst_dshape)
write_fragments(dst_path, dst_dshape, dst_num_frags, 11)
ts = tuple((t, t) for t in range(1, 21))
frags = tiledb.array_fragments(dst_path)
assert len(frags) == 10
assert frags.timestamp_range == ts[10:]
tiledb.copy_fragments_to_existing_array(src_path, dst_path, (3, 6))
frags = tiledb.FragmentInfoList(dst_path)
assert len(frags) == 14
assert frags.timestamp_range == ts[2:6] + ts[10:]
@pytest.mark.skipif(
sys.platform == "win32", reason="VFS.copy() does not run on windows"
)
def test_copy_fragments_to_existing_array_mismatch(self):
def create_array(target_path, attr_type):
dom = tiledb.Domain(tiledb.Dim(domain=(1, 3), tile=3))
att = tiledb.Attr(dtype=attr_type)
schema = tiledb.ArraySchema(domain=dom, attrs=(att,), sparse=True)
tiledb.libtiledb.Array.create(target_path, schema)
def write_fragments(target_path):
for i in range(10):
with tiledb.open(target_path, "w") as A:
A[[1, 2, 3]] = np.random.rand(3)
src_path = self.path("test_copy_fragments_to_existing_array_evolved_src")
create_array(src_path, "int64")
write_fragments(src_path)
dst_path = self.path("test_copy_fragments_to_existing_array_evolved_dst")
create_array(dst_path, "int32")
write_fragments(dst_path)
with self.assertRaises(tiledb.TileDBError):
tiledb.copy_fragments_to_existing_array(src_path, dst_path, (3, 6))
@pytest.mark.skipif(
sys.platform == "win32", reason="VFS.copy() does not run on windows"
)
def test_copy_fragments_to_existing_array_evolved(self):
def create_array(target_path):
dom = tiledb.Domain(tiledb.Dim(domain=(1, 3), tile=3))
att = tiledb.Attr(dtype="int64")
schema = tiledb.ArraySchema(domain=dom, attrs=(att,), sparse=True)
tiledb.libtiledb.Array.create(target_path, schema)
def write_fragments(target_path):
for i in range(10):
with tiledb.open(target_path, "w") as A:
A[[1, 2, 3]] = np.random.rand(3)
src_path = self.path("test_copy_fragments_to_existing_array_evolved_src")
create_array(src_path)
write_fragments(src_path)
dst_path = self.path("test_copy_fragments_to_existing_array_evolved_dst")
create_array(dst_path)
write_fragments(dst_path)
ctx = tiledb.default_ctx()
se = tiledb.ArraySchemaEvolution(ctx)
se.add_attribute(tiledb.Attr("a2", dtype=np.float64))
se.array_evolve(src_path)
with self.assertRaises(tiledb.TileDBError):
tiledb.copy_fragments_to_existing_array(src_path, dst_path, (3, 6))
class DeleteFragmentsTest(DiskTestCase):
@pytest.mark.parametrize("use_timestamps", [True, False])
def test_delete_fragments(self, use_timestamps):
dshape = (1, 3)
num_writes = 10
def create_array(target_path, dshape):
dom = tiledb.Domain(tiledb.Dim(domain=dshape, tile=len(dshape)))
att = tiledb.Attr(dtype="int64")
schema = tiledb.ArraySchema(domain=dom, attrs=(att,), sparse=True)
tiledb.libtiledb.Array.create(target_path, schema)
def write_fragments(target_path, dshape, num_writes):
for i in range(1, num_writes + 1):
with tiledb.open(
target_path, "w", timestamp=i if use_timestamps else None
) as A:
A[[1, 2, 3]] = np.random.rand(dshape[1])
path = self.path("test_delete_fragments")
ts = tuple((t, t) for t in range(1, 11))
create_array(path, dshape)
write_fragments(path, dshape, num_writes)
frags = tiledb.array_fragments(path)
assert len(frags) == 10
if use_timestamps:
assert frags.timestamp_range == ts
if use_timestamps:
tiledb.Array.delete_fragments(path, 3, 6)
else:
tiledb.Array.delete_fragments(
path, frags.timestamp_range[2][0], frags.timestamp_range[5][1]
)
frags = tiledb.array_fragments(path)
assert len(frags) == 6
if use_timestamps:
assert frags.timestamp_range == ts[:2] + ts[6:]
@pytest.mark.parametrize("use_timestamps", [True, False])
def test_delete_fragments_with_schema_evolution(self, use_timestamps):
path = self.path("test_delete_fragments_with_schema_evolution")
dshape = (1, 3)
dom = tiledb.Domain(tiledb.Dim(domain=dshape, tile=len(dshape)))
att = tiledb.Attr(name="a1", dtype=np.float64)
schema = tiledb.ArraySchema(domain=dom, attrs=(att,), sparse=True)
tiledb.libtiledb.Array.create(path, schema)
ts1_data = np.random.rand(3)
if use_timestamps:
with tiledb.open(path, "w", timestamp=1) as A:
A[[1, 2, 3]] = ts1_data
else:
with tiledb.open(path, "w") as A:
A[[1, 2, 3]] = ts1_data
ctx = tiledb.default_ctx()
se = tiledb.ArraySchemaEvolution(ctx)
se.add_attribute(tiledb.Attr("a2", dtype=np.float64))
se.array_evolve(path)
ts2_data = np.random.rand(3)
if use_timestamps:
with tiledb.open(path, "w", timestamp=2) as A:
A[[1, 2, 3]] = {"a1": ts2_data, "a2": ts2_data}
else:
with tiledb.open(path, "w") as A:
A[[1, 2, 3]] = {"a1": ts2_data, "a2": ts2_data}
frags = tiledb.array_fragments(path)
assert len(frags) == 2
with tiledb.open(path, "r") as A:
assert_array_equal(A[:]["a1"], ts2_data)
assert_array_equal(A[:]["a2"], ts2_data)
if use_timestamps:
tiledb.Array.delete_fragments(path, 2, 2)
else:
tiledb.Array.delete_fragments(
path, frags.timestamp_range[1][0], frags.timestamp_range[1][1]
)
frags = tiledb.array_fragments(path)
assert len(frags) == 1
with tiledb.open(path, "r") as A:
assert_array_equal(A[:]["a1"], ts1_data)
assert_array_equal(A[:]["a2"], [np.nan, np.nan, np.nan])
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