def test_copy_fragments_to_new(runner, uri, temp_rootdir, start_time,
end_time):
"""
Test for command
tiledb fragments copy [old_array_uri] [new_array_uri] [start_time] [end_time]
"""
old_uri = uri
new_uri = os.path.abspath(
os.path.join(
temp_rootdir,
f"test_copy_fragments_to_new_{start_time}_{end_time}",
))
result = runner.invoke(
root,
["fragments", "copy", "-f", old_uri, new_uri, start_time, end_time],
)
assert result.exit_code == 0
fragments = tiledb.array_fragments(old_uri)
assert len(fragments) == 3
assert fragments.timestamp_range == ((1, 1), (2, 2), (3, 3))
fragments = tiledb.array_fragments(new_uri)
assert len(fragments) == 2
assert fragments.timestamp_range == ((2, 2), (3, 3))
def test_delete_fragments_unix(runner, uri, ts):
"""
Test for command
tiledb fragments delete [array_uri] [start_time] [end_time]
"""
fragments = tiledb.array_fragments(uri)
assert len(fragments) == 3
assert fragments.timestamp_range == ((1, 1), (2, 2), (3, 3))
result = runner.invoke(root, ["fragments", "delete", "-f", uri, ts, ts])
assert result.exit_code == 0
fragments = tiledb.array_fragments(uri)
assert len(fragments) == 2
assert fragments.timestamp_range == ((2, 2), (3, 3))
def test_fragment_metadata_consolidate_and_vacuum(runner, uri):
"""
Test for command
tiledb consolidate fragment-metadata [array_uri]
tiledb vacuum fragment-metadata [array_uri]
"""
fragments = tiledb.array_fragments(uri)
assert fragments.unconsolidated_metadata_num == 2
result = runner.invoke(root, ["consolidate", "fragment-metadata", uri])
assert result.exit_code == 0
fragments = tiledb.array_fragments(uri)
assert fragments.unconsolidated_metadata_num == 0
result = runner.invoke(root, ["vacuum", "fragment-metadata", uri])
assert result.exit_code == 0
def test_copy_fragments_to_existing(runner, uri, temp_rootdir, start_time,
end_time):
"""
Test for command
tiledb fragments copy [old_array_uri] [new_array_uri] [start_time] [end_time]
"""
old_uri = uri
new_uri = os.path.abspath(
os.path.join(
temp_rootdir,
f"test_copy_fragments_to_existing_{start_time}_{end_time}",
))
rows_dim = tiledb.Dim(domain=(1, 25), dtype=np.int64)
cols_dim = tiledb.Dim(domain=(1, 12), dtype=np.int64)
dom = tiledb.Domain(rows_dim, cols_dim)
att1 = tiledb.Attr(name="a", dtype=np.float64)
att2 = tiledb.Attr(name="b", dtype=np.float64)
schema = tiledb.ArraySchema(domain=dom, attrs=(att1, att2))
tiledb.Array.create(new_uri, schema)
data = np.reshape(np.arange(300), (25, 12))
for ts in range(4, 6):
with tiledb.open(new_uri, mode="w", timestamp=ts) as A:
A[:] = {"a": data, "b": data}
result = runner.invoke(
root,
["fragments", "copy", "-f", old_uri, new_uri, start_time, end_time],
)
assert result.exit_code == 0
fragments = tiledb.array_fragments(old_uri)
assert len(fragments) == 3
assert fragments.timestamp_range == ((1, 1), (2, 2), (3, 3))
fragments = tiledb.array_fragments(new_uri)
assert len(fragments) == 4
assert fragments.timestamp_range == ((2, 2), (3, 3), (4, 4), (5, 5))
def test(self, runner, temp_rootdir, array_name, pp):
"""
Test for command
tiledb dump mbr [array_uri]
"""
uri = os.path.abspath(os.path.join(temp_rootdir, array_name))
result = runner.invoke(root, ["dump", "mbrs", uri])
assert result.exit_code == 0
fragments = tiledb.array_fragments(uri, include_mbrs=True)
assert result.stdout.split() == pp.pformat(fragments.mbrs).split()
def test_fragments_consolidate_and_vacuum(runner, uri):
"""
Test for command
tiledb consolidate fragments [array_uri]
tiledb vacuum fragments [array_uri]
"""
fragments = tiledb.array_fragments(uri)
assert len(fragments) == 2
result = runner.invoke(root, ["consolidate", "fragments", uri])
assert result.exit_code == 0
fragments = tiledb.array_fragments(uri)
assert len(fragments) == 1
assert len(fragments.to_vacuum) == 2
result = runner.invoke(root, ["vacuum", "fragments", uri])
assert result.exit_code == 0
fragments = tiledb.array_fragments(uri)
assert len(fragments) == 1
assert len(fragments.to_vacuum) == 0
def fragments(uri, index, number):
"""
Output the fragment information of a TileDB array located at uri.
"""
pp = pprint.PrettyPrinter()
fragments = tiledb.array_fragments(uri)
if number:
click.echo(len(fragments))
exit()
if index is not None:
fragments = fragments[index]
click.echo(pp.pformat(fragments))
def mbrs(uri, index):
"""
Output the minimum bounding rectangles of a sparse TileDB array located at uri.
"""
pp = pprint.PrettyPrinter()
fragments = tiledb.array_fragments(uri, include_mbrs=True)
if not hasattr(fragments, "mbrs"):
click.echo(
"Error: no MBRs found in the given array",
err=True,
)
mbrs = fragments.mbrs
if index is not None:
mbrs = mbrs[index]
click.echo(pp.pformat(mbrs))