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Support for appending to files larger than 5GB #541

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May 4, 2024
Merged

Support for appending to files larger than 5GB #541

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72 changes: 55 additions & 17 deletions pyathena/filesystem/s3.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,8 +39,11 @@

class S3FileSystem(AbstractFileSystem):
# https://docs.aws.amazon.com/AmazonS3/latest/userguide/qfacts.html
# The minimum size of a part in a multipart upload is 5MB.
MULTIPART_UPLOAD_MINIMUM_SIZE: int = 5 * 2**20 # 5MB
# The minimum size of a part in a multipart upload is 5MiB.
MULTIPART_UPLOAD_MINIMUM_PART_SIZE: int = 5 * 2**20 # 5MiB
# https://docs.aws.amazon.com/AmazonS3/latest/userguide/qfacts.html
# The maximum size of a part in a multipart upload is 5GiB.
MULTIPART_UPLOAD_MAXIMUM_PART_SIZE: int = 5 * 2**30 # 5GiB
DEFAULT_BLOCK_SIZE: int = 5 * 2**20 # 5MB
PATTERN_PATH: Pattern[str] = re.compile(
r"(^s3://|^s3a://|^)(?P<bucket>[a-zA-Z0-9.\-_]+)(/(?P<key>[^?]+)|/)?"
Expand Down Expand Up @@ -562,13 +565,13 @@ def _get_object(
self,
bucket: str,
key: str,
ranges: Optional[Tuple[int, int]],
ranges: Optional[Tuple[int, int]] = None,
version_id: Optional[str] = None,
**kwargs,
) -> Tuple[int, bytes]:
request = {"Bucket": bucket, "Key": key}
if ranges:
range_ = f"bytes={ranges[0]}-{ranges[1] - 1}"
range_ = S3File._format_ranges(ranges)
request.update({"Range": range_})
else:
ranges = (0, 0)
Expand Down Expand Up @@ -618,6 +621,7 @@ def _upload_part_copy(
copy_source: str,
upload_id: str,
part_number: int,
copy_source_ranges: Optional[Tuple[int, int]] = None,
**kwargs,
) -> S3MultipartUploadPart:
request = {
Expand All @@ -627,7 +631,9 @@ def _upload_part_copy(
"UploadId": upload_id,
"PartNumber": part_number,
}

if copy_source_ranges:
range_ = S3File._format_ranges(copy_source_ranges)
request.update({"CopySourceRange": range_})
_logger.debug(
f"Upload part copy from {copy_source} to s3://{bucket}/{key} as part {part_number}."
)
Expand Down Expand Up @@ -737,10 +743,12 @@ def __init__(
self.version_id = path_version_id
else:
self.version_id = version_id
if "r" not in mode and block_size < self.fs.MULTIPART_UPLOAD_MINIMUM_SIZE:
if "r" not in mode and block_size < self.fs.MULTIPART_UPLOAD_MINIMUM_PART_SIZE:
# When writing occurs, the block size should not be smaller
# than the minimum size of a part in a multipart upload.
raise ValueError(f"Block size must be >= {self.fs.MULTIPART_UPLOAD_MINIMUM_SIZE}MB.")
raise ValueError(
f"Block size must be >= {self.fs.MULTIPART_UPLOAD_MINIMUM_PART_SIZE}MB."
)

self.append_block = False
if "r" in mode:
Expand All @@ -752,7 +760,7 @@ def __init__(
self.append_block = True
info = self.fs.info(self.path, version_id=self.version_id)
loc = info.get("size", 0)
if loc < self.fs.MULTIPART_UPLOAD_MINIMUM_SIZE:
if loc < self.fs.MULTIPART_UPLOAD_MINIMUM_PART_SIZE:
self.write(self.fs.cat(self.path))
self.loc = loc
self.s3_additional_kwargs.update(info.to_api_repr())
Expand All @@ -778,16 +786,42 @@ def _initiate_upload(self) -> None:
**self.s3_additional_kwargs,
)
if self.append_block:
self.multipart_upload_parts.append(
self._executor.submit(
self.fs._upload_part_copy,
bucket=self.bucket,
key=self.key,
copy_source=self.path,
upload_id=cast(str, cast(S3MultipartUpload, self.multipart_upload).upload_id),
part_number=1,
if self.tell() > S3FileSystem.MULTIPART_UPLOAD_MAXIMUM_PART_SIZE:
info = self.fs.info(self.path, version_id=self.version_id)
ranges = self._get_ranges(
0,
# Set copy source file byte size
info.get("size", 0),
self.max_workers,
S3FileSystem.MULTIPART_UPLOAD_MAXIMUM_PART_SIZE,
)
for i, range in enumerate(ranges):
self.multipart_upload_parts.append(
self._executor.submit(
self.fs._upload_part_copy,
bucket=self.bucket,
key=self.key,
copy_source=self.path,
upload_id=cast(
str, cast(S3MultipartUpload, self.multipart_upload).upload_id
),
part_number=i + 1,
copy_source_ranges=range,
)
)
else:
self.multipart_upload_parts.append(
self._executor.submit(
self.fs._upload_part_copy,
bucket=self.bucket,
key=self.key,
copy_source=self.path,
upload_id=cast(
str, cast(S3MultipartUpload, self.multipart_upload).upload_id
),
part_number=1,
)
)
)

def _upload_chunk(self, final: bool = False) -> bool:
if self.tell() < self.blocksize:
Expand Down Expand Up @@ -906,6 +940,10 @@ def _fetch_range(self, start: int, end: int) -> bytes:
)[1]
return object_

@staticmethod
def _format_ranges(ranges: Tuple[int, int]):
return f"bytes={ranges[0]}-{ranges[1] - 1}"

@staticmethod
def _get_ranges(
start: int, end: int, max_workers: int, worker_block_size: int
Expand Down
17 changes: 15 additions & 2 deletions tests/pyathena/filesystem/test_s3.py
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Original file line number Diff line number Diff line change
Expand Up @@ -164,7 +164,12 @@ def test_read(self, fs, start, end, target_data):
(1, 2**20),
(10, 2**20),
(100, 2**20),
(1000, 2**20),
(1024, 2**20),
# TODO: Perhaps OOM is occurring and the worker is shutting down.
# The runner has received a shutdown signal.
# This can happen when the runner service is stopped,
# or a manually started runner is canceled.
# (5 * 1024 + 1, 2**20),
],
)
def test_write(self, fs, base, exp):
Expand All @@ -186,7 +191,12 @@ def test_write(self, fs, base, exp):
(1, 2**20),
(10, 2**20),
(100, 2**20),
(1000, 2**20),
(1024, 2**20),
# TODO: Perhaps OOM is occurring and the worker is shutting down.
# The runner has received a shutdown signal.
# This can happen when the runner service is stopped,
# or a manually started runner is canceled.
# (5 * 1024 + 1, 2**20),
],
)
def test_append(self, fs, base, exp):
Expand Down Expand Up @@ -298,3 +308,6 @@ def test_get_ranges(self, start, end, max_workers, worker_block_size, ranges):
)
== ranges
)

def test_format_ranges(self):
assert S3File._format_ranges((0, 100)) == "bytes=0-99"