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Added option to get file stats for requester-pays files #414

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Merged
merged 1 commit into from
Sep 28, 2021
Merged

Added option to get file stats for requester-pays files #414

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10 changes: 8 additions & 2 deletions gnomad/utils/file_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -154,19 +154,25 @@ def select_primitives_from_ht(ht: hl.Table) -> hl.Table:
)


def get_file_stats(url: str) -> Tuple[int, str, str]:
def get_file_stats(url: str, project_id: Optional[str] = None) -> Tuple[int, str, str]:
"""
Get size (as both int and str) and md5 for file at specified URL.

Typically used to get stats on VCFs.

:param url: Path to file of interest.
:param project_id: Google project ID. Specify if URL points to a requester-pays bucket.
:return: Tuple of file size and md5.
"""
one_gibibyte = 2 ** 30
one_mebibyte = 2 ** 20

output = subprocess.check_output(["gsutil", "stat", url]).decode("utf8")
if project_id:
output = subprocess.check_output(
["gsutil", "-u", project_id, "stat", url]
).decode("utf8")
else:
output = subprocess.check_output(["gsutil", "stat", url]).decode("utf8")
lines = output.split("\n")

info = {}
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