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FIX: DataSink to S3 buckets #3130

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Merged
merged 2 commits into from
Jan 18, 2020
Merged

FIX: DataSink to S3 buckets #3130

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3c78a54
fix DataSink to S3 buckets
Aksoo Jan 2, 2020
847553e
DataSink inputs changed from Directory to Str
kimsin98 Jan 13, 2020
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22 changes: 8 additions & 14 deletions nipype/interfaces/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -440,27 +440,20 @@ def _check_s3_base_dir(self):
is not a valid S3 path, defaults to '<N/A>'
"""

# Init variables
s3_str = "s3://"
# NOTE: due to pathlib.Path in traits.Directory, S3 bucket paths
# follow the format 's3:/bucket_name/...'
s3_str = "s3:/"
bucket_name = "<N/A>"
base_directory = self.inputs.base_directory

if not isdefined(base_directory):
s3_flag = False
return s3_flag, bucket_name

# Explicitly lower-case the "s3"
# Check for 's3:/' in base dir
if base_directory.lower().startswith(s3_str):
base_dir_sp = base_directory.split("/")
base_dir_sp[0] = base_dir_sp[0].lower()
base_directory = "/".join(base_dir_sp)

# Check if 's3://' in base dir
if base_directory.startswith(s3_str):
# Expects bucket name to be 's3://bucket_name/base_dir/..'
bucket_name = base_directory.split(s3_str)[1].split("/")[0]
bucket_name = base_directory[len(s3_str):].split("/")[0]
s3_flag = True
# Otherwise it's just a normal datasink
else:
s3_flag = False

Expand Down Expand Up @@ -618,8 +611,9 @@ def _upload_to_s3(self, bucket, src, dst):

from botocore.exceptions import ClientError

# Init variables
s3_str = "s3://"
# NOTE: due to pathlib.Path in traits.Directory, S3 bucket paths
# follow the format 's3:/bucket_name/...'
s3_str = "s3:/"
s3_prefix = s3_str + bucket.name

# Explicitly lower-case the "s3"
Expand Down