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Added md5 checking before uploading to S3 #2

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Merged
merged 3 commits into from
Oct 16, 2015
Merged

Added md5 checking before uploading to S3 #2

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0503c23
Added md5 checking for s3
pintohutch Oct 15, 2015
e3ad668
Merge pull request #1 from FCP-INDI/master
pintohutch Oct 15, 2015
f6cfad7
Added message about file already existsing
pintohutch Oct 15, 2015
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23 changes: 22 additions & 1 deletion nipype/interfaces/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -544,9 +544,12 @@ def _upload_to_s3(self, src, dst):
'''

# Import packages
import hashlib
import logging
import os

from botocore.exceptions import ClientError

# Init variables
bucket = self.bucket
iflogger = logging.getLogger('interface')
Expand All @@ -571,8 +574,26 @@ def _upload_to_s3(self, src, dst):
dst_f = dst_files[src_idx]
dst_k = dst_f.replace(s3_prefix, '').lstrip('/')

# See if same file is already up there
try:
dst_obj = bucket.Object(key=dst_k)
dst_md5 = dst_obj.e_tag.strip('"')

# See if same file is already there
src_read = open(src_f, 'rb').read()
src_md5 = hashlib.md5(src_read).hexdigest()
# Move to next loop iteration
if dst_md5 == src_md5:
iflogger.info('File %s already exists on S3, skipping...' % dst_f)
continue
else:
iflogger.info('Overwriting previous S3 file...')

except ClientError as exc:
iflogger.info('New file to S3')

# Copy file up to S3 (either encrypted or not)
iflogger.info('Copying %s to S3 bucket, %s, as %s...'\
iflogger.info('Uploading %s to S3 bucket, %s, as %s...'\
% (src_f, bucket.name, dst_f))
if self.inputs.encrypt_bucket_keys:
extra_args = {'ServerSideEncryption' : 'AES256'}
Expand Down