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Fix #300 by sorting output targets before uploading #340

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Fix #300 by sorting output targets before uploading #340

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10 changes: 10 additions & 0 deletions awsf3/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -392,6 +392,16 @@ def upload_to_output_target(prj_out, encrypt_s3_upload=False, kms_key_id=None, e
output_argnames = prj_out.output_files.keys()
output_target = prj_out.alt_output_target(output_argnames)

# sorting outputs by mtime in order to upload in the right order.
# arbitrary order created issues with workflow managers (snakemake)
# because S3 does not save the modification time of uploaded objects
output_target = dict(
sorted(
output_target.items(),
key=lambda i: os.path.getmtime(i[0].replace('file://', ''))
)
)

for k in output_target:
target = Target(output_bucket)

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