item = response['@graph'][0]
creds = item['upload_credentials']
- self.run_aws_cp(metadata['submitted_file_name'], creds)
+ run_aws_cp(metadata['submitted_file_name'], creds)
else:
LOGGER.info('%s already uploaded',
metadata['submitted_file_name'])
- def run_aws_cp(self, pathname, creds):
- env = os.environ.copy()
- env.update({
- 'AWS_ACCESS_KEY_ID': creds['access_key'],
- 'AWS_SECRET_ACCESS_KEY': creds['secret_key'],
- 'AWS_SECURITY_TOKEN': creds['session_token'],
- })
- start = time.time()
- try:
- subprocess.check_call(['aws', 's3', 'cp', pathname, creds['upload_url']], env=env)
- except subprocess.CalledProcessError as e:
- LOGGER.error('Upload of %s failed with exit code %d', pathname, e.returncode)
- return
- else:
- end = time.time()
- LOGGER.info('Upload of %s finished in %.2f seconds',
- pathname,
- end-start)
-
-
def get_metadata(self, analysis_node):
# convert our model names to encode project aliases
platform_alias = {
row['flowcell_details'] = [flowcell_details]
return results
+
+def run_aws_cp(pathname, creds):
+ env = os.environ.copy()
+ env.update({
+ 'AWS_ACCESS_KEY_ID': creds['access_key'],
+ 'AWS_SECRET_ACCESS_KEY': creds['secret_key'],
+ 'AWS_SECURITY_TOKEN': creds['session_token'],
+ })
+ start = time.time()
+ try:
+ subprocess.check_call(['aws', 's3', 'cp', pathname, creds['upload_url']], env=env)
+ except subprocess.CalledProcessError as e:
+ LOGGER.error('Upload of %s failed with exit code %d', pathname, e.returncode)
+ return
+ else:
+ end = time.time()
+ LOGGER.info('Upload of %s finished in %.2f seconds',
+ pathname,
+ end-start)