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Move ls to run-worker, one level only #219

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Move ls to run-worker, one level only #219

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7 changes: 0 additions & 7 deletions worker/cp-worker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -111,13 +111,6 @@ def printandlog(text,logger):
def runCellProfiler(message):
s3client=boto3.client('s3')

#List the directories in the bucket- this prevents a strange s3fs error
rootlist=os.listdir(DATA_ROOT)
for eachSubDir in rootlist:
subDirName=os.path.join(DATA_ROOT,eachSubDir)
if os.path.isdir(subDirName):
trashvar=os.system(f'ls {subDirName}')

# Configure the logs
logger = logging.getLogger(__name__)

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4 changes: 3 additions & 1 deletion worker/run-worker.sh
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Expand Up @@ -22,17 +22,19 @@ aws ec2 create-tags --resources $VOL_0_ID --tags Key=Name,Value=${APP_NAME}Worke
VOL_1_ID=$(aws ec2 describe-instance-attribute --instance-id $MY_INSTANCE_ID --attribute blockDeviceMapping --output text --query BlockDeviceMappings[1].Ebs.[VolumeId])
aws ec2 create-tags --resources $VOL_1_ID --tags Key=Name,Value=${APP_NAME}Worker

# 2. MOUNT S3
# 2. MOUNT S3 (and ls for s3fs bug - issues/214)
if [[ ${DOWNLOAD_FILES} == 'False' ]]; then
echo "Mounting S3 using S3FS"
if [[ -z "$AWS_ACCESS_KEY_ID" ]]; then
echo "Using role credentials to mount S3"
s3fs $SOURCE_BUCKET /home/ubuntu/bucket -o iam_role
ls /home/ubuntu/bucket/
else
echo "Using user credentials to mount S3"
echo $AWS_ACCESS_KEY_ID:$AWS_SECRET_ACCESS_KEY > /credentials.txt
chmod 600 /credentials.txt
s3fs $SOURCE_BUCKET /home/ubuntu/bucket -o passwd_file=/credentials.txt
ls /home/ubuntu/bucket/
fi
fi

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