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add try/except and error messages to file downloads #173

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Merged
merged 1 commit into from
Jul 15, 2024
Merged

add try/except and error messages to file downloads #173

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34 changes: 27 additions & 7 deletions worker/cp-worker.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import boto3
import botocore
import json
import logging
import os
Expand Down Expand Up @@ -186,8 +187,14 @@ def runCellProfiler(message):
subfolders = '/'.join((csv_insubfolders)[:-1])
if not os.path.exists(os.path.join(localIn,subfolders)):
os.makedirs(os.path.join(localIn,subfolders), exist_ok=True)
s3 = boto3.resource('s3')
s3.meta.client.download_file(WORKSPACE_BUCKET, message['data_file'], data_file_path)
s3client=boto3.client('s3')
try:
s3client.download_file(WORKSPACE_BUCKET, message['data_file'], data_file_path)
except botocore.exceptions.ClientError:
printandlog(f"Can't find load data file in S3. Looking for {message['data_file']} in {WORKSPACE_BUCKET}",logger)
printandlog("Aborting. Can't run without load data.",logger)
logger.removeHandler(watchtowerlogger)
return 'DOWNLOAD_PROBLEM'
if message['data_file'][-4:]=='.csv':
printandlog('Figuring which files to download', logger)
import pandas
Expand Down Expand Up @@ -222,8 +229,11 @@ def runCellProfiler(message):
os.makedirs(os.path.split(new_file_name)[0])
printandlog(f'Made directory {os.path.split(new_file_name)[0]}',logger)
if not os.path.exists(new_file_name):
s3.meta.client.download_file(SOURCE_BUCKET,prefix_on_bucket,new_file_name)
downloaded_files.append(new_file_name)
try:
s3client.download_file(SOURCE_BUCKET,prefix_on_bucket,new_file_name)
downloaded_files.append(new_file_name)
except botocore.exceptions.ClientError:
printandlog(f"Can't find file in S3. Looking for {prefix_on_bucket} in {SOURCE_BUCKET}",logger)
printandlog(f'Downloaded {str(len(downloaded_files))} files',logger)
import random
newtag = False
Expand Down Expand Up @@ -251,15 +261,25 @@ def runCellProfiler(message):
os.makedirs(os.path.split(new_file_name)[0])
printandlog(f'made directory {os.path.split(new_file_name)[0]}',logger)
if not os.path.exists(new_file_name):
s3.meta.client.download_file(SOURCE_BUCKET,prefix_on_bucket,new_file_name)
downloaded_files.append(new_file_name)
try:
s3client.download_file(SOURCE_BUCKET,prefix_on_bucket,new_file_name)
downloaded_files.append(new_file_name)
except botocore.exceptions.ClientError:
printandlog(f"Can't find file in S3. Looking for {prefix_on_bucket} in {SOURCE_BUCKET}",logger)
printandlog(f'Downloaded {str(len(downloaded_files))} files',logger)
else:
printandlog("Couldn't parse data file for file download. Not supported input of .csv or .txt",logger)
# Download pipeline and update pipeline path in message
printandlog(f"Downloading {message['pipeline']} from {WORKSPACE_BUCKET}", logger)
pipepath = os.path.join(localIn, message['pipeline'].split('/')[-1])
s3.meta.client.download_file(WORKSPACE_BUCKET, message['pipeline'], pipepath)
try:
s3client.download_file(WORKSPACE_BUCKET, message['pipeline'], pipepath)
except botocore.exceptions.ClientError:
printandlog(f"Can't find pipeline in S3. Looking for {message['pipeline']} in {WORKSPACE_BUCKET}",logger)
printandlog("Aborting. Can't run without pipeline.",logger)
logger.removeHandler(watchtowerlogger)
return 'DOWNLOAD_PROBLEM'

else:
data_file_path = os.path.join(DATA_ROOT,message['data_file'])
pipepath = os.path.join(DATA_ROOT,message["pipeline"])
Expand Down