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Update processing to be more general #26

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merged 2 commits into from
Oct 28, 2024
Merged

Update processing to be more general #26

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6ab7f4e
Update processing to be more general
lnauta Oct 11, 2024
737fd6f
Merge branch 'master' of github.com:sara-nl/picasclient into SPD-415
Oct 24, 2024
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19 changes: 13 additions & 6 deletions examples/local-example.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,11 +47,20 @@ def process_task(self, token):
print(key, value)
print("-----------------------")

# Start running the main job
# /usr/bin/time -v ./process_task.sh [input] [tokenid] 2> logs_[token_id].err 1> logs_[token_id].out
command = "/usr/bin/time -v ./process_task.sh " + "\"" +token['input'] + "\" " + token['_id'] + " 2> logs_" + str(token['_id']) + ".err 1> logs_" + str(token['_id']) + ".out"
# Start running the main job, the logging is done internally and saved below
# /usr/bin/time -v ./process_task.sh [input] [tokenid]
command = ["/usr/bin/time", "-v", "./process_task.sh", token['input'], token['_id']]
out = execute(command)

logsout = f"logs_{token['_id']}.out"
logserr = f"logs_{token['_id']}.err"

# write the logs
with open(logsout, 'w') as f:
f.write(out[2].decode('utf-8'))
with open(logserr, 'w') as f:
f.write(out[3].decode('utf-8'))

out = execute(command, shell=True)
self.subprocess = out[0]

# Get the job exit code and done in the token
Expand All @@ -61,11 +70,9 @@ def process_task(self, token):
# Attach logs in token
curdate = time.strftime("%d/%m/%Y_%H:%M:%S_")
try:
logsout = "logs_" + str(token['_id']) + ".out"
log_handle = open(logsout, 'rb')
token.put_attachment(logsout, log_handle.read())

logserr = "logs_" + str(token['_id']) + ".err"
log_handle = open(logserr, 'rb')
token.put_attachment(logserr, log_handle.read())
except:
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2 changes: 1 addition & 1 deletion examples/process_task.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ echo $TOKENID
echo $OUTPUT

#Start processing
eval $INPUT
bash -c "$INPUT"
if [[ "$?" != "0" ]]; then
echo "Program interrupted. Exit now..."
exit 1
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