Hi all, I've got some Python applications that I've hooked into Galaxy, which use the Python logging module for output. To capture this output in my Galaxy history I've created a wrapper that adds a logging.FileHandler to the root logger, which uses an Galaxy tool output argument as file to write to. This all works fine, up to a certain amount of logging output...
I've created a proof of concept Galaxy tool that uses my method of capturing logging output (30 lines in total for tool & config) and added that to this email. When run with the default settings on my Galaxy instance this tool only writes 6625 lines of logging output out of 10,000, after which I have to manually kill the process because it gets stuck. Could you please look into why producing more than a certain amount of logging output can lead to a tool getting stuck, and tell me what I can do to resolve this? (Preferably without changing the way I capture output: I don't think my use case is that much of a stretch) Greets, Tim
<tool id="logging_proof_of_concept" name="Get stuck capturing Python logging output">
<description>for no apparent reason</description>
<command interpreter="python">log-poc.py $logfile $countto</command>
<inputs>
<param name="countto" type="integer" value="10000" label="Count to: " help="" />
</inputs>
<outputs>
<data format="txt" name="logfile" label="Logfile for ${tool.name}" />
</outputs>
<help></help>
</tool>
log-poc.py
Description: Binary data
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