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