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ProtProtocols / IsoProt

Protocol of the analysis of iTRAQ/TMT proteomics data including quantification, statistical analysis and maybe clustering
https://protprotocols.github.io
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Save (search) output to log file #58

Closed jgriss closed 5 years ago

jgriss commented 6 years ago

Currently, when a running notebook is closed (in my case the search) the notebook is still executed, but the output is lost - and cannot be retrieved afterwards according to several bug reports.

A possible solution to this is to use a proper logging system in the search.ipy module and write every message to the notebook (using print) as well as to a log file.

Ideally, when the notebook is re-opened, we could display the contents of the log file.

veitveit commented 5 years ago

@jgriss Is it possible to write all SearchGUI and PeptideShaker output into a log-file? I cannot find this information anywhere which makes it very tricky to identify the error when something is going wrong.

Maybe just capture all output to stdout and stderr from the python script?

jgriss commented 5 years ago

@veitveit I'll start working on that

veitveit commented 5 years ago

@jgriss Can that be moved to the LOG folder?

jgriss commented 5 years ago

@veitveit I've now put the location of the log file to "OUT/LOG"

Is that OK?

veitveit commented 5 years ago

Yes, and better :+1: