fiji log goes to stderr

[atarkowska]

Would it be possible to correct logger level for the following commands?
Otherwise nextflow pipeline capture that as error

/opt/fiji/entrypoint.sh --update add-update-site PTBIOP http://biop.epfl.ch/Fiji-Update
/opt/fiji/entrypoint.sh --update update

seems to print to standard error of the system rather then out.

Updating the index of available files (Updating from ImageJ site: http://up...
Updating from ImageJ site: http://update.imagej.net/ done
...
Done: Checksummer

Updating the index of available files (Updating from ImageJ site: http://up...
Updating from ImageJ site: http://update.imagej.net/ done
...
Done: Checksummer

Downloading... (fiji-linux) 
...
plugins/JACoP_B-1.1.0.jar done
Done: Downloading...

Done: Downloading...

Temporarily I had to add >/dev/stdout 2>&1 to each command

[ctrueden]

It seems it has been that way for many years. See StderrProgress.

It was originally introduced here, but no explanation of the rationale for choosing stderr over stdout.

It is possible that changing it could break downstream projects, since people might be scraping the output. I also do not feel confident that stdout is a more "correct" choice than stderr for this purpose—there was probably a reason stderr was chosen. Since you already have a workaround—redirecting stderr to stdout—I'm in no hurry to make a change that entails effort without a clear technical benefit. But if this change would provide some tangible benefit, then we can do it.