[Biojava-dev] How are we supposed to log errors?

[LAW Andy]

The “beauty" of slf4j is that it provides a logging framework that doesn’t impose any downstream restrictions or requirements and will actually insulate users from logging dependencies that come from other third-party libraries that you may include. It allows the end user to include the logging framework of their choice, defaulting to a NOP version if none is specified.


On 26 May 2014, at 15:45, Andreas Prlic <andreas at sdsc.edu> wrote:

> I am always reluctant to add additional jar dependencies to the project. Is the basic logging API that is part of Java sufficient?
> 
> Andreas
> 
> 
> 
> 
> On Mon, May 26, 2014 at 2:37 AM, LAW Andy <andy.law at roslin.ed.ac.uk> wrote:
> If I had a vote, then SLF4J (www.slf4j.org) would get it.
> 
> Later,
> 
> Andy
> 
> 
> On 26 May 2014, at 09:43, Spencer Bliven <sbliven at ucsd.edu> wrote:
> 
> > I wouldn't be opposed to using one of the standard logging apis in biojava
> > (apache log4j, for instance). The downside of this is that users would have
> > to include one of the implementation jars in their classpath, and failure
> > to do so leads to fairly opaque error messages.
> >
> > -Spencer
> >
> >
> > On Mon, May 26, 2014 at 8:21 AM, Paolo Bizzarri <pibizza at gmail.com> wrote:
> >
> >> Hi Andreas,
> >>
> >> it depends on the use case of biojava, I think - something that I don't
> >> know very well at the moment.
> >>
> >> If biojava is going to be used for short running processes with a limited
> >> output, you can clearly rely on the standard error for logging errors and
> >> exceptions.
> >>
> >> On the other side, if your process is a long running one, potentially
> >> producing lots of output, you do not want to miss any error just because
> >> things scroll up, or because you forgot to redirect your standard error to
> >> a file.
> >>
> >> I could provide a patch some of the System.out invocations to a logger, so
> >> that we can see how the code will work.
> >>
> >> What do you think?
> >>
> >> Regards.
> >>
> >> Paolo
> >>
> >>
> >>
> >>
> >> On Mon, May 26, 2014 at 7:17 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> >>
> >>> Hi Paolo,
> >>>
> >>> We don't have strict standards how to log throughout the code base. The
> >>> topic has come up on and off, but so far we have not agreed on any
> >>> convention.
> >>>
> >>> Andreas
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Sun, May 25, 2014 at 12:43 AM, Paolo Bizzarri <pibizza at gmail.com
> >>> wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> I am looking at the code inside
> >>>> org.biojava.bio.structure.align.util.AtomCache.
> >>>>
> >>>> I see that many times the code prints the stack trace on the standard
> >>>> error.
> >>>>
> >>>> I understand that in other parts of the code we use to a standard logger
> >>>> instead.
> >>>>
> >>>> Which of the two is the expected approach?
> >>>>
> >>>> Regards.
> >>>>
> >>>> Paolo
> >>>> _______________________________________________
> >>>> biojava-dev mailing list
> >>>> biojava-dev at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >>>>
> >>>
> >>>
> >>>
> >>>
> >> _______________________________________________
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> >>
> > _______________________________________________
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> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
> 
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> 
> 


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The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.