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

[Spencer Bliven]

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
> >> _______________________________________________
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> >> biojava-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >>
> >
> >
> >
> >
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