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

[Paolo Bizzarri]

My understanding is that the basic Java logging is typically perceived as
too limited.

I think it is really important to keep the dependecies of a package to a
bare minimum.

However, logging is such a fundamental feature for a library that I would
pay the price of a extra dependecy for a good package for logging.

slf4j could be a good choice.

Regards

Paolo


On Mon, May 26, 2014 at 4:45 PM, 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
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> > >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > >>>>
> > >>>
> > >>>
> > >>>
> > >>>
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