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

[Andreas Prlic]

ok, slf4j has been suggested here before, so I take this as a clear vote
towards starting to use that. Anybody opposed to this?

We have an empty wiki page for this topic already
http://www.biojava.org/wiki/BioJava3_logging

Anybody willing to add some docu and recommendations for how to use it?

Andreas




On Mon, May 26, 2014 at 11:35 AM, Paolo Bizzarri <pibizza at gmail.com> wrote:

> 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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