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

[LAW Andy]

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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