[Biojava-dev] How are we supposed to log errors?
LAW Andy
andy.law at roslin.ed.ac.uk
Mon May 26 09:37:40 UTC 2014
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
>>>>
>>>
>>>
>>>
>>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
More information about the biojava-dev
mailing list