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

[Jose Manuel Duarte]

Agree, slf4j sounds like the best choice.

Jose



On 26/05/14 16:57, LAW Andy wrote:
> The “beauty" of slf4j is that it provides a logging framework that doesn’t impose any downstream restrictions or requirements and will actually insulate users from logging dependencies that come from other third-party libraries that you may include. It allows the end user to include the logging framework of their choice, defaulting to a NOP version if none is specified.
>
>
> On 26 May 2014, at 15:45, 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
>>>>>> _______________________________________________
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>>>>>>
>>>>>
>>>>>
>>>>>
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