OK to use GPLed class libraries in DNA sequencers ( was Re: [dna-dev] Required headers on all files)

Michael Neale michael.neale at gmail.com
Sun Jun 15 00:50:33 EDT 2008 

If you like antlr, you will love antlrworks. A graphical ui to debut  
and build you grammar. No need to fear wierd legacy text formats again.

Sent from my iPhone

On 14/06/2008, at 0:58, Randall Hauch <rhauch at redhat.com> wrote:

> I would like us to seriously consider Smooks.  I've not had any time  
> to take a look (other than reading some documentation), but it seems  
> very powerful and worth us understanding and leveraging.  Like you  
> said, it could provide a consistent solution for a number of  
> sequencers.  Great idea, Stefano!
>
> BTW, another pattern several sequencers will follow are those that  
> need to parse a grammar-based file, and I'd like those to use  
> ANTLR.  We're still investigating the first one (DNA-73), but the  
> goal is that we can use ANTLR grammar to create an abstract syntax  
> tree (AST) of the file, then an ANTLR tree grammar to transform the  
> AST into another AST that has the same structure as the sequencer  
> output graph.  Then, a common library would do the work of writing  
> that second AST into the SequencerOutput.  If we can do this, then a  
> sequencer would consist almost entirely of two ANTLR grammar files  
> in a Maven project.  (We could even create a Maven archetype that  
> would allow Maven to generate the stub of that project.)
>
> Best regards,
>
> Randall
>
> On Jun 13, 2008, at 9:46 AM, Gregory Haber wrote:
>
>> That is a great idea!  Especially since we are considering using it  
>> for
>> DNA-31, DNA-32, and DNA-33 - so it would give us a consistent  
>> solution
>> across a number of use cases.
>>
>> Are the developers assigned to those JIRAs (you for DNA-33 and Johnny
>> Verhaeg for DNA-31) still considering using Smooks?
>>
>> Thanks,
>>
>> Greg
>>
>> On Fri, 2008-06-13 at 08:59 +0200, Stefano Maestri wrote:
>>> Hi,
>>> why don't use smooks?
>>>
>>> http://milyn.codehaus.org/Smooks
>>>
>>> It could solve csv and a lot of other use case and it's LGPL. It's
>>> indeed a great toy.
>>>
>>> bye
>>> S.
>>>
>>> Gregory Haber wrote on 12/06/08 19:18:
>>>> Yeah, there are plenty of other alternatives - in particular,  
>>>> Apache
>>>> Commons project has one in the works:
>>>>
>>>> http://commons.apache.org/sandbox/csv/
>>>>
>>>> So there is not really a problem for implementing this specific
>>>> sequencer, this is more idle curiousity...no rush on finding the  
>>>> answer.
>>>> I asked one of the JBoss Developer Studio developers about this  
>>>> and he
>>>> thought that the answer was probably "no", unless they make a  
>>>> specific
>>>> GPL exception for linking(which they don't in this case).   
>>>> Otherwise I
>>>> think it pollutes the whole code base, forcing it all to be GPL.
>>>>
>>>> Regards,
>>>>
>>>> Greg
>>>>
>>>> On Thu, 2008-06-12 at 12:10 -0500, Randall Hauch wrote:
>>>>
>>>>> Greg:
>>>>>
>>>>> Have you looked at http://sourceforge.net/projects/javacsv/?  Are
>>>>> there other alternatives?
>>>>>
>>>>> On Jun 12, 2008, at 11:55 AM, Randall Hauch wrote:
>>>>>
>>>>>
>>>>>> Greg:
>>>>>>
>>>>>> I don't know the answer to that.  I know we're using some  
>>>>>> projects
>>>>>> with MIT or Apache license, but no GPL to date (that I'm aware  
>>>>>> of).
>>>>>> I'll look into it and get back to you.  (Unless someone else on  
>>>>>> the
>>>>>> list already knows.)
>>>>>>
>>>>>> Randall
>>>>>>
>>>>>> On Jun 12, 2008, at 11:47 AM, Gregory Haber wrote:
>>>>>>
>>>>>>
>>>>>>> Hi Randall,
>>>>>>>
>>>>>>> I've made a first pass at DNA-105 (delimited text sequencer).   
>>>>>>> In
>>>>>>> it I
>>>>>>> use the Ostermiller Utils classes
>>>>>>> (http://ostermiller.org/utils/download.html) to do the  
>>>>>>> delimited text
>>>>>>> parsing.
>>>>>>>
>>>>>>> Before I do any more work on it (and "officially" pick it up  
>>>>>>> from the
>>>>>>> JIRA queue), though, it occurred to me - these classes are  
>>>>>>> GPL, where
>>>>>>> DNA is LGPL.
>>>>>>>
>>>>>>> Is it OK to build sequencers using class libraries that are  
>>>>>>> GPL? or
>>>>>>> do
>>>>>>> they need a less restrictive license like LGPL or Apache?
>>>>>>>
>>>>>>> It isn't a problem to implement this individual connector  
>>>>>>> (there are
>>>>>>> lots of good delimited text parsing classes out there under a
>>>>>>> variety of
>>>>>>> licenses - and although this is something I could do myself,  
>>>>>>> this
>>>>>>> parsing is actually a lot more difficult a problem than it  
>>>>>>> appears
>>>>>>> initially, so I would prefer not to do it), but I was curious  
>>>>>>> as to
>>>>>>> whether using GPLed libraries is OK.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Greg
>>>>>>>
>>>>>>> On Tue, 2008-06-10 at 16:58 -0500, Randall Hauch wrote:
>>>>>>>
>>>>>>>> Please make sure that add the correct JBoss header to all  
>>>>>>>> files in
>>>>>>>> JBoss DNA.  We're not being consistent with our commits, so  
>>>>>>>> please
>>>>>>>> go
>>>>>>>> through code you've recently created and make the appropriate
>>>>>>>> changes.
>>>>>>>>
>>>>>>>>
>>>>>>>> The easiest way to do this is to set up your development  
>>>>>>>> environment
>>>>>>>> to automatically add the following header to all Java classes:
>>>>>>>>
>>>>>>>>
>>>>>>>> /*
>>>>>>>> * JBoss, Home of Professional Open Source.
>>>>>>>> * Copyright 2008, Red Hat Middleware LLC, and individual
>>>>>>>> contributors
>>>>>>>> * as indicated by the @author tags. See the copyright.txt  
>>>>>>>> file in
>>>>>>>> the
>>>>>>>> * distribution for a full listing of individual contributors.
>>>>>>>> *
>>>>>>>> * This is free software; you can redistribute it and/or  
>>>>>>>> modify it
>>>>>>>> * under the terms of the GNU Lesser General Public License as
>>>>>>>> * published by the Free Software Foundation; either version  
>>>>>>>> 2.1 of
>>>>>>>> * the License, or (at your option) any later version.
>>>>>>>> *
>>>>>>>> * This software is distributed in the hope that it will be  
>>>>>>>> useful,
>>>>>>>> * but WITHOUT ANY WARRANTY; without even the implied warranty  
>>>>>>>> of
>>>>>>>> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See  
>>>>>>>> the GNU
>>>>>>>> * Lesser General Public License for more details.
>>>>>>>> *
>>>>>>>> * You should have received a copy of the GNU Lesser General  
>>>>>>>> Public
>>>>>>>> * License along with this software; if not, write to the Free
>>>>>>>> * Software Foundation, Inc., 51 Franklin St, Fifth Floor,  
>>>>>>>> Boston, MA
>>>>>>>> * 02110-1301 USA, or see the FSF site: http://www.fsf.org.
>>>>>>>> */
>>>>>>>>
>>>>>>>>
>>>>>>>> We also have to add it to all property files:
>>>>>>>>
>>>>>>>>
>>>>>>>> #
>>>>>>>> # JBoss, Home of Professional Open Source.
>>>>>>>> # Copyright 2008, Red Hat Middleware LLC, and individual
>>>>>>>> contributors
>>>>>>>> # as indicated by the @author tags. See the copyright.txt  
>>>>>>>> file in
>>>>>>>> the
>>>>>>>> # distribution for a full listing of individual contributors.
>>>>>>>> #
>>>>>>>> # This is free software; you can redistribute it and/or  
>>>>>>>> modify it
>>>>>>>> # under the terms of the GNU Lesser General Public License as
>>>>>>>> # published by the Free Software Foundation; either version  
>>>>>>>> 2.1 of
>>>>>>>> # the License, or (at your option) any later version.
>>>>>>>> #
>>>>>>>> # This software is distributed in the hope that it will be  
>>>>>>>> useful,
>>>>>>>> # but WITHOUT ANY WARRANTY; without even the implied warranty  
>>>>>>>> of
>>>>>>>> # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See  
>>>>>>>> the GNU
>>>>>>>> # Lesser General Public License for more details.
>>>>>>>> #
>>>>>>>> # You should have received a copy of the GNU Lesser General  
>>>>>>>> Public
>>>>>>>> # License along with this software; if not, write to the Free
>>>>>>>> # Software Foundation, Inc., 51 Franklin St, Fifth Floor,  
>>>>>>>> Boston, MA
>>>>>>>> # 02110-1301 USA, or see the FSF site: http://www.fsf.org.
>>>>>>>> #
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
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