Re: [Savannah-hackers] submission of BioDB - savannah.nongnu.org

[Dan Bolser]

Thanks very much, this is all clear now.

Is MySQL free software?

Cheers,
Dan.

On Sat, 23 Oct 2004, Michael Casadevall wrote:

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>The requirements for Savannah hosting for Java projects is that the  
>project must be free software and be licensed under a GPL-compatiable  
>license, and that everything the project requires can be used in a free  
>environment. Sun's Java license does not constitute a free (as in  
>speech) license. Basically, you must be able to compile and install in  
>a free environment. This also includes all JAR files your project uses.  
>If you can't compile the dependencies, error reports should be sent to  
>both the GCJ and the project's administrators.
>Michael
>
>On Oct 23, 2004, at 1:36 PM, Dan Bolser wrote:
>
>>
>> I think I emailed you the src code (for building the SCOP
>> database) already?
>>
>> I have a question about the .jar files included with the Prova
>> installation (not necessarily essential for this project). Basically I
>> would like to know if each .jar is OK to use at Savannah, i.e. if it is
>> 'free software'...
>>
>> Aside from looking for these (or equivalent) .jar files under the
>> Classpath project, is there a way to rapidly determine if the  
>> dependencies
>> are free software or not? i.e. compatible for use with a Savannah  
>> project
>> or not?
>>
>> I count 84 .jar files in total, including...
>>
>> ant.jar
>> commons-collections-2.1.jar
>> junit-3.8.1.jar
>> biojava.jar
>> j2ssh-core.jar
>> jade.jar
>> jms.jar
>> joram.jar
>> mandarax.jar
>>
>> Given what you have said below, would I have to check that every piece  
>> of
>> java code packaged with the project is compile-able using GCJ and  
>> runnable
>> under Kaffe (or equivalent free JVM)?
>>
>> Also I would like to know about how to deal with GCJ compile problems.
>> Should I report the problem to the specific code vendor (org/mandarax  
>> in
>> this case) or to GCJ mailing lists?
>>
>> Thanks very much for your help, and sorry for my lack of experience in
>> these issues,
>>
>> All the best,
>> Dan.
>>
>> On Tue, 19 Oct 2004, Michael McTails wrote:
>>
>>> I'm evaluating the project you submitted for approval in Savannah.
>>>
>>> You must determine whether your project and it's dependencies
>>> can run on a Free Software Java suite (see
>>> http://www.gnu.org/software/java/
>>> for more information).
>>>
>>> We recommend you to test your project using GCJ and GNU Classpath, and
>>> ensure that your Java code runs on this Free Software Java suite.
>>>
>>> GCJ is the GNU Compiler for Java, part of the GCC (GNU Compiler
>>> Collection).  The Classpath project aims to develop a free and  
>>> portable
>>> implementation of the Java API (the classes in the 'java' package).
>>>
>>> More information is available at http://gcc.gnu.org/ and
>>> http://www.gnu.org/software/classpath/,
>>>
>>> Furthermore, please include an (perhaps temporary)
>>> URL pointing to the source code. We wish to review your source code,
>>> even if it is not functional, to catch potential legal issues early.
>>> The description you gave whenregistering will not be read by the
>>> general public.
>>> If you are still concerned with privacy, however, you can forward the
>>> code to me by email
>>> address@hidden
>>>
>>> Please provide us with more information about this point.
>>>
>>>> A package was submitted to savannah.nongnu.org
>>>> This mail was sent to address@hidden,
>>>> address@hidden
>>>>
>>>>
>>>> Dan Bolser <address@hidden> described the package as
>>>> follows:
>>>> License: gpl
>>>> Other License:
>>>> Package: BioDB
>>>> System name: biodb
>>>> Type: non-GNU
>>>>
>>>> Description:
>>>> This project aims to produce very simple software to produce and
>>>> maintain a set
>>>> of biological databases in relational form. The software will  
>>>> download
>>>> text
>>>> versions of various databases, and produce a 'standardized'  
>>>> relational
>>>> version
>>>> of that database in tab delimited form, suitable for loading into any
>>>> relational database system (such as mysql).
>>>>
>>>> The standard versions of these databases can then form components of
>>>> other
>>>> projects.
>>>>
>>>> First, the SCOP databases will be 'processed'
>>>> (http://scop.mrc-lmb.cam.ac.uk/scop/) which is open access.
>>>>
>>>> We will then consider looking at ENZYME
>>>> (http://www.expasy.org/enzyme/),
>>>> SwissProt (http://us.expasy.org/sprot/) and GO
>>>> (http://www.geneontology.org/),
>>>> based on the evaluation of the licence.
>>>>
>>>> Initally Perl will be used.
>>>>
>>>> This rather simple project may form a test bed for the new  
>>>> experimental
>>>> software language, Prova.
>>>> http://osdn.dl.sourceforge.net/sourceforge/mandarax/ 
>>>> prova_all_1.7.1.zip
>>>>
>>>>
>>>>
>>>> Other Software Required:
>>>> Mandarax (http://mandarax.sourceforge.net/)
>>>> Prova (http://comas.soi.city.ac.uk/prova/)
>>>>
>>>> Other Comments:
>>>> I previously submitted this project some time last year. SCOP is  
>>>> freely
>>>> available and open source (the old licence has elapsed). Prova is
>>>> LPGL. The
>>>> code is trivial.
>>
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