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

[Dan Bolser]

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.