Re: [Gusdev-gusdev] Re: plugin for XML

[Terry C. <tw...@cs...>]

>  - would this be able to work for the more common, non-trivial case 
> where the object models differ more significantly?  Angel has done a lot 
> of thinking about this for his object mapper which maps MAGE-ML into GUS.

I'm looking forward to hearing Angel's comments. The mapper I'm proposing
targets XML schema to relational schema (and GUS Objects). 
I have used the notation only for simple schemas, but
Bourret describes the method as a complete mapping from W3C XML schemas 
to relationl schemas.
    http://www.xml.com/pub/a/2001/05/09/dtdtodbs.html
    http://www.rpbourret.com/xml/SchemaMap.htm
The simplicity of the notation is a plus for error and overhead
reduction in writing mappings. 


>  - will you go directly to SQL or will you go to gus objects?  In a 
> simple case like this, it might make sense to go to SQL for efficiency 
> reasons, if you are expecting huge inputs.

It seems preferable to go to GUS objects through the object layer to enforce 
adherence to GUS policies.  Basically, I see this mapper plugin approach as 
a front end to the object layer driven by XML-to-DB maps (supplied in XML files) 
that are intrepretted by the plugin to map into the GUS object model.
Our inputs will not be larger than what GuS has used in other projects I think,
but the SQL route could be a good way to go -- I'm not clear on the tradeoffs.


>  - is the power offered by Bourret's transformer sufficient to justify 
> us packaging his product with the GUS distribution, which is what we 
> would probably have to do if we write certified plugins that use it.

I did not plan to use the existing XMLtoDBMS transformer, in part because
I'm thinking along the lines of mapping to GUS objects, not DB-SQL, so the
backends would be different.  Instead the plan is to write a  mapper in the 
GUS universe using code fragments as possible from existing work 
by Nick Semenov, who wrote the Perl port of the Java code. 
Maybe it will be possible to lightly hack XML::XMLtoDBMS and change the backend.
I plan to look carefully at Semenov's package, which I have used but did not analyze.


>  - what other third-party software (eg, xml parsers) does bourret 
> depend on?

The Perl module XML::XMLtoDBMS uses XML::Parser::PerlSAX;



>  - since the transform in the case you are handling is so simple, does 
> it make sense to deploy a third-party transformer rather than just write 
> some simple brute force perl code

The mappings are simple, but there are many of them. Another example
on our end is the retroelement database we are planning for GUS.
The retroelements will use several tables in addition to NASequeneImp. 
Without a general strategy, we would need to craft yet another plugin. 
On the other hand, the XML-to-GUS mapping approach would handle this readily, 
making for a swift, general-purpose implementation of the retroelement plugin.

One could conceivably use a single plugin for both our current task (unanchored sequences)
and the retroelement database. It seems though that the idiosyncracies of GUS objects
and objects built on GUS objects calls for separate plugins of this type (mappers).


Terry





On  0, Steve Fischer <st...@pc...> wrote:
> Terry-
> 
> In general, schema transformation is a hard problem.  It looks like, in 
> the immediate case, the transform from the agave sequence file to gus is 
> relatively simple:  a one-to-one transform of a single data type, but 
> requiring mapping some foreign keys.  It seems that Bourret's XML-DBMS 
> can handle this gracefully.
> 
> What i am not clear on is:
>  - would this be able to work for the more common, non-trivial case 
> where the object models differ more significantly?  Angel has done a lot 
> of thinking about this for his object mapper which maps MAGE-ML into GUS.
>  - will you go directly to SQL or will you go to gus objects?  In a 
> simple case like this, it might make sense to go to SQL for efficiency 
> reasons, if you are expecting huge inputs.
>  - is the power offered by Bourret's transformer sufficient to justify 
> us packaging his product with the GUS distribution, which is what we 
> would probably have to do if we write certified plugins that use it.
>  - since the transform in the case you are handling is so simple, does 
> it make sense to deploy a third-party transformer rather than just write 
> some simple brute force perl code
>  - what other third-party software (eg, xml parsers) does bourret 
> depend on?
> 
> In sum, i think it is an excellent idea to consider third party 
> solutions, and to provide general solutions instead of one-off plugins. 
> I also want to make sure that the extra effort we put into making this a 
> general solution will have a comensurate payoff.
> 
> steve
> 
> 
> Terry Clark wrote:
> 
> >Posted for discussion at 
> >   http://flora.uchicago.edu/ 
> >is a short specification  sketched (working draft) 
> >for an XML-to-GUS Plugin for GUS' NASequenceImp, LoadSeqFromXML.pm.
> >
> >The idea, based on the XML to DB/SQL work by Ron Bourret,
> >is to give a flexible way to map various sequence
> >data management projects into GUS using the same source.
> >The Plugin operates from 1) an XML formatted sequence file
> >and 2) a mapping from the sequence file to GUS space. 
> >
> >The method is generally applicable to GUS objects/tables,
> >but the idiosyncracies of objects probably calls for
> >individual mappers, like  LoadSeqFromXML.pm 
> >(better named as LoadNASequenceFromXML.pm).  
> >
> >Are there any thoughts, variations, existing work, etc.,
> >about the idea?
> >
> >Terry
> > 
> >
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> Data Reports, E-commerce, Portals, and Forums are available now.
> Download today and enter to win an XBOX or Visual Studio .NET.
> http://aspnet.click-url.com/go/psa00100003ave/direct;at.aspnet_072303_01/01
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev