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Re: [Gmod-architecture] [Gmod-schema] stag-storenode.pl for Chado CRUD

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Re: [Gmod-architecture] [Gmod-schema] stag-storenode.pl for Chado CRUD

Chris Mungall
I'm cc-ing gmod-arch, I'm not sure if that group is already subsumed by gmod-schema

DBStag does implement the original XORT specification for updates, but not deletes:

        http://search.cpan.org/~cmungall/DBIx-DBStag/DBIx/DBStag.pm#Operations

 I don't know if this would be sufficient for your purposes.

I would recommend all newer GMOD software goes a more conventional ORM route:

* For java, hibernate, using something like the GSOL layer (I don't recall if this covers the nd module, it could be extended quite easily I imagine)
* For perl, Bio::Chado::Schema



On Jan 23, 2012, at 12:29 PM, Scott Cain wrote:

> Hi Bob,
>
> I'm certainly agree that a delete and reload is ugly!  I'm honestly
> not sure about stag-storenode and deletes.  I've cc'ed Chris Mungall
> in hopes that he can shed some light.  I also cc'ed Naama Menda; she
> wrote an ontology loader/updater based (I'm pretty sure) on
> Bio::Chado::Schema, so she may have some useful advice on how to
> proceed.
>
> Scott
>
>
> On Thu, Jan 19, 2012 at 6:53 PM, Bob MacCallum
> <[hidden email]> wrote:
>> Hi,
>>
>> We have some Bio::Chado::Schema/DBIx::Class code for doing a one-shot
>> load of natural diversity data into Chado from "master" tab delimited
>> files (ISA-Tab and Phenote - chosen for their GUI editors).
>>
>> Now I'm looking at making this more sophisticated - loading the same
>> (but potentially edited) files again should update/create/delete as
>> necessary.  The alternative would be delete and reload - but this just
>> seems nasty to me.
>>
>> I'm wondering if creating Chado-XML and using stag-storenode.pl is the
>> way to go.  The script handles all the deletes and updates already,
>> doesn't it?  That would save me a lot of wheel reinventing.  I've
>> looked but can't find any DBIC modules to help with the task of
>> cascading update_or_create (_or_delete) - have I missed something?
>>
>> Grateful for any thoughts on the matter!
>>
>> cheers,
>> Bob.
>>
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>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research


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