[MOBY-dev] data by reference - a request for comments

[Pieter Neerincx]

Hi José,

I don't understand how references could be security risk. And if they  
do why the level at which you could use them would impact security.  
Could you please explain?

If references to mobyData blocks are not an option having at least  
references to BioMoby articles would already be a big help.  
Secondaries are usually very small so I wouldn't need / use references  
there, but for primary Simple and especially for primary Collection  
articles it would be a big plus!

Cheers,

Pi

On 23 Jul 2008, at 19:47, José María Fernández González wrote:

> IMHO it can be dangerous for the MOBY payload integrity using  
> XInclude at mobyContent childs (mobyData) level, but it can be  
> needed in scenarios like the one described by Pieter. For security  
> reasons, XInclude / XLink / XPointer should be restricted to the  
> contents of mobyData, not to MOBY Data itself. For instance,  
> references to Simples or Collections, Collections composed by a  
> mixure of Simples and references to Simples, or Secondary parameters  
> copied from run to run.
>
> 	Best Regards,
> 		José María
>
> Mark Wilkinson wrote:
>> On Wed, 23 Jul 2008 08:06:38 -0700, Pieter Neerincx <pieter.neerincx at gmail.com 
>> > wrote:
>>> That doesn't sound very appealing to me. I use quite large data  
>>> structures and can have tens of thousands of them in a collection  
>>> (think of oligos for micro arrays.) If I can only replace the  
>>> primitives with references, I would still have to send a BioMoby  
>>> XML structure with hundreds of thousands of references replacing  
>>> the primitives.
>> Hmmm... that's a situation that we had NEVER considered!  Putting  
>> xlinks into a component of the Moby message higher than the  
>> mobyData block was not a scenario that came up during our  
>> discussions in Tokyo.  the xlink was really only intended to carry  
>> data, not data + moby message structure...  but I suppose it COULD!
>> How do others feel about this?
>> M
>
> -- 
> "There is no reason why anybody would want a computer in their home" -
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>
> "Premature optimization is the root of all evil." - Donald Knuth
>
> José María Fernández González
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