[MOBY-dev] Decisions from the BioHackathon

[Pieter Neerincx]

Hi All,

This is very good news*4! Looks like it's been a fruitful event :).

Cheers,

Pi


On  13 Feb 2008, at 03:54, Mark Wilkinson wrote:

> Hi all,
>
> Since we have a quorum of the RFC committee here at the Open  
> BioHackathon, we've managed to make quite a few decisions, and  
> we're now in the process of coding them.
>
> Here are the decisions in a nutshell:
>
> 1)  The RFC from INB regarding mirroring of services was accepted  
> with a few changes.  We'll get a copy of the revised proposal from  
> Oswaldo in the next few days.  Apparently they have already coded  
> support for these changes at INB so it will quickly get into the  
> codebase.
>
> 2)  Moby will *immediately* start supporting document-literal  
> services.  These services will be identified using the "Category"  
> tag in the service registration/discovery XML.  Two new categories  
> will be "doc-literal" and "doc-literal-async".  Until we get better  
> support for document-literal services in Perl it is likely that  
> these will not be available to Perl clients, but apparently it's no  
> problem in Java.  Some considerations that arise from this are:   
> (a) you must now remove the XML header from your data if you're  
> using document-literal, and therefore (b) clients and services need  
> to specify the appropriate character encoding (e.g. UTF-8) in the  
> SOAP XML header.
>
> 3)  Sending data by reference:  we have decided to allow the  
> sending of data by reference rather than as the content of an  
> object.  We'll write-up the formal specification of how to do this  
> soon, but briefly the idea is that we will use the xlink XML  
> attribute in a Moby Object XML  <.... xlink=''/>.  When that tag is  
> present, it is assumed that the content of that node is available  
> at the URI in that reference.  During service registration a  
> provider will indicate the various transport protocols they provide  
> for creating references (e.g. http, ftp) and this will be  
> discoverable during a registry query.  If you don't indicate a  
> protocol, then you are saying that you do not support pass-by- 
> reference, and therefore all existing services are supported.  When  
> accessing a service, you indicate to the service provider that you  
> want data to be passed by reference by adding an attribute in the  
> mobyData block <mobyData acceptRefs="http ftp">.  The service  
> provider then has the option of providing you references for any  
> data they wish.  The xlink attribute can appear at any level in  
> your Moby object, such that some data may be passed in the object  
> itself, while other data from the same object may be passed by  
> reference.
>
> 4)  Validating services:  Moby will have several levels of  
> validation:  (1) ping, (2) does the service crash when accesed with  
> sample data?  (3)  does the service output the correct object  
> type?  (4)  does the service output data that validates against  
> XPath and/or REGEX.  The sample input data will be in the service  
> provider's RDF, and there will be several new predicates added to  
> the RDF (I'll provide the OWL file shortly that defines how these  
> predicates are to be used):  unit_test, example_input, valid_xpath,  
> valid_regex, valid_output_xml.  The validation of output XML will  
> be canonicalized (i.e. xmldiff, not byte-identity)
>
>
> Hackers - please correct me if I have mis-represented anything.   
> I'm working from Eddie's scribbled notes ;-)
>
> Hopefully we'll find time to document these changes between our  
> hacking sessions :-)
>
> Cheers all!  Greetings from Tokyo!
>
> Mark
>
>
>
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>

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