[MOBY-dev] Strange inconsistence (bug?) in MobyCentral

[Mark]

Hi Dmitry,

It's almost certainly a bug.  I wont be able to fix it for a few days,  
though, as I've got other deadlines to meet this week.

If you want to fix it yourself and commit (or send me) the fix that would  
be fine... but be very very careful because I know that those attributes  
are often used by other methods, so it may be that other routines are now  
coded to compensate for this bug!  :-P

otherwise, give me a week or so and I'll fix it myself.

Mark



On Tue, 07 Jul 2009 19:25:03 -0700, Dmitry Repchevsky  
<dmitry.repchevski at bsc.es> wrote:

> Hello,
>
> Trying to optimize a little bit my MobyCentral API I found a strange a
> thing:
>
> According the "specification"
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/XMLPayloads.html#retrieveObjectDefinition
>
> There are two ways to get the relationships for an object:
>
> first way is to get Relationships directly (through "Relationships"
> operation):
>
> Output:
>
>         <Relationships>
>            <Relationship relationshipType="RelationshipOntologyTerm1"
> 	   lsid='urn:lsid:authority.uri:namespace:id'>
>                 [ <objecctType lsid='...'  
> articleName='foo'>OntologyTerm</objectType> |
> 		<serviceType lsid='...'>OntologyTerm</serviceType> ]
>                        ...
>            </Relationship>
>            ...
>         </Relationships>
>
> This one I used to use...
>
> But there is another way using "retrieveObjectDefinition" method:
>
> Output:
>
>         <retrieveObjectDefinition>
>             <objectType  
> lsid='urn:lsid:authority.uri:namespace:id'>ObjectClassName</objectType>
>             <Description><![CDATA[
>                     human readable description
>                     of data type]]>
>             </Description>
>             <Relationship relationshipType="RelationshipOntologyTerm"
> 	    lsid='urn:lsid:authority.uri:namespace:id'>
>                <objectType articleName="SomeName"  
> lsid='urn:lsid:authority.uri:namespace:id'>ExistingObjectType</objectType>
>             </Relationship>
>             ...
>             <authURI>your.URI.here  
> <http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Authorities.html></authURI>
>             <contactEmail>owner at their.address.com</contactEmail>
>         </retrieveObjectDefinition>
>
>
> The problem is that instead of  
> [relationshipType="RelationshipOntologyTerm"] it returns lsid!!!
>
> Here is the output:
>
> <retrieveObjectDefinition>
>   <objectType  
> lsid='urn:lsid:biomoby.org:objectclass:Zip_Encoded:2007-11-16T11-34-07Z'>Zip_Encoded</objectType>
>   <Description><![CDATA[A Zip file encoded in Base-64.]]></Description>
>   <authURI>inb.bsc.es</authURI>
>   <contactEmail>romina.royo at bsc.es</contactEmail>
>
>   <Relationship  
> relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
>     <objectType articleName=''  
> lsid='urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z'>Object</objectType>
>   </Relationship>
>   <Relationship  
> relationshipType='urn:lsid:biomoby.org:objectrelation:hasa'>
>     <objectType articleName='rawdata'  
> lsid='urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z'>String</objectType>
>     <objectType articleName='mimeTypte'  
> lsid='urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z'>String</objectType>
>   </Relationship>
> </retrieveObjectDefinition>
>
> As far as I understand from the specification it should be:
>
> <Relationship relationshipType='ISA'  
> lsid='urn:lsid:biomoby.org:objectrelation:isa'>
>
> Could someone clarify please...
>
> Dmitry
>
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