[moby] Re: [MOBY-dev] Migration of database to new API

Fri Oct 7 09:16:23 UTC 2005

On 6-Oct-2005, at 6:08 PM, Mark Wilkinson wrote:

> As you have noticed, the change has already happened at the code level
> just to prevent any more registrations of what will soon be illegal
> objects.

That would be fine, but I have upgraded my service and objects to  
conform to the new standard and can not register legal stuff :(.

> I have a script that will update the database records of the
> ontologies and deprecate the old nodes, but we haven't yet run it  
> on the
> public registry.  Eddie is going to make a couple of changes to it  
> over
> the next day or two, and then will send out a heads-up that the
> ontologies are changing forever, and a tutorial on how to do the  
> update
> for service providers.  We'll give a reasonable amount of time for
> people to update their services (say, 6 weeks) and then we will delete
> the old nodes from the ontology completely.  The script is in the  
> CVS so
> anyone running a registry can do the same thing.

I'll run that script on my local central to see if I can register  
after the change.

>
> When I went to update my own services it took me less than 5  
> minutes to
> do so, so 6 weeks should be more than enough time for anyone who is
> actively concerned about their service :-)

IMHO it might be even a bit too much. Personally I opt for

2)  If we change to _2 temporarily, deprecate, delete, and then rename
the _2's back again after 6 weeks:
      with:
         i) update their services and NOT re-register, and
         ii) their services will be "illegal" for 6 weeks,

This keeps the ontology clean. This change was announced long enough  
ago to give people a chance to update their services. For me it took  
even less time. I didn't have to update my services at all. When I  
extract for example text from a CustomObject ISA String object I was  
already assuming it would not have any HASA relations, because it is  
a primitive. So I was getting the text from that node and any childs  
it might have. After the change, if my service fetches text from  
CustomObject I get the text from it's HASA String. No recoding  
needed; painless change :). I did spend the 5 minutes though on the  
scripts I use to register my services at a central.

Anyway, for the DateTime primitive things are still a bit strange.  
Currently DateTime ISA String ISA Object. All other primitives are  
simply ISA Object. This will change to DateTime ISA Object and HASA  
String. According to the spec DateTime shouldn't have a String,  
because it is by itself already a primitive... In the current  
situation DateTime is not a primitive, but just yet another type of  
String.

just my 2c,

Pi

>
> Cheers!
>
> M
>
>
>
> On Thu, 2005-10-06 at 17:32 +0200, Pieter Neerincx wrote:
>
>> On 27-Aug-2005, at 12:20 AM, Mark Wilkinson wrote:
>>
>>
>>> Hi all,
>>>
>>> As we move toward deploying the new API, there are some serious
>>> consequences on the underlying databases.
>>>
>>> Let me first re-cap the new API features that I am discussing and  
>>> what
>>> effects they have on the databases:
>>>
>>> 1)  Inheritence from primitives through ISA relationships is no  
>>> longer
>>> allowed.  e.g. plain-text ISA String  is no longer allowed.  To
>>> achieve
>>> the same result, you now create an object that inherits from Object
>>> and
>>> contains the primitive.  e.g. plain-text ISA Object; plain-text HASA
>>> String.
>>>
>>
>> Hi Mark et al.,
>>
>> Any idea when this change will happen? If I look in the Central that
>> is running the latest and greatest codebase, the forbidden ISA [some
>> primitive] relationships are still in place :(. What is even worse is
>> that the primitive DateTime ISA String. As a result I can not get one
>> of my Objects (that plays by the rules of the latest specs)
>> registered. At least I suspect this to be the problem. I don't get an
>> error message when register my object, but it has amongst others a
>> HASA DataTime and that relationship is not getting registered...
>>
>> Cheers,
>>
>> Pi
>>
>>
>>
>>
>> Wageningen University and Research centre (WUR)
>> Laboratory of Bioinformatics
>> Transitorium (building 312) room 1034
>> Dreijenlaan 3
>> 6703 HA Wageningen
>> The Netherlands
>> phone: 0317-483 060
>> fax: 0317-483 584
>> mobile: 06-143 66 783
>> pieter.neerincx at wur.nl
>>
>>
>>
>> _______________________________________________
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>>
> -- 
> "Ontologists do it with the edges!"
>
> Mark Wilkinson
> Asst. Professor
> Dept. of Medical Genetics
> University of British Columbia
> PI in Bioinformatics
> iCAPTURE Centre
> St. Paul's Hospital
> Rm. 166, 1081 Burrard St.
> Vancouver, BC, V6Z 1Y6
> tel: 604 682 2344 x62129
> fax: 604 806 9274
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at biomoby.org
> http://www.biomoby.org/mailman/listinfo/moby-dev
>

Wageningen University and Research centre (WUR)
Laboratory of Bioinformatics
Transitorium (building 312) room 1034
Dreijenlaan 3
6703 HA Wageningen
The Netherlands
phone: 0317-483 060
fax: 0317-483 584
mobile: 06-143 66 783
pieter.neerincx at wur.nl