[MOBY-dev] Changes in the 0.86API

[Martin Senger]

> 1)  *all* parameters going into a service must now be named (currently using the
> articleName attribute of the Simple/Collection/Parameter tag, but I want to
> migrate this to componentName if possible)
>
   Generally it is a good idea (to have things named). I also remember
that we had asked for in in Vancouver. But the change, even though may not
be big in the code, is big in the documentation, in the API description. I
would rather see first an updated API documentation, read it and only then
have here a discussion about it. This is mainly we used the name 'article'
not only as an XML attribute, but we had/have also an XML tag called
'secondaryArticle', we often speak about 'parameters' (as you just done
above) but we mean by that actually all input data... and so on.
   Other issue is that the biomoby.org now has API086 from the August
3. But it does not have the changes described in your last email - and the
email is labeled 'changes in the 0.86' - so you are actually describing
changes that will be in 0.87API? I am confused... The normal practice -
which I strongly suggest - is to keep on biomoby.org an API which works
currently - and to have a separate page, where we can see 'proposed API' -
which is not yet implemented, even it is not yet approved by us/developers
and it serves for these discussions. I know that it is boring to keep docs
updated but that is one of the issues we discussed in V. when we said that
the current biomoby does not have enough of the 'project management' :-)
   Back to article names: I remember that in Malaga the ICN people had
talked about their incoming proposal for more decent error handling in
biomoby messages. For that, the article names were mandatory (so it is
good that we are thinking about it in the same way) - but I think that
they wanted to name also individual Simples in Collection. So it may be
worth to make sure that they are listening now...
 
> 2)  Inheritence from primitive classes is now forbidden and this is enforced by
> the MOBY Central code.
>
   Again, this need to be documented first...
 
> 4)  a new method "retrieveResourceURLs" has been added to the API that provides
> you with a list of the URLs from which you can retrieve the RDF versions of all
> of the ontologies.
>
   Here comes my previous email (send only to Mark) about how to make
these (BIG) RDF documents compressed. One solution is to allow registry
providers to specify two URLs for each resource type, one for normal and
one for zipped document.
 
> I will be moving the production server to the new codebase next week sometime.
> 
   No, don't do it so soon... Please... Describe it first in the API in
details...

   Martin

-- 
Martin Senger    martin.senger at gmail.com

International Rice Research Institute
Biometrics and Bioinformatics Unit
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