[MOBY-dev] more on graphs

[Rebecca Ernst]

Hi Martin and Mark!

If I understand it right the graphic should connect two services if one 
service uses as input the output of another service. I just had a look 
at the cgi-client (sorry mark but there it's easy to see !).  I executed 
get AGICodeByKeyword and then getSequenceByAGI. That gives me a 
ProteinSequence. With this in hand the cgi-client offers me the services 
that can deal with this (e.g. Blast it). So I expect a connection 
between getSequenceByAGI and that Blast-Service.

There is no such connection in the graphic. Why? does it have to do with 
missing namespaces or with collection/simple (the problems you discussed 
before) ?

Rebecca.

Martin Senger wrote:

>Mark,
>   I have the second version of graphs.
>
>   The data types graph got better arrow symbols (those used in the UML,
>at least I hope I got it right):
>   http://industry.ebi.ac.uk/~senger/jMoby/images/data-types-newer.png
>
>   The services graph looks worse. That's why I am asking if it is
>correct, or not. The main problem is with services getGoTermAssociations
>and PBI_Cluster_Blast because they do not specify any namespaces for their
>input and output. Therefore they are connected with many services that
>have just 'Object'.
>   This is the question I am asking:
>   * if a service claims that it has an input of type "X" but does not
>define any namespace for it, then any service with output of type "X",
>even if specified with some namespaces, can connect to it?
>   * or the true is rather that services with a missing namespace in their
>input/output data can matched again only with services with missing
>namespaces (with the corresponding data types, of course)?
>
>   Please let me know, I will continue to work on it asap.
>
>   BTW, it's a pity that the API does not support yet the retrieving of
>the full ServiceType object. If you add it there (as mentioned for the
>future in the API documentation) I can easily add yet another graph
>displaying the tree of service types.
>
>   Regards,
>   Martin
>

-- 
Rebecca Ernst
MIPS, Inst. for Bioinformatics
GSF Research Center for Environment and Health
Ingolstaedter Landstr. 1
85764 Neuherberg
fon: +49 89 3187 3583
email: Rebecca.Ernst at gsf.de