[MOBY-dev] Services in registry

[Edward Kawas]

Hi Ola,

> After trying to programmatically access several services I 
> turned to using the dashboard and found that there are many 
> in "default"  
> registry which answer with "Connection refused", "Operation 
> timed out" etc. Shouldn't the purpose of service discovery be 
> that you only discover available services? How does this 
> process work? Doesn't the registry poll (from time to time) 
> if services are available?
The registry does do such polling, but many of the clients do not use this
information yet. One client that does is gBrowse_moby
(http://mobycentral.icapture.ubc.ca/cgi-bin/gbrowse_moby)

For a list of services and whether they respond to a 'ping' (true/false),
try the following link:
http://mobycentral.icapture.ubc.ca:8090/authority/ValidateService

> 
> There are also some (I have tried several) services which 
> answer "Response could not be parsed", "(500)Internal Server 
> Error", and some respond with a stacktrace in the 
> moby:serviceNotes tag. 
I am not sure what services you tried, but one thing to keep in mind is that
most of the services require a namespace, in addition to the amino acid
sequence, and the service may fail ungracefully when one doesn't exist.

> Many services also have poor or 
> limited description, which makes it hard (almost impossible 
> for novice users) to interpret what they actually do. I guess 

This blame here lies with the people that register the services.
Unfortunately, the only option available to a user of these services would
be to contact the service provider and ask them to possibly update the
description to make it more descriptive.


> the solution to this is to require unit tests of a service 
> upon registration, which the server can test the service with 
> from time to time and make sure that it is operational. It 
> should at least be quite simple to just send e.g. a 
> predefined AminoAcidSequence to all services which accept 
> them as inputs and verify that you get a valid result back.
This is actually harder than it sounds. What does valid mean? A service may
return seemingly random data or nothing at all and still be considered
operational ...

> I am wondering how to use BioMoby in our rich client Bioclipse
> (www.bioclipse.net) at present. Is the resolution to set up 
> our own central repository which we manually curate? How can 
> I in that case synchronize this with the BioMoby registry but 
> only include services which are actually available and return 
> something useful (and omit all services meant for testing)?
One thing to try would be including only those services that link mentioned
above stated where 'alive'. This information is available in RDF/XML from
http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances, with the predicate
'isAlive'.


> How are things done for the different registries available in 
> the dashboard? Is it even possible for a person to document 
> someone else's services?
Not really. the only thing to do is email the service provider and ask them
to nicely update their descriptions. Unless of course you plan to host your
own moby registry. In that case, you could mirror the services (using a
variety of ways, but one would be using the RDFAgent and the RDF mentioned
above). You could edit the RDF document as much as you wanted and the
changes would appear in your clone. 

> 
> It is not my intention to sound negative. BioMoby looks 
> extremely promising and will be an integral part of our 
> project's future. Maybe I have just been unlucky with 
> choosing services for testing. Could someone give me a few 
> names of services which accept 1-2 AminoAcidSequence's and 
> are fully operational from the dashboard?
I found a few, of the ones that didn't work, I emailed the provider.
Inb.bsc.es
	searchInterPro, runEmboss(AntigenicFromSequence | ChargeFromSequence
| PepstatsFromSequence | PepstatswindowFromSequence | ...) 

(In dashboard, I sorted the services by input and attempted to run a few of
the ones under the branch 'AminoAcidSequence'), etc. 

I used the amino acid sequence: RFCFDRLCF 

> 
> Cheers,
> 
> Ola
> 

Thanks,

Eddie

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