[MOBY-l] Re: [Mygrid-developers] "BioMoby in Java" updated

[Alan Robinson]

Hi Martin,

I've been having a first go at using the Java "MobyCmdLineClient" tool.

I can use it to easily get a view of the different service names, types
providers, names spaces, data types & WSDL, as well as search on keywords
('-f') & service types ('-ft').

However, I'm having trouble with the other find options (apart from '-f' &
'-ft'), e.g. the '-fs-in' option to query services by their inputs didn't
work as I expected. It seemed whatever valid values(*) I put in, I just
got back a list of services that had no inputs specified.

(*) Actually I'm having trouble figuring out what are valid data type &
    authority value combinations.

> java MobyCmdLineClient -fs-in GO_Term=GO/Acc
Looking for services with the following pattern:
Name:     dummy
Type:
Category: moby
Auth:
Desc:
URL:
ID:       null
Inputs:  GO_Term (GO/Acc)
Outputs:
-----------------------------------------------
Name:     retrieveGOannotations
Type:     Retrieve
Category: moby
Auth:     www.arabidopsis.org
Desc:     Retrieval of Sequences that are annotated to a specific GO term
URL:
ID:       null
Inputs:
Outputs: Sequence

Name:     Servicetest2
Type:     Retrieve
Category: moby
Auth:     illuminate.com
Desc:     this is a test
URL:
ID:       null
Inputs:
Outputs: Object

[...]

Also the following:

> java MobyCmdLineClient -f illuminae.com-Servicetest_22
Looking for services related to: 'illuminae.com-Servicetest_22':
--------------------------------
Name:     Servicetest_22
Type:     Retrieve
Category: cgi
Auth:     illuminae.com
Desc:     this is a test
URL:
ID:       null
Inputs:
Outputs: illuminae.com-Servicetest_22


But if I search on that output type with 'java MobyCmdLineClient -fs-out
illuminae.com-Servicetest_22', I don't get any hits.

Also 'java MobyCmdLineClient -fs-auth illuminae.com' didn't return any
hits.

I haven't looked at the source yet - At which point things may be clearer.


Alan.


--
============================================================
Alan J. Robinson, D.Phil.             Tel:+44-(0)1223 494444
European Bioinformatics Institute     Fax:+44-(0)1223 494468
EMBL Outstation - Hinxton             Email:  alan at ebi.ac.uk
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD, UK                http://industry.ebi.ac.uk/~alan/
============================================================

On Mon, 3 Mar 2003, Martin Senger wrote:

> Dear Moby-users,
>    I have updated Java client accessing the Moby registry. The clients are
> available for download and playing with normally from the BioMoby CVS, but
> also separately from a convenient distribution package.
>    Please see details in the updated documentation. Before it appears on
> the main BioMoby homepage, you can find it also at
> http://industry.ebi.ac.uk/~senger/jMoby/.
> 
>    I am looking forward for any comments, suggestions and bug reports.
> 
>    Martin
> 
> -- 
> Martin Senger
> 
> EMBL Outstation - Hinxton                Senger at EBI.ac.uk     
> European Bioinformatics Institute        Phone: (+44) 1223 494636      
> Wellcome Trust Genome Campus             (Switchboard:     494444)
> Hinxton                                  Fax  : (+44) 1223 494468
> Cambridge CB10 1SD
> United Kingdom                           http://industry.ebi.ac.uk/~senger
> 
> 
> 
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