[MOBY-dev] [MOBY-l] DataInputs for complex services

[Andreas Groscurth]

Hi Ola,

I answer for Paul, who had to answer me also that one :-)

Hi Andreas,

Yes, there is a class that allows you to cache these...

*org.biomoby.registry.meta.RegistryCache*

You can see how I use it in the source code for
*
ca.ucalgary.seahawk.gui.MobyContentGUI

*Though I should probably add a doc about that too :-)*

cheers
andreas

On Friday 10 August 2007 14:36, Ola Spjuth wrote:
> Thanks a lot Paul, that got me going.
>
> Another question:
> Is there a way to cache the data type and namespace ontologies and
> get rid of the annoying
>
> Fetching data type ontology from http://biomoby.org/RESOURCES/MOBY-S/
> Objects
>   ... done
> Fetching namespace ontology from http://biomoby.org/RESOURCES/MOBY-S/
> Namespaces
>
> which happens on every startup? Can I download the ontologies and
> tell jMoby where it is located locally?
>
> Cheers,
>
>     ../Ola
>
> On Aug 9, 2007, at 16:51 , Paul Gordon wrote:
> > Hi Ola,
> >
> > The key, if you are using the org.biomoby.shared.data package, is that
> > everything is a primitive, or a composite.
> > Composites are Java Maps, with member article names as the keys.  See
> > the examples below.  May I suggest, if you have
> > not already, to join the moby-dev mailing list, as the moby-l mailing
> > list is primarily for non-technical discussion
> > (I'm cross-posting this reply just in case you are not on moby-dev,
> > and
> > to show the moby-l-only folks that we are
> > doing real work ;-)).
> >
> >> Hello,
> >>
> >> Thanks for a great framework, I am excited to add BioMoby features to
> >> Bioclipse (http://www.bioclipse.net). However, I have some questions
> >> to get things running:
> >>
> >> How do I set up the PrimaryDataInput and SecondaryDatainputs for a
> >> more advanced service in jMoby?
> >> For example, the service 'runClustalwFast':
> >>
> >> MobyService templateService = new MobyService("runClustalwFast");
> >> MobyService[] validServices = worker.findService(templateService);
> >>
> >> This gives me the following info from the service:
> >>
> >> Primary inputs:
> >> Name: 'sequences' - DataType: 'GenericSequence'
> >
> > /** Here is the 'Generic' solution, untested and off the cuff */
> >
> > MobyDataComposite seq = new MobyDataComposite("GenericSequence");
> > for(MobyRelationship child: seq.getDataType().getAllChildren()){
> >   String childTypeName = child.getDataTypeName();
> >   // Things are either primitive, or composite
> >   if(PrimitiveType.isPrimitive(childTypeName)){
> >     seq.put(child.getName(),
> >                 MobyDataObject.createInstanceFromString(childTypeName,
> >
> > sourceDataStringForThisField));
> >   }
> >   else{
> >     // recursively populate the child as a MobyDataComposite
> >   }
> > }
> >
> >> Primary outputs:
> >> Name: 'alignment' - DataType: 'Clustalw_Text'
> >
> > You don't need to do anything, the service will populate this for
> > you (via MobyRequest.invokeService()).
> >
> >> Secondary inputs:
> >> Name: 'ktup' - DataType: 'Integer'
> >> Name: 'gapext' - DataType: 'Float'
> >> Name: 'transitions_weight' - DataType: 'Float'
> >> Name: 'window' - DataType: 'Integer'
> >> Name: 'topdiag' - DataType: 'Integer'
> >> Name: 'matrix' - DataType: 'String'
> >> Name: 'pairgap' - DataType: 'Integer'
> >> Name: 'endgaps' - DataType: 'String'
> >> Name: 'gapdist' - DataType: 'Integer'
> >> Name: 'gapopen' - DataType: 'Float'
> >
> >    public static void setSecondaries(MobyRequest mr, MobyService
> > service){
> >         MobySecondaryData[] secondaryData =
> > service.getSecondaryInputs();
> >         MobyDataSecondaryInstance[] secondaryInstances =
> >             new MobyDataSecondaryInstance[secondaryData.length];
> >
> >         for(int i = 0; i < secondaryData.length; i++){
> >             MobySecondaryData param = secondaryData[i];
> >             // Set specific values for the following param, just as an
> > example
> >             if(param.getName().equals("strand")){
> >                 secondaryInstances[i] = new
> > MobyDataSecondaryInstance(param, "Reverse");
> >             }
> >             // Use default value for other parameters (if any), is set
> > to the registered default value automagically
> >             else{
> >                 secondaryInstances[i] = new
> > MobyDataSecondaryInstance(param);
> >             }
> >         }
> >
> >         mr.setSecondaryInput(secondaryInstances);
> >     }
> >
> >> How do I set up the inputs with MobyDataObject's for this service?
> >> The sample clients in CVS only deal with simple setups (id and
> >> namespace) so some lines of example code would be really helpful.
> >>
> >> Another question: How can I from the MobyDataType tell what format I
> >> should expect to fill in? If it is 'GenericSequence', how can I tell
> >> if i'm supposed to add a String? Can I look that up somewhere?
> >
> > This is covered in the first example, mobyDataType.getAllChildren();
> >
> >> And do
> >> the MobyDataType's have constraints (like min/max values) etc?
> >
> > No, only Secondary parameters have constraints on values in Moby.
> >
> >> I have
> >> also not really understood the key-value-datatype. Is it possible to
> >> get the allowed keys from the MobyDataType in some way?
> >
> > Do you mean namespace/id?  You can get the list of valid namespaces
> > with
> > Central..|*getFullNamespaces
> > <http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/
> > org/biomoby/shared/Central.html#getFullNamespaces%28%29>*()|
> > .
> > There is no way to validate IDs except by submitting them to services
> > are seeing if they work.
> >
> > Hope this helps!
> >
> > -Paul
> >
> >> Cheers,
> >>
> >>     .../Ola Spjuth
> >>
> >>
> >>
> >>
> >> _______________________________________________
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> >>
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> >
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>
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-- 
Andreas Groscurth
Diplom Bioinformatik - PhD Student
Max Planck Institute for Plant Breeding Research
Carl-von-Linné-Weg 10
50829 Cologne
Germany
E-mail:    groscurt at mpiz-koeln.mpg.de
Phone:    +49(0)221-5062-447