[MOBY-dev] Problems with http://biomoby.org/RESOURCES/MOBY-S/Objects

[Andreas Groscurth]

hi,

mhm...

running it from the parser it also works for me... the following not:

public class TestMoby {
    public static void main( String[] args ) throws Exception {
       Central central =  new CentralCachedCallsImpl( );
       MobyService mobyService = new MobyService();
       mobyService.setCategory("");
       mobyService.setAuthority("arabidopsis.info");
       mobyService.setName("NASCArraysGeneswingerByAGI");
       mobyService = central.findService(mobyService)[0];
       
       MobyRequest request = new MobyRequest( central );
       request.setService( mobyService );
       request.setInput( new MobyDataObject( "AGI_LocusCode", "At2g21050" ) );
       
       MobyContentInstance contentInstance = request.invokeService();
    }
}

First it takes a eternity to get the data types - maybe this is just a current 
(and also a local) issue, but thats the feeling i get, compared to the calles 
some weeks ago.

Second - this is the output I get:
 Fetching data type ontology from http://biomoby.org/RESOURCES/MOBY-S/Objects
Cannot parse MOBY Service Type Ontology: java.lang.NullPointerException
java.lang.NullPointerException
	at 
org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF(DataTypeParser.java:182)
	at org.biomoby.shared.MobyDataType.loadDataTypes(MobyDataType.java:103)
	at org.biomoby.shared.MobyDataType.getDataType(MobyDataType.java:144)
	at org.biomoby.shared.data.MobyDataObject.<init>(MobyDataObject.java:78)
	at org.biomoby.shared.data.MobyDataObject.<init>(MobyDataObject.java:73)
	at test.TestMoby.main(TestMoby.java:28)
Fetching namespace ontology from 
http://biomoby.org/RESOURCES/MOBY-S/Namespaces
There are 1 collections in response 1
Fetching data type ontology from http://biomoby.org/RESOURCES/MOBY-S/Objects

So - the namespaces are apparently ok - but it keeps trying to get the data 
types.... and always ends up in the Nullpointer.

Any ideas?
thanks
andreas


On Monday 26 November 2007 15:22, Edward Kawas wrote:
> Hi Andreas,
>
> I cannot reproduce this error. I have tried running the 'main' for each of
> the classes in the package org.biomoby.shared.extended and each of them
> worked ...
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: November-26-07 6:05 AM
> To: Core developer announcements
> Subject: [MOBY-dev] Problems with
> http://biomoby.org/RESOURCES/MOBY-S/Objects
>
> Hi,
>
> I'm using CentralCachedCallsImpl to send calls to the Central.
>
> The first time i'm calling it it collects the service types from the url
> http://biomoby.org/RESOURCES/MOBY-S/Objects
>
> For the last months this worked fine, but as I tried to today i receive
> error
> by error:
>
> Cannot parse MOBY Service Type Ontology:
> com.hp.hpl.jena.shared.JenaException:
> rethrew: ARP interrupted
> 15:00:48,230 ERROR [STDERR] java.io.InterruptedIOException: ARP interrupted
> 15:00:48,231 ERROR [STDERR]     at
> com.hp.hpl.jena.rdf.arp.WrappedException.throwMe(WrappedException.java:74)
> 15:00:48,231 ERROR [STDERR]     at
> com.hp.hpl.jena.rdf.arp.ARPFilter.parse(ARPFilter.java:316)
> 15:00:48,231 ERROR [STDERR]     at
> com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:221)
> 15:00:48,231 ERROR [STDERR]     at
> com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:209)
> 15:00:48,231 ERROR [STDERR]     at
> com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:239)
> 15:00:48,231 ERROR [STDERR]     at
> org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF(DataType
>P arser.java:161)
>
> or
>
> Cannot parse MOBY Service Type Ontology: java.lang.NullPointerException
> 15:00:02,396 ERROR [STDERR] java.lang.NullPointerException
> 15:00:02,396 ERROR [STDERR]     at
> org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF(DataType
>P arser.java:182)
>
> is this a current or general error ?
>
> Does the moving of MobyCentral requires an cvs update ?
>
> thanks
> andreas

-- 
Andreas Groscurth
Bioinformatics Developer
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)221-5062-449