local installation of validator not working

[Karin]

Hi everybody,

I just got the latest code version from SVN (revision 372) and am now
trying to locally validate XML files. I already did this a couple
weeks ago, and it worked just fine. But now I'm getting the error
below, no matter what kind of file I feed it (correct/broken XML, non-
XML, ..).

Any input and thoughts on this are much appreciated!

Thanks,
Karin



I'm running:

./validate-mimix.sh myFile.xml

resulting in:

[..]
Parse Done!
10355 [main] WARN (AbstractLoader,129) - Total Terms to process:
1342
10358 [main] WARN (AbstractLoader,390) - MOD:00000 is a root term
10441 [main] WARN (AbstractLoader,144) - Processing done
10441 [main] WARN (AbstractLoader,147) - Creating relationships
10449 [main] WARN (AbstractLoader,692) - Created unkonwn relation
type: has_functional_parent
10460 [main] WARN (AbstractLoader,692) - Created unkonwn relation
type: derives_from
10466 [main] WARN (AbstractLoader,692) - Created unkonwn relation
type: contains
10476 [main] WARN (AbstractLoader,162) - Processing done
10484 [main] INFO (LocalOntology,96) - Successfully created
LocalOntology from values: ontology=MOD name=PSI-MOD version=1.x
format=OBO location=http://psidev.sourceforge.net/mod/data/PSI-MOD.obo
10484 [main] INFO (OntologyManager,185) - Loading ontology:
name=Gene Ontology, ID= GO, format=OBO, version=latest in OLS, uri=
using source: OLS
10487 [main] INFO (OlsOntology,54) - Creating new OlsOntology...
10487 [main] INFO (OlsOntology,59) - Setting up cache
administrator...
10487 [main] INFO (OlsOntology,72) - Using custom cache
configuration from file: olsontology-oscache.properties
10498 [main] INFO (OlsOntology,77) - Creating new OLS query client.
10710 [main] INFO (OlsOntology,106) - setOntologyDirectory does not
have any effect on the OlsOntology.
psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException:
Failed loading ontology source: OLS
at
psidev.psi.tools.ontology_manager.OntologyManager.loadOntologies(OntologyManager.java:
206)
at
psidev.psi.tools.ontology_manager.OntologyManager.<init>(OntologyManager.java:
74)
at
psidev.psi.tools.validator.Validator.setOntologyManager(Validator.java:
141)
at psidev.psi.tools.validator.Validator.<init>(Validator.java:118)
at psidev.psi.tools.validator.Validator.<init>(Validator.java:104)
at psidev.psi.tools.validator.Validator.<init>(Validator.java:96)
at
psidev.psi.mi.validator.extension.Mi25Validator.<init>(Mi25Validator.java:
70)
at psidev.psi.mi.ValidatorClient.buildValidator(ValidatorClient.java:
77)
at psidev.psi.mi.ValidatorClient.main(ValidatorClient.java:374)
Caused by: java.lang.IllegalStateException: RemoteException while
trying to connect to OLS.
at
psidev.psi.tools.ontology_manager.impl.ols.OlsOntology.loadOntology(OlsOntology.java:
94)
at
psidev.psi.tools.ontology_manager.OntologyManager.loadOntologies(OntologyManager.java:
203)
... 8 more
[INFO]
------------------------------------------------------------------------
[INFO] BUILD SUCCESSFUL
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 17 seconds
[INFO] Finished at: Thu Jul 14 14:27:52 PDT 2011
[INFO] Final Memory: 29M/323M
[INFO]
------------------------------------------------------------------------

[Marine]

Hello Karin,

It seems that the validator cannot connect to OLS to collect some
ontology terms...

I will see what I can do.

Regards,

Marine