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podd / podd-redesign

The redesigned PODD
http://podd.plantphenomics.org.au/podd/
GNU Affero General Public License v3.0
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Fix schema migration #129

Closed ansell closed 10 years ago

ansell commented 10 years ago

Schema migration in testing seems to work well. However, in production when operating on the migrated artifacts it gives the following in logs:

[2014-01-13 15:51:16,991] INFO (com.github.podd.restlet.ApplicationUtils:645) About to update schema imports for: OntologyID(OntologyIRI(http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact) VersionIRI(http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact:version:1))urn:podd:inferred:ontologyiriprefix:http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact:version:1 [2014-01-13 15:51:17,009] INFO (com.github.podd.impl.PoddArtifactManagerImpl:2271) Starting exporting artifact to RDF: OntologyID(OntologyIRI(http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact) VersionIRI(http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact:version:1))urn:podd:inferred:ontologyiriprefix:http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact:version:1 [2014-01-13 15:51:17,045] INFO (com.github.podd.impl.PoddArtifactManagerImpl:2277) Finished exporting artifact to RDF: OntologyID(OntologyIRI(http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact) VersionIRI(http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact:version:1))urn:podd:inferred:ontologyiriprefix:http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact:version:1 [2014-01-13 15:51:17,045] INFO (com.github.podd.impl.PoddArtifactManagerImpl:2303) Started caching schema ontologies for artifact migration: OntologyID(OntologyIRI(http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact) VersionIRI(http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact:version:1))urn:podd:inferred:ontologyiriprefix:http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact:version:1 [2014-01-13 15:51:17,046] INFO (com.github.podd.impl.PoddArtifactManagerImpl:2325) Starting reload of artifact to Repository: OntologyID(OntologyIRI(http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact) VersionIRI(http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact:version:1))urn:podd:inferred:ontologyiriprefix:http://purl.org/podd-csiro/56a1ce27-edaf-4186-a12a-15211cb0dcf3/3075/ontology/artifact:version:1 [2014-01-13 15:51:17,062] ERROR (com.github.podd.restlet.ApplicationUtils:652) Could not update schema imports automatically due to exception: com.github.podd.exception.EmptyOntologyException: Loaded ontology is empty at com.github.podd.impl.PoddOWLManagerImpl.loadOntologyInternal(PoddOWLManagerImpl.java:860) at com.github.podd.impl.PoddOWLManagerImpl.loadAndInfer(PoddOWLManagerImpl.java:708) at com.github.podd.impl.PoddOWLManagerImpl.loadAndInfer(PoddOWLManagerImpl.java:681) at com.github.podd.impl.PoddArtifactManagerImpl.loadInferStoreArtifact(PoddArtifactManagerImpl.java:1659) at com.github.podd.impl.PoddArtifactManagerImpl.updateSchemaImports(PoddArtifactManagerImpl.java:2329) at com.github.podd.restlet.ApplicationUtils.setupSchemas(ApplicationUtils.java:646) at com.github.podd.restlet.ApplicationUtils.setupApplication(ApplicationUtils.java:416) at au.org.plantphenomics.podd.PoddCSIRORestletComponent.initialise(PoddCSIRORestletComponent.java:146) at au.org.plantphenomics.podd.PoddCSIRORestletComponent.(PoddCSIRORestletComponent.java:76) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:526) at java.lang.Class.newInstance(Class.java:374) at org.restlet.ext.servlet.ServerServlet.createComponent(ServerServlet.java:439) at org.restlet.ext.servlet.ServerServlet.getComponent(ServerServlet.java:812) at org.restlet.ext.servlet.ServerServlet.init(ServerServlet.java:930) at javax.servlet.GenericServlet.init(GenericServlet.java:160) at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1266) at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1185) at org.apache.catalina.core.StandardWrapper.allocate(StandardWrapper.java:857) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:135) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98) at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407) at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:200) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579) at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:307) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:724)

ansell commented 10 years ago

Seems to be working now