[InterMine Dev] Error on integrate malariamine interpro.xml.

Loke Kok Keong kkloke86 at zetilab.org
Tue Mar 4 15:36:00 GMT 2014


Hi,

     I have error when try to run build_project on malariamine tutorial.
May I know how to fix this?

 [ant] -retrieve-tgt-from-custom-file:
  [ant] [integrate] Processing file:
/var/www/intermine/malariamine/malaria/interpro/interpro.xml
  [ant] [integrate] org.xml.sax.SAXException: Error while storing
  [ant] [integrate] org.intermine.objectstore.ObjectStoreException: Error
while storing
  [ant] [integrate]     at
org.intermine.bio.dataconversion.InterProConverter$InterProHandler.endElement(InterProConverter.java:168)
  [ant] [integrate]     at
org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
  [ant] [integrate]     at
org.apache.xerces.impl.dtd.XMLDTDValidator.endNamespaceScope(Unknown Source)
  [ant] [integrate]     at
org.apache.xerces.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
  [ant] [integrate]     at
org.apache.xerces.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
  [ant] [integrate]     at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown
Source)
  [ant] [integrate]     at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown
Source)
  [ant] [integrate]     at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
Source)
  [ant] [integrate]     at
org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
  [ant] [integrate]     at
org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
  [ant] [integrate]     at
org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
  [ant] [integrate]     at
org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
  [ant] [integrate]     at
org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
  [ant] [integrate]     at
org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
  [ant] [integrate]     at
org.intermine.util.SAXParser.parse(SAXParser.java:59)
  [ant] [integrate]     at
org.intermine.util.SAXParser.parse(SAXParser.java:42)
  [ant] [integrate]     at
org.intermine.bio.dataconversion.InterProConverter.process(InterProConverter.java:56)
  [ant] [integrate]     at
org.intermine.task.FileConverterTask.execute(FileConverterTask.java:116)
  [ant] [integrate]     at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
  [ant] [integrate]     at
sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
  [ant] [integrate]     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  [ant] [integrate]     at java.lang.reflect.Method.invoke(Method.java:622)
  [ant] [integrate]     at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
  [ant] [integrate]     at org.apache.tools.ant.Task.perform(Task.java:348)
  [ant] [integrate]     at
org.apache.tools.ant.Target.execute(Target.java:390)
  [ant] [integrate]     at
org.apache.tools.ant.Target.performTasks(Target.java:411)
  [ant] [integrate]     at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
  [ant] [integrate]     at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
  [ant] [integrate]     at
org.apache.tools.ant.Project.executeTargets(Project.java:1251)


Regards,
Kok Keong

-- 
Candidate PhD. Computational Systems Biology
Zetilab
Universiti Kebangsaan Malaysia(UKM)kkloke86 at zetilab.org
0102266792
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