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

Julie Sullivan julie at flymine.org
Tue Mar 4 15:39:46 GMT 2014


Hello! Sorry you are having problems.

The process seems to have failed when it was trying to write to the 
database, but it doesn't say why.

Can you run the command again but add the "verbose" flag, -v? That will 
hopefully give us a better error message.

Thanks!
Julie

On 04/03/14 15:36, Loke Kok Keong wrote:
> 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  <mailto:kkloke86 at zetilab.org>
> 0102266792
>
>
>
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> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>



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