[InterMine Dev] Intermine tutorial - Duplicate 'gff3-query' in web.xml

sergio contrino sergio at modencode.org
Mon Mar 3 14:38:31 GMT 2014

dear paulo,
you did the right thing, there has been a change in the code that does 
not allow duplication any longer. an empty web-model.xml is fine.
it is not related to the ignoreDuplicates FAQ.
we will correct the tutorial.
thank you for letting us know

On 03/03/14 14:30, Paulo Almeida wrote:
> Hi,
> I followed the intermine tutorial and got this error when deploying the
> webapp with 'ant remove-webapp release-webapp':
> ---
> Parse error in application web.xml file at
> jndi:/localhost/malariamine/WEB-INF/web.xml
> org.xml.sax.SAXParseException; systemId:
> jndi:/localhost/malariamine/WEB-INF/web.xml; lineNumber: 226;
> columnNumber: 11; Error at (226, 11: addChild:  Child name 'gff3-query'
> is not unique
> ---
> I noticed one of the gff3-query definitions in web.xml was after the
> comment about allowing other modules to define their own nodes, so I got
> around the error by deleting everything from
> $INTERMINE_HOME/malariamine/webapp/resources/web-model.xml . Then I
> redeployed the application and it worked, but this left me wondering
> whether I did something wrong, and if I am missing something, because I
> deleted everything from web-model.xml (I did that to avoid a potentially
> long cycle of deleting nodes, testing, failing and deleting more).
> Can you advise me on this situation? Should I have removed the node
> definition from the additional module, instead of web-model.xml? If so,
> how can I find where to do that, and how can I find which module is
> trying to add a redundant definition?
> I saw this phrase on the FAQ:
> «So if possible, you should make sure that there are no duplicated
> objects at all in each data source, and then switch off
> "ignoreDuplicates".»
> But I don't know if it's relevant in this case, and even if it is, I
> couldn't figure out where to configure ignoreDuplicates.
> Thanks for any help,
> Paulo Almeida
> Instituto Gulbenkian de Ciência
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