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

Paulo Almeida palmeida at igc.gulbenkian.pt
Mon Mar 3 14:30:33 GMT 2014


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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