[flymine-dev] flymine 11 - ant build-db-userprofile problem

[Richard Smith]

Hi Wolfgang,
Yes, Sorry.  The problem was with tags on classes that had been removed
from the model appearing in default-template-queries.xml.  I've updated
it on the branch.  In general it is fine to delete invalid tags, we
should really change the code to ignore them instead of throwing an
exception.

We never load that file for FlyMine and instead upgrade the existing
userprofile each time.

Richard.




Wolfgang Lugmayr wrote:
> Hi,
> 
> when building flymine 11 from scratch the following error occurs when
> calling:
> (ant build-db-userprofile 2>&1) | tee ant-userprofile.log
> :
> [load-default-templates] Adding template "gene_agLifecycleExpression"
> [load-default-templates] Adding template
> "gene_downstreamAdjacentgene_FlyAtlas" [invalid]
> [load-default-templates] Adding template "mRNAlocalisationTerm_Genes"
> 
> BUILD FAILED
> /bioinfodev1/flymine/flymine11/imbuild/application.xml:87:
> java.lang.RuntimeException: unknown class name
> "org.flymine.model.genomic.Paralogue" while tagging:
> org.flymine.model.genomic.Paralogue
> 
> 
> doing some ant compile, jar, war etc. ...
> and running the same again the error is:
> /bioinfodev1/flymine/flymine11/imbuild/application.xml:87:
> java.lang.RuntimeException: unknown class name
> "org.flymine.model.genomic.ProteinFeature" while tagging:
> org.flymine.model.genomic.ProteinFeature
> 
> The classes/tables existed in flymine9 but not in 11?
> 
> Attached is the logfile of the first run.
> 
> Is there an error in
> ./webapp/src/default-template-queries.xml?
> 
> Cheers,
> Wolfgang
> 
>